Build/check report for BioC 3.24 - CHECK results for sangeranalyseR on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.4 LTS)	x86_64	4.6.0 RC (2026-04-17 r89917) -- "Because it was There"	4894
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

CHECK results for sangeranalyseR on nebbiolo2

To the developers/maintainers of the sangeranalyseR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/sangeranalyseR.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: sangeranalyseR

Version: 1.23.0

Command: /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:sangeranalyseR.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings sangeranalyseR_1.23.0.tar.gz

StartedAt: 2026-05-16 04:00:48 -0400 (Sat, 16 May 2026)

EndedAt: 2026-05-16 04:08:07 -0400 (Sat, 16 May 2026)

EllapsedTime: 439.8 seconds

RetCode: 0

Status: OK

CheckDir: sangeranalyseR.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:sangeranalyseR.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings sangeranalyseR_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.24-bioc/meat/sangeranalyseR.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-16 08:00:48 UTC
* checking for file ‘sangeranalyseR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sangeranalyseR’ version ‘1.23.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘sangeranalyseR’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* checking installed package size ... INFO
  installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data      1.0Mb
    extdata   5.5Mb
    libs      1.2Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... INFO
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
SangerAlignment-class 37.533  8.969  43.846
SangerAlignment        9.243  2.856  11.394
SangerContig-class     8.898  2.336  10.573
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

sangeranalyseR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD INSTALL sangeranalyseR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.24-bioc/R/site-library’
* installing *source* package ‘sangeranalyseR’ ...
** this is package ‘sangeranalyseR’ version ‘1.23.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.24-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.24-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.24-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.24-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c peakvalues.cpp -o peakvalues.o
g++ -std=gnu++20 -shared -L/home/biocbuild/bbs-3.24-bioc/R/lib -L/usr/local/lib -o sangeranalyseR.so RcppExports.o peakvalues.o -L/home/biocbuild/bbs-3.24-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.24-bioc/R/site-library/00LOCK-sangeranalyseR/00new/sangeranalyseR/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Note: wrong number of arguments to '==' 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (sangeranalyseR)

Tests output

sangeranalyseR.Rcheck/tests/testthat.Rout


R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(sangeranalyseR)
Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: XVector
Loading required package: Seqinfo

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: DECIPHER
Loading required package: sangerseqR
Loading required package: pwalign
Loading required package: stringr
Welcome to sangeranalyseR
> 
> test_check("sangeranalyseR")
INFO [2026-05-16 04:04:21] #################################################
INFO [2026-05-16 04:04:21] #### Start creating SangerAlignment instance ####
INFO [2026-05-16 04:04:21] #################################################
INFO [2026-05-16 04:04:21]   >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-16 04:04:21] ========================================================
INFO [2026-05-16 04:04:21] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:04:21] ========================================================
INFO [2026-05-16 04:04:21]   >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-16 04:04:22] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:22] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:04:22] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:22]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).

SUCCESS [2026-05-16 04:04:22] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:22] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:04:22] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:22]    >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).

INFO [2026-05-16 04:04:22]    >> The number of reads detected: 2
================================================================================

Time difference of 0.05 secs

SUCCESS [2026-05-16 04:04:24] ==========================================================
SUCCESS [2026-05-16 04:04:24] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:04:24] ==========================================================
INFO [2026-05-16 04:04:24]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:04:24]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:04:24]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:04:24] ========================================================
INFO [2026-05-16 04:04:24] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:04:24] ========================================================
INFO [2026-05-16 04:04:24]   >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-16 04:04:24] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:24] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:04:24] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:24]    >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).

SUCCESS [2026-05-16 04:04:25] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:25] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:04:25] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:25]    >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).

INFO [2026-05-16 04:04:25]    >> The number of reads detected: 2
================================================================================

Time difference of 0.03 secs

SUCCESS [2026-05-16 04:04:26] ==========================================================
SUCCESS [2026-05-16 04:04:26] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:04:26] ==========================================================
INFO [2026-05-16 04:04:26]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:04:26]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:04:26]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:04:26] ========================================================
INFO [2026-05-16 04:04:26] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:04:26] ========================================================
INFO [2026-05-16 04:04:26]   >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-16 04:04:28] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:28] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:04:28] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:28]    >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).

SUCCESS [2026-05-16 04:04:29] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:29] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:04:29] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:29]    >> 'Achl_ACHLO040-09_2_R.ab1' is created (Reverse Read; ABIF).

INFO [2026-05-16 04:04:29]    >> The number of reads detected: 2
================================================================================

Time difference of 0.04 secs

SUCCESS [2026-05-16 04:04:31] ==========================================================
SUCCESS [2026-05-16 04:04:31] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:04:31] ==========================================================
INFO [2026-05-16 04:04:31]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:04:31]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:04:31]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:04:31] ========================================================
INFO [2026-05-16 04:04:31] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:04:31] ========================================================
INFO [2026-05-16 04:04:31]   >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-16 04:04:32] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:32] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:04:32] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:32]    >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).

SUCCESS [2026-05-16 04:04:32] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:32] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:04:32] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:32]    >> 'Achl_ACHLO041-09_2_R.ab1' is created (Reverse Read; ABIF).

INFO [2026-05-16 04:04:32]    >> The number of reads detected: 2
================================================================================

Time difference of 0.03 secs

SUCCESS [2026-05-16 04:04:33] ==========================================================
SUCCESS [2026-05-16 04:04:33] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:04:33] ==========================================================
INFO [2026-05-16 04:04:33]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:04:33]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:04:33]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:04:33] Aligning consensus reads ... 
SUCCESS [2026-05-16 04:04:34] #############################################################
SUCCESS [2026-05-16 04:04:34] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-16 04:04:34] #############################################################
INFO [2026-05-16 04:04:34]   >> 4 contigs detected from 'regular expression'.
INFO [2026-05-16 04:04:34]       >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-16 04:04:34]           >> 1 forward reads.
INFO [2026-05-16 04:04:34]           >> 1 reverse reads.
INFO [2026-05-16 04:04:34]       >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-16 04:04:34]           >> 1 forward reads.
INFO [2026-05-16 04:04:34]           >> 1 reverse reads.
INFO [2026-05-16 04:04:34]       >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-16 04:04:34]           >> 1 forward reads.
INFO [2026-05-16 04:04:34]           >> 1 reverse reads.
INFO [2026-05-16 04:04:34]       >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-16 04:04:34]           >> 1 forward reads.
INFO [2026-05-16 04:04:34]           >> 1 reverse reads.
INFO [2026-05-16 04:04:34]   >> 8 reads created from ABIF file.
INFO [2026-05-16 04:04:34]   >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:04:34]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:04:34]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-16 04:04:34] #################################################
INFO [2026-05-16 04:04:35] #### Start creating SangerAlignment instance ####
INFO [2026-05-16 04:04:35] #################################################
INFO [2026-05-16 04:04:35] **** You are using Regular Expression Method to group reads in FASTA file (No CSV file)!
INFO [2026-05-16 04:04:35] ========================================================
INFO [2026-05-16 04:04:35] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:04:35] ========================================================
INFO [2026-05-16 04:04:35]   >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-16 04:04:35] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:35] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:04:35] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:35]    >> 'Achl_ACHLO006-09_1_F' is created (Forward Read; FASTA).

SUCCESS [2026-05-16 04:04:35] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:35] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:04:35] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:35]    >> 'Achl_ACHLO006-09_2_R' is created (Reverse Read; FASTA).

INFO [2026-05-16 04:04:35]    >> The number of reads detected: 2
================================================================================

Time difference of 0.03 secs

SUCCESS [2026-05-16 04:04:37] ==========================================================
SUCCESS [2026-05-16 04:04:37] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:04:37] ==========================================================
INFO [2026-05-16 04:04:37]    >> 2 read(s) created from FASTA file.
INFO [2026-05-16 04:04:37]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:04:37]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:04:37] ========================================================
INFO [2026-05-16 04:04:37] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:04:37] ========================================================
INFO [2026-05-16 04:04:37]   >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-16 04:04:37] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:37] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:04:37] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:37]    >> 'Achl_ACHLO007-09_1_F' is created (Forward Read; FASTA).

SUCCESS [2026-05-16 04:04:37] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:37] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:04:37] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:37]    >> 'Achl_ACHLO007-09_2_R' is created (Reverse Read; FASTA).

INFO [2026-05-16 04:04:37]    >> The number of reads detected: 2
================================================================================

Time difference of 0.04 secs

SUCCESS [2026-05-16 04:04:39] ==========================================================
SUCCESS [2026-05-16 04:04:39] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:04:39] ==========================================================
INFO [2026-05-16 04:04:39]    >> 2 read(s) created from FASTA file.
INFO [2026-05-16 04:04:39]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:04:39]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:04:39] ========================================================
INFO [2026-05-16 04:04:39] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:04:39] ========================================================
INFO [2026-05-16 04:04:39]   >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-16 04:04:39] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:39] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:04:39] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:39]    >> 'Achl_ACHLO040-09_1_F' is created (Forward Read; FASTA).

SUCCESS [2026-05-16 04:04:39] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:39] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:04:39] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:39]    >> 'Achl_ACHLO040-09_2_R' is created (Reverse Read; FASTA).

INFO [2026-05-16 04:04:39]    >> The number of reads detected: 2
================================================================================

Time difference of 0.04 secs

SUCCESS [2026-05-16 04:04:40] ==========================================================
SUCCESS [2026-05-16 04:04:40] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:04:40] ==========================================================
INFO [2026-05-16 04:04:40]    >> 2 read(s) created from FASTA file.
INFO [2026-05-16 04:04:40]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:04:40]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:04:40] ========================================================
INFO [2026-05-16 04:04:40] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:04:40] ========================================================
INFO [2026-05-16 04:04:40]   >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-16 04:04:40] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:40] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:04:40] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:40]    >> 'Achl_ACHLO041-09_1_F' is created (Forward Read; FASTA).

SUCCESS [2026-05-16 04:04:41] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:41] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:04:41] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:41]    >> 'Achl_ACHLO041-09_2_R' is created (Reverse Read; FASTA).

INFO [2026-05-16 04:04:41]    >> The number of reads detected: 2
================================================================================

Time difference of 0.04 secs

SUCCESS [2026-05-16 04:04:42] ==========================================================
SUCCESS [2026-05-16 04:04:42] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:04:42] ==========================================================
INFO [2026-05-16 04:04:42]    >> 2 read(s) created from FASTA file.
INFO [2026-05-16 04:04:42]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:04:42]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:04:42] Aligning consensus reads ... 
SUCCESS [2026-05-16 04:04:43] #############################################################
SUCCESS [2026-05-16 04:04:43] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-16 04:04:43] #############################################################
INFO [2026-05-16 04:04:43]   >> 4 contigs detected from 'regular expression'.
INFO [2026-05-16 04:04:43]       >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-16 04:04:43]           >> 1 forward reads.
INFO [2026-05-16 04:04:43]           >> 1 reverse reads.
INFO [2026-05-16 04:04:43]       >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-16 04:04:43]           >> 1 forward reads.
INFO [2026-05-16 04:04:43]           >> 1 reverse reads.
INFO [2026-05-16 04:04:43]       >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-16 04:04:43]           >> 1 forward reads.
INFO [2026-05-16 04:04:43]           >> 1 reverse reads.
INFO [2026-05-16 04:04:43]       >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-16 04:04:43]           >> 1 forward reads.
INFO [2026-05-16 04:04:43]           >> 1 reverse reads.
INFO [2026-05-16 04:04:43]   >> 8 reads created from FASTA file.
DEBUG [2026-05-16 04:04:43]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:04:43]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-16 04:04:43] ========================================================
INFO [2026-05-16 04:04:43] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:04:43] ========================================================
INFO [2026-05-16 04:04:43]   >> Contig Name: 'Achl_ACHLO006-09'
INFO [2026-05-16 04:04:43]   >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-16 04:04:43] >> Your contig name is Achl_ACHLO006-09
SUCCESS [2026-05-16 04:04:44] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:44] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:04:44] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:44]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).

SUCCESS [2026-05-16 04:04:44] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:44] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:04:44] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:44]    >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).

INFO [2026-05-16 04:04:44]    >> The number of reads detected: 2
INFO [2026-05-16 04:04:44] Correcting frameshifts in reads using amino acidreference sequence
================================================================================

Time difference of 0.03 secs

SUCCESS [2026-05-16 04:04:45] ==========================================================
SUCCESS [2026-05-16 04:04:45] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:04:45] ==========================================================
INFO [2026-05-16 04:04:45]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:04:45]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:04:45]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:04:45]    >> Trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:04:45]    >> For more information, please run 'object'
DEBUG [2026-05-16 04:04:45]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-16 04:04:45] ========================================================
INFO [2026-05-16 04:04:45] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:04:45] ========================================================
INFO [2026-05-16 04:04:45]   >> Contig Name: 'Achl_RBNII384-13'
INFO [2026-05-16 04:04:46]   >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-16 04:04:46] >> Your contig name is Achl_RBNII384-13
SUCCESS [2026-05-16 04:04:46] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:46] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:04:46] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:46]    >> 'Achl_RBNII384-13_1_F.ab1' is created (Forward Read; ABIF).

SUCCESS [2026-05-16 04:04:47] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:47] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:04:47] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:47]    >> 'Achl_RBNII384-13_2_R.ab1' is created (Reverse Read; ABIF).

INFO [2026-05-16 04:04:47]    >> The number of reads detected: 2
INFO [2026-05-16 04:04:47] Correcting frameshifts in reads using amino acidreference sequence
================================================================================

Time difference of 0.04 secs

SUCCESS [2026-05-16 04:04:48] ==========================================================
SUCCESS [2026-05-16 04:04:48] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:04:48] ==========================================================
INFO [2026-05-16 04:04:48]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:04:48]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:04:48]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:04:48]    >> Trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:04:48]    >> For more information, please run 'object'
DEBUG [2026-05-16 04:04:48]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-16 04:04:48] ========================================================
INFO [2026-05-16 04:04:48] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:04:48] ========================================================
INFO [2026-05-16 04:04:48]   >> Contig Name: 'Achl_ACHLO006-09'
INFO [2026-05-16 04:04:49]   >> You are using Regular Expression Method to group reads in FASTA file (No CSV file)!
INFO [2026-05-16 04:04:49] >> Your contig name is Achl_ACHLO006-09
SUCCESS [2026-05-16 04:04:49] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:49] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:04:49] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:49]    >> 'Achl_ACHLO006-09_1_F' is created (Forward Read; FASTA).

SUCCESS [2026-05-16 04:04:49] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:49] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:04:49] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:49]    >> 'Achl_ACHLO006-09_2_R' is created (Reverse Read; FASTA).

INFO [2026-05-16 04:04:49]    >> The number of reads detected: 2
INFO [2026-05-16 04:04:49] Correcting frameshifts in reads using amino acidreference sequence
================================================================================

Time difference of 0.04 secs

SUCCESS [2026-05-16 04:04:50] ==========================================================
SUCCESS [2026-05-16 04:04:50] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:04:50] ==========================================================
INFO [2026-05-16 04:04:50]    >> 2 read(s) created from FASTA file.
INFO [2026-05-16 04:04:50]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:04:50]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
DEBUG [2026-05-16 04:04:50]    >> For more information, please run 'object'
DEBUG [2026-05-16 04:04:50]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-16 04:04:50] ========================================================
INFO [2026-05-16 04:04:50] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:04:50] ========================================================
INFO [2026-05-16 04:04:50]   >> Contig Name: 'Achl_RBNII384-13'
INFO [2026-05-16 04:04:51]   >> You are using CSV Name Conversion Method to group reads in FASTA file (with Csv file)!
INFO [2026-05-16 04:04:51] >> Your contig name is Achl_RBNII384-13
SUCCESS [2026-05-16 04:04:51] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:51] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:04:51] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:51]    >> 'Achl_RBNII384-13_1_F' is created (Forward Read; FASTA).

SUCCESS [2026-05-16 04:04:51] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:51] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:04:51] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:51]    >> 'Achl_RBNII384-13_2_R' is created (Reverse Read; FASTA).

INFO [2026-05-16 04:04:51]    >> The number of reads detected: 2
INFO [2026-05-16 04:04:51] Correcting frameshifts in reads using amino acidreference sequence
================================================================================

Time difference of 0.04 secs

SUCCESS [2026-05-16 04:04:52] ==========================================================
SUCCESS [2026-05-16 04:04:52] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:04:52] ==========================================================
INFO [2026-05-16 04:04:52]    >> 2 read(s) created from FASTA file.
INFO [2026-05-16 04:04:52]      >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-16 04:04:52]      >> 1 reads assigned to 'reverse reads' according to 'csv file'.
DEBUG [2026-05-16 04:04:52]    >> For more information, please run 'object'
DEBUG [2026-05-16 04:04:52]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-16 04:04:52] ------------------------------------------------
INFO [2026-05-16 04:04:52] -------- Creating 'SangerRead' instance --------
INFO [2026-05-16 04:04:52] ------------------------------------------------
INFO [2026-05-16 04:04:52] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-16 04:04:52]     >> Creating Forward Read raw abif ...
INFO [2026-05-16 04:04:52]     >> Creating Forward Read raw sangerseq ...
INFO [2026-05-16 04:04:52]           * Making basecall !!
INFO [2026-05-16 04:04:52]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-16 04:04:53] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:53] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:04:53] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:53]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-16 04:04:53]    >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:04:53]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:04:53]    >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-16 04:04:53] ------------------------------------------------
INFO [2026-05-16 04:04:53] -------- Creating 'SangerRead' instance --------
INFO [2026-05-16 04:04:53] ------------------------------------------------
INFO [2026-05-16 04:04:53] >> Reverse Read: Creating abif & sangerseq ...
INFO [2026-05-16 04:04:53]     >> Creating Reverse Read raw abif ...
INFO [2026-05-16 04:04:53]     >> Creating Reverse Read raw sangerseq ...
INFO [2026-05-16 04:04:53]           * Making basecall !!
INFO [2026-05-16 04:04:53]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-16 04:04:53] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:53] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:04:53] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:53]    >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:04:53]    >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:04:53]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:04:53]    >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-16 04:04:53] ------------------------------------------------
INFO [2026-05-16 04:04:53] -------- Creating 'SangerRead' instance --------
INFO [2026-05-16 04:04:53] ------------------------------------------------
INFO [2026-05-16 04:04:53] Forward Read: Creating SangerRead from FASTA ...
SUCCESS [2026-05-16 04:04:54] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:54] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:04:54] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:54]    >> 'Achl_ACHLO006-09_1_F' is created (Forward Read; FASTA).
INFO [2026-05-16 04:04:54]    >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:04:54]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:04:54]    >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-16 04:04:54] ------------------------------------------------
INFO [2026-05-16 04:04:54] -------- Creating 'SangerRead' instance --------
INFO [2026-05-16 04:04:54] ------------------------------------------------
INFO [2026-05-16 04:04:54] Reverse Read: Creating SangerRead from FASTA ...
SUCCESS [2026-05-16 04:04:54] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:54] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:04:54] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:54]    >> 'Achl_ACHLO006-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-16 04:04:54]    >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:04:54]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:04:54]    >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
ERROR [2026-05-16 04:04:54] FILE_NOT_EXIST_ERROR
'/home/biocbuild/bbs-3.24-bioc/R/site-library/sangeranalyseR/extdata//Allolobophora_chlorotica/ACHLO/TEST_Achl_ACHLO006-09_2_R.ab1' file does not exist.
DEBUG [2026-05-16 04:04:54]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:04:54]    >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-16 04:04:54] ------------------------------------------------
INFO [2026-05-16 04:04:54] -------- Creating 'SangerRead' instance --------
INFO [2026-05-16 04:04:54] ------------------------------------------------
INFO [2026-05-16 04:04:54] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-16 04:04:54]     >> Creating Forward Read raw abif ...
INFO [2026-05-16 04:04:54]     >> Creating Forward Read raw sangerseq ...
INFO [2026-05-16 04:04:54]           * Making basecall !!
INFO [2026-05-16 04:04:54]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-16 04:04:54] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:54] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:04:54] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:54]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-16 04:04:54]    >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:04:54]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:04:54]    >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-16 04:04:54] ========================================================
INFO [2026-05-16 04:04:54] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:04:54] ========================================================
INFO [2026-05-16 04:04:54]   >> Contig Name: 'Achl_ACHLO006-09'
INFO [2026-05-16 04:04:54]   >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-16 04:04:54] >> Your contig name is Achl_ACHLO006-09
SUCCESS [2026-05-16 04:04:54] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:54] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:04:54] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:54]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:04:54] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:54] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:04:54] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:54]    >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:04:54]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:04:55] ==========================================================
SUCCESS [2026-05-16 04:04:55] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:04:55] ==========================================================
INFO [2026-05-16 04:04:55]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:04:55]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:04:55]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:04:55]    >> Trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:04:55]    >> For more information, please run 'object'
DEBUG [2026-05-16 04:04:55]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-16 04:04:55] #################################################
INFO [2026-05-16 04:04:55] #### Start creating SangerAlignment instance ####
INFO [2026-05-16 04:04:55] #################################################
INFO [2026-05-16 04:04:55]   >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-16 04:04:55] ========================================================
INFO [2026-05-16 04:04:55] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:04:55] ========================================================
INFO [2026-05-16 04:04:55]   >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-16 04:04:55] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:55] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:04:55] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:55]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:04:55] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:55] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:04:55] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:55]    >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:04:55]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:04:55] ==========================================================
SUCCESS [2026-05-16 04:04:55] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:04:55] ==========================================================
INFO [2026-05-16 04:04:55]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:04:55]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:04:55]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:04:55] ========================================================
INFO [2026-05-16 04:04:55] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:04:55] ========================================================
INFO [2026-05-16 04:04:55]   >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-16 04:04:55] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:55] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:04:55] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:55]    >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:04:55] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:55] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:04:55] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:55]    >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:04:55]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:04:56] ==========================================================
SUCCESS [2026-05-16 04:04:56] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:04:56] ==========================================================
INFO [2026-05-16 04:04:56]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:04:56]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:04:56]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:04:56] ========================================================
INFO [2026-05-16 04:04:56] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:04:56] ========================================================
INFO [2026-05-16 04:04:56]   >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-16 04:04:56] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:56] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:04:56] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:56]    >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:04:56] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:56] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:04:56] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:56]    >> 'Achl_ACHLO040-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:04:56]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:04:56] ==========================================================
SUCCESS [2026-05-16 04:04:56] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:04:56] ==========================================================
INFO [2026-05-16 04:04:56]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:04:56]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:04:56]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:04:56] ========================================================
INFO [2026-05-16 04:04:56] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:04:56] ========================================================
INFO [2026-05-16 04:04:56]   >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-16 04:04:56] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:56] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:04:56] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:56]    >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:04:56] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:56] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:04:57] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:57]    >> 'Achl_ACHLO041-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:04:57]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:04:57] ==========================================================
SUCCESS [2026-05-16 04:04:57] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:04:57] ==========================================================
INFO [2026-05-16 04:04:57]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:04:57]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:04:57]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:04:57] Aligning consensus reads ... 
INFO [2026-05-16 04:04:57] Before building!!
INFO [2026-05-16 04:04:57] After building!!
SUCCESS [2026-05-16 04:04:57] #############################################################
SUCCESS [2026-05-16 04:04:57] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-16 04:04:57] #############################################################
INFO [2026-05-16 04:04:57]   >> 4 contigs detected from 'regular expression'.
INFO [2026-05-16 04:04:57]       >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-16 04:04:57]           >> 1 forward reads.
INFO [2026-05-16 04:04:57]           >> 1 reverse reads.
INFO [2026-05-16 04:04:57]       >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-16 04:04:57]           >> 1 forward reads.
INFO [2026-05-16 04:04:57]           >> 1 reverse reads.
INFO [2026-05-16 04:04:57]       >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-16 04:04:57]           >> 1 forward reads.
INFO [2026-05-16 04:04:57]           >> 1 reverse reads.
INFO [2026-05-16 04:04:57]       >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-16 04:04:57]           >> 1 forward reads.
INFO [2026-05-16 04:04:57]           >> 1 reverse reads.
INFO [2026-05-16 04:04:57]   >> 8 reads created from ABIF file.
INFO [2026-05-16 04:04:57]   >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:04:57]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:04:57]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-16 04:04:57]           * Making basecall !!
INFO [2026-05-16 04:04:57]           * Updating slots in 'SangerRead' instance !!
INFO [2026-05-16 04:04:58] ********************************************
INFO [2026-05-16 04:04:58] ******** SangerRead readTable print ********
INFO [2026-05-16 04:04:58] ********************************************
  ------------------------------
  --- SangerRead S4 instance ---
  ------------------------------
                  Input source :  ABIF 
                   Read feature :  Forward Read 
            Read fileName (abs) :  /Library/Frameworks/R.framework/Versions/4.1/Resources/library/sangeranalyseR/extdata//Allolobophora_chlorotica/ACHLO/Achl_ACHLO006-09_1_F.ab1 
           Read fileName (base) :  Achl_ACHLO006-09_1_F.ab1 
                Trimming method :  M1 
                Trimming cutoff :  1e-04 
       Trimming start base pair :  16 
      Trimming finish base pair :  477 
    Read length before trimming :  702 
     Read length after trimming :  461 
   Read quality before trimming :  52.87607 
    Read quality after trimming :  58.21041 
          Secondary peak cutoff :  0.33 
               Primary Sequence :  CTGGGCGTCTGAGCAGGAATGGTTGGAGCCGGTATAAGACTTCTAATTCGAATCGAGCTAAGACAACCAGGAGCGTTCCTGGGCAGAGACCAACTATACAATACTATCGTTACTGCACACGCATTTGTAATAATCTTCTTTCTAGTAATGCCTGTATTCATCGGGGGATTCGGAAACTGGCTTTTACCTTTAATACTTGGAGCCCCCGATATAGCATTCCCTCGACTCAACAACATGAGATTCTGACTACTTCCCCCATCACTGATCCTTTTAGTGTCCTCTGCGGCGGTAGAAAAAGGCGCTGGTACGGGGTGAACTGTTTATCCGCCTCTAGCAAGAAATCTTGCCCACGCAGGCCCGTCTGTAGATTTAGCCATCTTTTCCCTTCATTTAGCGGGTGCGTCTTCTATTCTAGGGGCTATTAATTTTATCACCACAGTTATTAATATGCGTTGAAGAGG 
             Secondary Sequence :  CTGGGCGTCTGAGCAGGAATGGTTGGAGCCGGTATAAGACTTCTAATTCGAATCGAGCTAAGACAACCAGGAGCGTTCCTGGGCAGAGACCAACTATACAATACTATCGTTACTGCACACGCATTTGTAATAATCTTCTTTCTAGTAATGCCTGTATTCATCGGGGGATTCGGAAACTGGCTTTTACCTTTAATACTTGGAGCCCCCGATATAGCATTCCCTCGACTCAACAACATGAGATTCTGACTACTTCCCCCATCACTGATCCTTTTAGTGTCCTCTGCGGCGGTAGAAAAAGGCGCTGGTACGGGGTGAACTGTTTATCCGCCTCTAGCAAGAAATCTTGCCCACGCAGGCCCGTCTGTAGATTTAGCCATCTTTTCCCTTCATTTAGCGGGTGCGTCTTCTATTCTAGGGGCTATTAATTTTATCACCACAGTTATTAATATGCGTTGAAGAGG 
INFO [2026-05-16 04:04:58] **********************************************
INFO [2026-05-16 04:04:58] ******** SangerContig readTable print ********
INFO [2026-05-16 04:04:58] **********************************************
 ================================
 === SangerContig S4 instance ===
 ================================
                  Input source :  ABIF 
      Names conversion CSV file :  
                    Contig name :  Achl_ACHLO006-09 
           Suffix forward regex :  _[0-9]*_F.ab1$ 
           Suffix reverse regex :  _[0-9]*_R.ab1$ 
           Minimum reads number :  2 
            Minimum read length :  20 
          Minimum fraction call :  0.5 
  Reference amino acid sequence :  SRQWLFSTNHKDIGTLYFIFGAWAGMVGTSLSILIRAELGHPGALIGDDQIYNVIVTAHAFIMIFFMVMPIMIGGFGNWLVPLMLGAPDMAFPRMNNMSFWLLPPALSLLLVSSMVENGAGTGWTVYPPLSAGIAHGGASVDLAIFSLHLAGISSILGAVNFITTVINMRSTGISLDRMPLFVWSVVITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGMISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKIFSWLATLHGTQLSYSPAILWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAGFIHWYPLFTGLTLNNKWLKSHFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNIVSTIGSTISLLGILFFFFIIWESLVSQRQVIYPIQLNSSIEWYQNTPPAEHSYSELPLLTN 
          Maximum fraction lost :  0.5 
             Accept stop codons :  TRUE 
                  Reading frame :  1 
                Contig sequence :  TTATATTTTATTCTGGGCGTCTGAGCAGGAATGGTTGGAGCCGGTATAAGACTTCTAATTCGAATCGAGCTAAGACAACCAGGAGCGTTCCTGGGCAGAGACCAACTATACAATACTATCGTTACTGCACACGCATTTGTAATAATCTTCTTTCTAGTAATGCCTGTATTCATCGGGGGATTCGGAAACTGGCTTTTACCTTTAATACTTGGAGCCCCCGATATAGCATTCCCTCGACTCAACAACATGAGATTCTGACTACTTCCCCCATCACTGATCCTTTTAGTGTCCTCTGCGGCGGTAGAAAAAGGCGCTGGTACGGGGTGAACTGTTTATCCGCCTCTAGCAAGAAATCTTGCCCACGCAGGCCCGTCTGTAGATTTAGCCATCTTTTCCCTTCATTTAGCGGGTGCGTCTTCTATTCTAGGGGCTATTAATTTTATCACCACAGTTATTAATATGCGTTGAAGAGGATTACGTCTTGAACGAATTCCCCTGTTTGTCTGAGCTGTGCTAATTACAGTTGTTCTTCTACTTCTATCTTTACCAGTGCTAGCAGGTGCCATTACCATACTTCTTACCGACCGAAACCTCAATACTTCATTCTTTGATCCTGCCGGTGGTGGAGACCCCATCCTC 

   ------------------------------
   --- SangerRead S4 instance ---
   ------------------------------
                   Input source :  ABIF 
                    Read feature :  Forward Read 
             Read fileName (abs) :  /Library/Frameworks/R.framework/Versions/4.1/Resources/library/sangeranalyseR/extdata/Allolobophora_chlorotica/ACHLO/Achl_ACHLO006-09_1_F.ab1 
            Read fileName (base) :  Achl_ACHLO006-09_1_F.ab1 
                 Trimming method :  M1 
                 Trimming cutoff :  1e-04 
        Trimming start base pair :  16 
       Trimming finish base pair :  477 
     Read length before trimming :  702 
      Read length after trimming :  461 
    Read quality before trimming :  52.87607 
     Read quality after trimming :  58.21041 
           Secondary peak cutoff :  0.33 
                Primary Sequence :  CTGGGCGTCTGAGCAGGAATGGTTGGAGCCGGTATAAGACTTCTAATTCGAATCGAGCTAAGACAACCAGGAGCGTTCCTGGGCAGAGACCAACTATACAATACTATCGTTACTGCACACGCATTTGTAATAATCTTCTTTCTAGTAATGCCTGTATTCATCGGGGGATTCGGAAACTGGCTTTTACCTTTAATACTTGGAGCCCCCGATATAGCATTCCCTCGACTCAACAACATGAGATTCTGACTACTTCCCCCATCACTGATCCTTTTAGTGTCCTCTGCGGCGGTAGAAAAAGGCGCTGGTACGGGGTGAACTGTTTATCCGCCTCTAGCAAGAAATCTTGCCCACGCAGGCCCGTCTGTAGATTTAGCCATCTTTTCCCTTCATTTAGCGGGTGCGTCTTCTATTCTAGGGGCTATTAATTTTATCACCACAGTTATTAATATGCGTTGAAGAGG 
              Secondary Sequence :  CTGGGCGTCTGAGCAGGAATGGTTGGAGCCGGTATAAGACTTCTAATTCGAATCGAGCTAAGACAACCAGGAGCGTTCCTGGGCAGAGACCAACTATACAATACTATCGTTACTGCACACGCATTTGTAATAATCTTCTTTCTAGTAATGCCTGTATTCATCGGGGGATTCGGAAACTGGCTTTTACCTTTAATACTTGGAGCCCCCGATATAGCATTCCCTCGACTCAACAACATGAGATTCTGACTACTTCCCCCATCACTGATCCTTTTAGTGTCCTCTGCGGCGGTAGAAAAAGGCGCTGGTACGGGGTGAACTGTTTATCCGCCTCTAGCAAGAAATCTTGCCCACGCAGGCCCGTCTGTAGATTTAGCCATCTTTTCCCTTCATTTAGCGGGTGCGTCTTCTATTCTAGGGGCTATTAATTTTATCACCACAGTTATTAATATGCGTTGAAGAGG 
   ------------------------------
   --- SangerRead S4 instance ---
   ------------------------------
                   Input source :  ABIF 
                    Read feature :  Reverse Read 
             Read fileName (abs) :  /Library/Frameworks/R.framework/Versions/4.1/Resources/library/sangeranalyseR/extdata/Allolobophora_chlorotica/ACHLO/Achl_ACHLO006-09_2_R.ab1 
            Read fileName (base) :  Achl_ACHLO006-09_2_R.ab1 
                 Trimming method :  M1 
                 Trimming cutoff :  1e-04 
        Trimming start base pair :  18 
       Trimming finish base pair :  658 
     Read length before trimming :  705 
      Read length after trimming :  640 
    Read quality before trimming :  54.85106 
     Read quality after trimming :  57.29531 
           Secondary peak cutoff :  0.33 
                Primary Sequence :  GAGGATGGGGTCTCCACCACCGGCAGGATCAAAGAATGAAGTATTGAGGTTTCGGTCGGTAAGAAGTATGGTAATGGCACCTGCTAGCACTGGTAAAGATAGAAGTAGAAGAACAACTGTAATTAGCACAGCTCAGACAAACAGGGGAATTCGTTCAAGACGTAATCCTCTTCAACGCATATTAATAACTGTGGTGATAAAATTAATAGCCCCTAGAATAGAAGACGCACCCGCTAAATGAAGGGAAAAGATGGCTAAATCTACAGACGGGCCTGCGTGGGCAAGATTTCTTGCTAGAGGCGGATAAACAGTTCACCCCGTACCAGCGCCTTTTTCTACCGCCGCAGAGGACACTAAAAGGATCAGTGATGGGGGAAGTAGTCAGAATCTCATGTTGTTGAGTCGAGGGAATGCTATATCGGGGGCTCCAAGTATTAAAGGTAAAAGCCAGTTTCCGAATCCCCCGATGAATACAGGCATTACTAGAAAGAAGATTATTACAAATGCGTGTGCAGTAACGATAGTATTGTATAGTTGGTCTCTGCCCAGGAACGCTCCTGGTTGTCTTAGCTCGATTCGAATTAGAAGTCTTATACCGGCTCCAACCATTCCTGCTCAGACGCCCAGAATAAAATATAAA 
              Secondary Sequence :  GAGGATGGGGTCTCCACCACCGGCAGGATCAAAGAATGAAGTATTGCGGTTTCGGTCGGTAAGAAGTATGGTAATGGCACCTGCTAGCACTGGTAAAGATAGAAGTAGAAGAACAACTGTAATTAGCACAGCTCAGACAAACAGGGGAATTCGTTCAAGACGTAATCCTCTTCAACGCATATTAATAACTGTGGTGATAAAATTAATAGCCCCTAGAATAGAAGACGCACCCGCTAAATGAAGGGAAAAGATGGCTAAATCTACAGACGGGCCTGCGTGGGCAAGATTTCTTGCTAGAGGCGGATAAACAGTTCACCCCGTACCAGCGCCTTTTTCTACCGCCGCAGAGGACACTAAAAGGATCAGTGATGGGGGAAGTAGTCAGAATCTCATGTTGTTGAGTCGAGGGAATGCTATATCGGGGGCTCCAAGTATTAAAGGTAAAAGCCAGTTTCCGAATCCCCCGATGAATACAGGCATTACTAGAAAGAAGATTATTACAAATGCGTGTGCAGTAACGATAGTATTGTATAGTTGGTCTCTGCCCAGGAACGCTCCTGGTTGTCTTAGCTCGATTCGAATTAGAAGTCTTATACCGGCTCCAACCATTCCTGCTCAGACGCCCAGAATAAAATATAAA 
INFO [2026-05-16 04:04:58] Your input is 'SangerRead' S4 instance
INFO [2026-05-16 04:04:58] >>> outputDir : /tmp/RtmpeZL3QC/file113f963cfa58ad
INFO [2026-05-16 04:04:58] Start writing '/Library/Frameworks/R.framework/Versions/4.1/Resources/library/sangeranalyseR/extdata//Allolobophora_chlorotica/ACHLO/Achl_ACHLO006-09_1_F.ab1' to FASTA format ...
INFO [2026-05-16 04:04:58] >> '/tmp/RtmpeZL3QC/file113f963cfa58ad/Achl_ACHLO006-09_1_F.fa' is written
INFO [2026-05-16 04:04:58] Your input is 'SangerContig' S4 instance
INFO [2026-05-16 04:04:58] >>> outputDir : /tmp/RtmpeZL3QC/file113f963cfa58ad
INFO [2026-05-16 04:04:58] Start to write 'Achl_ACHLO006-09' to FASTA format ...
INFO [2026-05-16 04:04:58] >> Writing alignment to FASTA ...
INFO [2026-05-16 04:04:58] >> Writing all single reads to FASTA ...
INFO [2026-05-16 04:04:58] >> Writing consensus read to FASTA ...
INFO [2026-05-16 04:04:58] Finish writing 'Achl_ACHLO006-09' to FASTA format
INFO [2026-05-16 04:04:58] Your input is 'SangerAlignment' S4 instance
INFO [2026-05-16 04:04:58] >>> outputDir : /tmp/RtmpeZL3QC/file113f963cfa58ad
INFO [2026-05-16 04:04:58] Start to write 'SangerAlignment' to FASTA format ...
INFO [2026-05-16 04:04:58] >> Writing 'alignment' to FASTA ...
INFO [2026-05-16 04:04:58] >> Writing 'contigs' to FASTA ...
INFO [2026-05-16 04:04:58] >> Writing all single reads to FASTA ...
INFO [2026-05-16 04:04:58] Finish writing 'SangerAlignment' to FASTA format
INFO [2026-05-16 04:04:58] #################################################
INFO [2026-05-16 04:04:58] #### Start creating SangerAlignment instance ####
INFO [2026-05-16 04:04:58] #################################################
INFO [2026-05-16 04:04:58]   >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-16 04:04:58] ========================================================
INFO [2026-05-16 04:04:58] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:04:58] ========================================================
INFO [2026-05-16 04:04:58]   >> Contig Name: 'Top'
SUCCESS [2026-05-16 04:04:59] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:59] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:04:59] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:59]    >> 'Top_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:04:59] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:59] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:04:59] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:59]    >> 'Top_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:04:59]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:04:59] ==========================================================
SUCCESS [2026-05-16 04:04:59] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:04:59] ==========================================================
INFO [2026-05-16 04:04:59]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:04:59]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:04:59]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:04:59] ========================================================
INFO [2026-05-16 04:04:59] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:04:59] ========================================================
INFO [2026-05-16 04:04:59]   >> Contig Name: 'Nested'
SUCCESS [2026-05-16 04:04:59] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:59] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:04:59] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:59]    >> 'Nested_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:04:59] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:59] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:04:59] --------------------------------------------------------
SUCCESS [2026-05-16 04:04:59]    >> 'Nested_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:04:59]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:05:00] ==========================================================
SUCCESS [2026-05-16 04:05:00] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:05:00] ==========================================================
INFO [2026-05-16 04:05:00]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:05:00]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:05:00]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:05:00] Aligning consensus reads ... 
INFO [2026-05-16 04:05:00] Before building!!
INFO [2026-05-16 04:05:00] After building!!
INFO [2026-05-16 04:05:00] The number of contigs is less than 3 or quality of reads are too low. 'Contigs Tree' cannot be created.
SUCCESS [2026-05-16 04:05:00] #############################################################
SUCCESS [2026-05-16 04:05:00] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-16 04:05:00] #############################################################
INFO [2026-05-16 04:05:00]   >> 2 contigs detected from 'regular expression'.
INFO [2026-05-16 04:05:00]       >> Contig 'Top':
INFO [2026-05-16 04:05:00]           >> 1 forward reads.
INFO [2026-05-16 04:05:00]           >> 1 reverse reads.
INFO [2026-05-16 04:05:00]       >> Contig 'Nested':
INFO [2026-05-16 04:05:00]           >> 1 forward reads.
INFO [2026-05-16 04:05:00]           >> 1 reverse reads.
INFO [2026-05-16 04:05:00]   >> 4 reads created from ABIF file.
INFO [2026-05-16 04:05:00]   >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:05:00]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:05:00]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-16 04:05:00] #################################################
INFO [2026-05-16 04:05:00] #### Start creating SangerAlignment instance ####
INFO [2026-05-16 04:05:00] #################################################
INFO [2026-05-16 04:05:00]   >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-16 04:05:00] ========================================================
INFO [2026-05-16 04:05:00] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:05:00] ========================================================
INFO [2026-05-16 04:05:00]   >> Contig Name: 'Top'
SUCCESS [2026-05-16 04:05:00] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:00] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:00] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:00]    >> 'Top_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:05:00] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:00] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:00] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:00]    >> 'Top_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:05:00]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:05:00] ==========================================================
SUCCESS [2026-05-16 04:05:00] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:05:00] ==========================================================
INFO [2026-05-16 04:05:00]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:05:00]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:05:00]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:05:00] ========================================================
INFO [2026-05-16 04:05:00] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:05:00] ========================================================
INFO [2026-05-16 04:05:00]   >> Contig Name: 'Nested'
SUCCESS [2026-05-16 04:05:00] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:00] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:00] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:00]    >> 'Nested_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:05:00] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:00] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:00] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:00]    >> 'Nested_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:05:00]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:05:01] ==========================================================
SUCCESS [2026-05-16 04:05:01] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:05:01] ==========================================================
INFO [2026-05-16 04:05:01]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:05:01]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:05:01]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:05:01] Aligning consensus reads ... 
INFO [2026-05-16 04:05:01] Before building!!
INFO [2026-05-16 04:05:01] After building!!
INFO [2026-05-16 04:05:01] The number of contigs is less than 3 or quality of reads are too low. 'Contigs Tree' cannot be created.
SUCCESS [2026-05-16 04:05:01] #############################################################
SUCCESS [2026-05-16 04:05:01] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-16 04:05:01] #############################################################
INFO [2026-05-16 04:05:01]   >> 2 contigs detected from 'regular expression'.
INFO [2026-05-16 04:05:01]       >> Contig 'Top':
INFO [2026-05-16 04:05:01]           >> 1 forward reads.
INFO [2026-05-16 04:05:01]           >> 1 reverse reads.
INFO [2026-05-16 04:05:01]       >> Contig 'Nested':
INFO [2026-05-16 04:05:01]           >> 1 forward reads.
INFO [2026-05-16 04:05:01]           >> 1 reverse reads.
INFO [2026-05-16 04:05:01]   >> 4 reads created from ABIF file.
INFO [2026-05-16 04:05:01]   >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:05:01]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:05:01]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-16 04:05:01] #################################################
INFO [2026-05-16 04:05:01] #### Start creating SangerAlignment instance ####
INFO [2026-05-16 04:05:01] #################################################
INFO [2026-05-16 04:05:01]   >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-16 04:05:01] ========================================================
INFO [2026-05-16 04:05:01] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:05:01] ========================================================
INFO [2026-05-16 04:05:01]   >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-16 04:05:01] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:01] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:01] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:01]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:05:01] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:01] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:01] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:01]    >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:05:01]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:05:01] ==========================================================
SUCCESS [2026-05-16 04:05:01] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:05:01] ==========================================================
INFO [2026-05-16 04:05:01]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:05:01]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:05:01]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:05:01] ========================================================
INFO [2026-05-16 04:05:01] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:05:01] ========================================================
INFO [2026-05-16 04:05:01]   >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-16 04:05:01] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:02] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:02] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:02]    >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:05:02] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:02] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:02] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:02]    >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:05:02]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:05:02] ==========================================================
SUCCESS [2026-05-16 04:05:02] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:05:02] ==========================================================
INFO [2026-05-16 04:05:02]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:05:02]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:05:02]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:05:02] ========================================================
INFO [2026-05-16 04:05:02] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:05:02] ========================================================
INFO [2026-05-16 04:05:02]   >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-16 04:05:02] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:02] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:02] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:02]    >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:05:02] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:02] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:02] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:02]    >> 'Achl_ACHLO040-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:05:02]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:05:02] ==========================================================
SUCCESS [2026-05-16 04:05:02] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:05:02] ==========================================================
INFO [2026-05-16 04:05:02]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:05:02]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:05:02]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:05:02] ========================================================
INFO [2026-05-16 04:05:02] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:05:02] ========================================================
INFO [2026-05-16 04:05:02]   >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-16 04:05:03] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:03] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:03] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:03]    >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:05:03] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:03] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:03] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:03]    >> 'Achl_ACHLO041-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:05:03]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:05:03] ==========================================================
SUCCESS [2026-05-16 04:05:03] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:05:03] ==========================================================
INFO [2026-05-16 04:05:03]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:05:03]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:05:03]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:05:03] Aligning consensus reads ... 
INFO [2026-05-16 04:05:03] Before building!!
INFO [2026-05-16 04:05:03] After building!!
SUCCESS [2026-05-16 04:05:03] #############################################################
SUCCESS [2026-05-16 04:05:03] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-16 04:05:03] #############################################################
INFO [2026-05-16 04:05:03]   >> 4 contigs detected from 'regular expression'.
INFO [2026-05-16 04:05:03]       >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-16 04:05:03]           >> 1 forward reads.
INFO [2026-05-16 04:05:03]           >> 1 reverse reads.
INFO [2026-05-16 04:05:03]       >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-16 04:05:03]           >> 1 forward reads.
INFO [2026-05-16 04:05:03]           >> 1 reverse reads.
INFO [2026-05-16 04:05:03]       >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-16 04:05:03]           >> 1 forward reads.
INFO [2026-05-16 04:05:03]           >> 1 reverse reads.
INFO [2026-05-16 04:05:03]       >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-16 04:05:03]           >> 1 forward reads.
INFO [2026-05-16 04:05:03]           >> 1 reverse reads.
INFO [2026-05-16 04:05:03]   >> 8 reads created from ABIF file.
INFO [2026-05-16 04:05:03]   >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:05:03]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:05:03]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-16 04:05:04] ------------------------------------------------
INFO [2026-05-16 04:05:04] -------- Creating 'SangerRead' instance --------
INFO [2026-05-16 04:05:04] ------------------------------------------------
INFO [2026-05-16 04:05:04] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-16 04:05:04]     >> Creating Forward Read raw abif ...
INFO [2026-05-16 04:05:04]     >> Creating Forward Read raw sangerseq ...
INFO [2026-05-16 04:05:04]           * Making basecall !!
INFO [2026-05-16 04:05:04]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-16 04:05:04] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:04] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:04] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:04]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-16 04:05:04]    >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:05:04]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:05:04]    >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-16 04:05:04] ------------------------------------------------
INFO [2026-05-16 04:05:04] -------- Creating 'SangerRead' instance --------
INFO [2026-05-16 04:05:04] ------------------------------------------------
INFO [2026-05-16 04:05:04] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-16 04:05:04]     >> Creating Forward Read raw abif ...
INFO [2026-05-16 04:05:04]     >> Creating Forward Read raw sangerseq ...
INFO [2026-05-16 04:05:04]           * Making basecall !!
INFO [2026-05-16 04:05:04]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-16 04:05:04] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:04] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:04] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:04]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-16 04:05:04]    >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:05:04]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:05:04]    >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-16 04:05:04] ------------------------------------------------
INFO [2026-05-16 04:05:04] -------- Creating 'SangerRead' instance --------
INFO [2026-05-16 04:05:04] ------------------------------------------------
INFO [2026-05-16 04:05:04] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-16 04:05:04]     >> Creating Forward Read raw abif ...
INFO [2026-05-16 04:05:04]     >> Creating Forward Read raw sangerseq ...
INFO [2026-05-16 04:05:04]           * Making basecall !!
INFO [2026-05-16 04:05:04]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-16 04:05:04] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:04] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:04] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:04]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-16 04:05:04]    >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:05:04]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:05:04]    >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-16 04:05:04] ------------------------------------------------
INFO [2026-05-16 04:05:04] -------- Creating 'SangerRead' instance --------
INFO [2026-05-16 04:05:04] ------------------------------------------------
INFO [2026-05-16 04:05:04] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-16 04:05:04]     >> Creating Forward Read raw abif ...
INFO [2026-05-16 04:05:04]     >> Creating Forward Read raw sangerseq ...
INFO [2026-05-16 04:05:04]           * Making basecall !!
INFO [2026-05-16 04:05:04]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-16 04:05:05] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:05] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:05] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:05]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-16 04:05:05]    >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:05:05]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:05:05]    >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-16 04:05:05] ------------------------------------------------
INFO [2026-05-16 04:05:05] -------- Creating 'SangerRead' instance --------
INFO [2026-05-16 04:05:05] ------------------------------------------------
INFO [2026-05-16 04:05:05] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-16 04:05:05]     >> Creating Forward Read raw abif ...
INFO [2026-05-16 04:05:05]     >> Creating Forward Read raw sangerseq ...
INFO [2026-05-16 04:05:05]           * Making basecall !!
INFO [2026-05-16 04:05:05]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-16 04:05:06] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:06] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:06] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:06]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-16 04:05:06]    >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:05:06]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:05:06]    >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-16 04:05:06] #################################################
INFO [2026-05-16 04:05:06] #### Start creating SangerAlignment instance ####
INFO [2026-05-16 04:05:06] #################################################
INFO [2026-05-16 04:05:06]   >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-16 04:05:06] ========================================================
INFO [2026-05-16 04:05:06] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:05:06] ========================================================
INFO [2026-05-16 04:05:06]   >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-16 04:05:06] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:06] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:06] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:06]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:05:06] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:06] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:06] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:06]    >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:05:06]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:05:07] ==========================================================
SUCCESS [2026-05-16 04:05:07] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:05:07] ==========================================================
INFO [2026-05-16 04:05:07]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:05:07]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:05:07]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:05:07] ========================================================
INFO [2026-05-16 04:05:07] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:05:07] ========================================================
INFO [2026-05-16 04:05:07]   >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-16 04:05:07] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:07] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:07] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:07]    >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:05:07] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:07] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:07] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:07]    >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:05:07]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:05:07] ==========================================================
SUCCESS [2026-05-16 04:05:07] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:05:07] ==========================================================
INFO [2026-05-16 04:05:07]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:05:07]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:05:07]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:05:07] ========================================================
INFO [2026-05-16 04:05:07] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:05:07] ========================================================
INFO [2026-05-16 04:05:07]   >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-16 04:05:07] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:07] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:07] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:07]    >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:05:07] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:07] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:07] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:07]    >> 'Achl_ACHLO040-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:05:07]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:05:08] ==========================================================
SUCCESS [2026-05-16 04:05:08] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:05:08] ==========================================================
INFO [2026-05-16 04:05:08]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:05:08]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:05:08]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:05:08] ========================================================
INFO [2026-05-16 04:05:08] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:05:08] ========================================================
INFO [2026-05-16 04:05:08]   >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-16 04:05:08] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:08] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:08] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:08]    >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:05:08] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:08] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:08] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:08]    >> 'Achl_ACHLO041-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:05:08]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:05:08] ==========================================================
SUCCESS [2026-05-16 04:05:08] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:05:08] ==========================================================
INFO [2026-05-16 04:05:08]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:05:08]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:05:08]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:05:08] Aligning consensus reads ... 
INFO [2026-05-16 04:05:08] Before building!!
INFO [2026-05-16 04:05:08] After building!!
SUCCESS [2026-05-16 04:05:08] #############################################################
SUCCESS [2026-05-16 04:05:08] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-16 04:05:08] #############################################################
INFO [2026-05-16 04:05:08]   >> 4 contigs detected from 'regular expression'.
INFO [2026-05-16 04:05:08]       >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-16 04:05:08]           >> 1 forward reads.
INFO [2026-05-16 04:05:08]           >> 1 reverse reads.
INFO [2026-05-16 04:05:08]       >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-16 04:05:08]           >> 1 forward reads.
INFO [2026-05-16 04:05:08]           >> 1 reverse reads.
INFO [2026-05-16 04:05:08]       >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-16 04:05:08]           >> 1 forward reads.
INFO [2026-05-16 04:05:08]           >> 1 reverse reads.
INFO [2026-05-16 04:05:08]       >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-16 04:05:08]           >> 1 forward reads.
INFO [2026-05-16 04:05:08]           >> 1 reverse reads.
INFO [2026-05-16 04:05:08]   >> 8 reads created from ABIF file.
INFO [2026-05-16 04:05:08]   >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:05:08]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:05:08]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-16 04:05:09] #################################################
INFO [2026-05-16 04:05:09] #### Start creating SangerAlignment instance ####
INFO [2026-05-16 04:05:09] #################################################
INFO [2026-05-16 04:05:09]   >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-16 04:05:09] ========================================================
INFO [2026-05-16 04:05:09] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:05:09] ========================================================
INFO [2026-05-16 04:05:09]   >> Contig Name: 'Achl_ACHLO006-09'
INFO [2026-05-16 04:05:09]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:05:10] ==========================================================
SUCCESS [2026-05-16 04:05:10] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:05:10] ==========================================================
INFO [2026-05-16 04:05:10]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:05:10]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:05:10]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:05:10] ========================================================
INFO [2026-05-16 04:05:10] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:05:10] ========================================================
INFO [2026-05-16 04:05:10]   >> Contig Name: 'Achl_ACHLO007-09'
INFO [2026-05-16 04:05:10]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:05:10] ==========================================================
SUCCESS [2026-05-16 04:05:10] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:05:10] ==========================================================
INFO [2026-05-16 04:05:10]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:05:10]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:05:10]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:05:10] ========================================================
INFO [2026-05-16 04:05:10] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:05:10] ========================================================
INFO [2026-05-16 04:05:10]   >> Contig Name: 'Achl_ACHLO040-09'
INFO [2026-05-16 04:05:11]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:05:11] ==========================================================
SUCCESS [2026-05-16 04:05:11] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:05:11] ==========================================================
INFO [2026-05-16 04:05:11]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:05:11]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:05:11]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:05:11] ========================================================
INFO [2026-05-16 04:05:11] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:05:11] ========================================================
INFO [2026-05-16 04:05:11]   >> Contig Name: 'Achl_ACHLO041-09'
INFO [2026-05-16 04:05:12]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:05:12] ==========================================================
SUCCESS [2026-05-16 04:05:12] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:05:12] ==========================================================
INFO [2026-05-16 04:05:12]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:05:12]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:05:12]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:05:12] Aligning consensus reads ... 
INFO [2026-05-16 04:05:12] Before building!!
INFO [2026-05-16 04:05:12] After building!!
SUCCESS [2026-05-16 04:05:12] #############################################################
SUCCESS [2026-05-16 04:05:12] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-16 04:05:12] #############################################################
INFO [2026-05-16 04:05:12]   >> 4 contigs detected from 'regular expression'.
INFO [2026-05-16 04:05:12]       >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-16 04:05:12]           >> 1 forward reads.
INFO [2026-05-16 04:05:12]           >> 1 reverse reads.
INFO [2026-05-16 04:05:12]       >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-16 04:05:12]           >> 1 forward reads.
INFO [2026-05-16 04:05:12]           >> 1 reverse reads.
INFO [2026-05-16 04:05:12]       >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-16 04:05:12]           >> 1 forward reads.
INFO [2026-05-16 04:05:12]           >> 1 reverse reads.
INFO [2026-05-16 04:05:12]       >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-16 04:05:12]           >> 1 forward reads.
INFO [2026-05-16 04:05:12]           >> 1 reverse reads.
INFO [2026-05-16 04:05:12]   >> 8 reads created from ABIF file.
INFO [2026-05-16 04:05:12]   >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:05:12]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:05:12]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-16 04:05:12] #################################################
INFO [2026-05-16 04:05:12] #### Start creating SangerAlignment instance ####
INFO [2026-05-16 04:05:12] #################################################
INFO [2026-05-16 04:05:12]   >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-16 04:05:12] ========================================================
INFO [2026-05-16 04:05:12] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:05:12] ========================================================
INFO [2026-05-16 04:05:12]   >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-16 04:05:12] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:12] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:12] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:12]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:05:13] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:13] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:13] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:13]    >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:05:13]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:05:13] ==========================================================
SUCCESS [2026-05-16 04:05:13] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:05:13] ==========================================================
INFO [2026-05-16 04:05:13]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:05:13]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:05:13]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:05:13] ========================================================
INFO [2026-05-16 04:05:13] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:05:13] ========================================================
INFO [2026-05-16 04:05:13]   >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-16 04:05:13] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:13] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:13] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:13]    >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:05:13] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:13] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:13] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:13]    >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:05:13]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:05:13] ==========================================================
SUCCESS [2026-05-16 04:05:13] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:05:13] ==========================================================
INFO [2026-05-16 04:05:13]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:05:13]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:05:13]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:05:13] ========================================================
INFO [2026-05-16 04:05:13] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:05:13] ========================================================
INFO [2026-05-16 04:05:13]   >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-16 04:05:14] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:14] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:14] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:14]    >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:05:14] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:14] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:14] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:14]    >> 'Achl_ACHLO040-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:05:14]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:05:14] ==========================================================
SUCCESS [2026-05-16 04:05:14] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:05:14] ==========================================================
INFO [2026-05-16 04:05:14]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:05:14]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:05:14]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:05:14] ========================================================
INFO [2026-05-16 04:05:14] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:05:14] ========================================================
INFO [2026-05-16 04:05:14]   >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-16 04:05:14] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:14] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:14] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:14]    >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:05:14] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:14] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:14] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:14]    >> 'Achl_ACHLO041-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:05:14]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:05:14] ==========================================================
SUCCESS [2026-05-16 04:05:14] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:05:14] ==========================================================
INFO [2026-05-16 04:05:14]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:05:14]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:05:14]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:05:14] Aligning consensus reads ... 
INFO [2026-05-16 04:05:14] Before building!!
INFO [2026-05-16 04:05:14] After building!!
SUCCESS [2026-05-16 04:05:15] #############################################################
SUCCESS [2026-05-16 04:05:15] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-16 04:05:15] #############################################################
INFO [2026-05-16 04:05:15]   >> 4 contigs detected from 'regular expression'.
INFO [2026-05-16 04:05:15]       >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-16 04:05:15]           >> 1 forward reads.
INFO [2026-05-16 04:05:15]           >> 1 reverse reads.
INFO [2026-05-16 04:05:15]       >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-16 04:05:15]           >> 1 forward reads.
INFO [2026-05-16 04:05:15]           >> 1 reverse reads.
INFO [2026-05-16 04:05:15]       >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-16 04:05:15]           >> 1 forward reads.
INFO [2026-05-16 04:05:15]           >> 1 reverse reads.
INFO [2026-05-16 04:05:15]       >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-16 04:05:15]           >> 1 forward reads.
INFO [2026-05-16 04:05:15]           >> 1 reverse reads.
INFO [2026-05-16 04:05:15]   >> 8 reads created from ABIF file.
INFO [2026-05-16 04:05:15]   >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:05:15]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:05:15]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-16 04:05:15] ------------------------------------------------
INFO [2026-05-16 04:05:15] -------- Creating 'SangerRead' instance --------
INFO [2026-05-16 04:05:15] ------------------------------------------------
INFO [2026-05-16 04:05:15] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-16 04:05:15]     >> Creating Forward Read raw abif ...
INFO [2026-05-16 04:05:15]     >> Creating Forward Read raw sangerseq ...
INFO [2026-05-16 04:05:15]           * Making basecall !!
INFO [2026-05-16 04:05:15]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-16 04:05:15] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:15] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:15] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:15]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-16 04:05:15]    >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:05:15]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:05:15]    >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-16 04:05:15] ------------------------------------------------
INFO [2026-05-16 04:05:15] -------- Creating 'SangerRead' instance --------
INFO [2026-05-16 04:05:15] ------------------------------------------------
INFO [2026-05-16 04:05:15] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-16 04:05:15]     >> Creating Forward Read raw abif ...
INFO [2026-05-16 04:05:15]     >> Creating Forward Read raw sangerseq ...
INFO [2026-05-16 04:05:15]           * Making basecall !!
INFO [2026-05-16 04:05:15]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-16 04:05:15] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:15] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:15] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:15]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-16 04:05:15]    >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:05:15]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:05:15]    >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-16 04:05:16] ------------------------------------------------
INFO [2026-05-16 04:05:16] -------- Creating 'SangerRead' instance --------
INFO [2026-05-16 04:05:16] ------------------------------------------------
INFO [2026-05-16 04:05:16] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-16 04:05:16]     >> Creating Forward Read raw abif ...
INFO [2026-05-16 04:05:16]     >> Creating Forward Read raw sangerseq ...
INFO [2026-05-16 04:05:16]           * Making basecall !!
INFO [2026-05-16 04:05:16]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-16 04:05:16] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:16] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:16] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:16]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-16 04:05:16]    >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:05:16]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:05:16]    >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-16 04:05:17] ------------------------------------------------
INFO [2026-05-16 04:05:17] -------- Creating 'SangerRead' instance --------
INFO [2026-05-16 04:05:17] ------------------------------------------------
INFO [2026-05-16 04:05:17] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-16 04:05:17]     >> Creating Forward Read raw abif ...
INFO [2026-05-16 04:05:17]     >> Creating Forward Read raw sangerseq ...
INFO [2026-05-16 04:05:17]           * Making basecall !!
INFO [2026-05-16 04:05:17]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-16 04:05:17] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:17] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:17] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:17]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-16 04:05:17]    >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:05:17]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:05:17]    >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-16 04:05:17] #################################################
INFO [2026-05-16 04:05:17] #### Start creating SangerAlignment instance ####
INFO [2026-05-16 04:05:17] #################################################
INFO [2026-05-16 04:05:17]   >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-16 04:05:17] ========================================================
INFO [2026-05-16 04:05:17] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:05:17] ========================================================
INFO [2026-05-16 04:05:17]   >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-16 04:05:18] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:18] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:18] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:18]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:05:18] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:18] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:18] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:18]    >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:05:18]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:05:18] ==========================================================
SUCCESS [2026-05-16 04:05:18] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:05:18] ==========================================================
INFO [2026-05-16 04:05:18]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:05:18]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:05:18]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:05:18] ========================================================
INFO [2026-05-16 04:05:18] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:05:18] ========================================================
INFO [2026-05-16 04:05:18]   >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-16 04:05:18] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:18] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:18] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:18]    >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:05:18] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:18] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:18] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:18]    >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:05:18]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:05:19] ==========================================================
SUCCESS [2026-05-16 04:05:19] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:05:19] ==========================================================
INFO [2026-05-16 04:05:19]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:05:19]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:05:19]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:05:19] ========================================================
INFO [2026-05-16 04:05:19] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:05:19] ========================================================
INFO [2026-05-16 04:05:19]   >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-16 04:05:19] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:19] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:19] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:19]    >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:05:19] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:19] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:19] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:19]    >> 'Achl_ACHLO040-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:05:19]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:05:19] ==========================================================
SUCCESS [2026-05-16 04:05:19] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:05:19] ==========================================================
INFO [2026-05-16 04:05:19]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:05:19]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:05:19]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:05:19] ========================================================
INFO [2026-05-16 04:05:19] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:05:19] ========================================================
INFO [2026-05-16 04:05:19]   >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-16 04:05:20] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:20] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:20] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:20]    >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:05:20] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:20] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:20] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:20]    >> 'Achl_ACHLO041-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:05:20]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:05:20] ==========================================================
SUCCESS [2026-05-16 04:05:20] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:05:20] ==========================================================
INFO [2026-05-16 04:05:20]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:05:20]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:05:20]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:05:20] Aligning consensus reads ... 
INFO [2026-05-16 04:05:20] Before building!!
INFO [2026-05-16 04:05:20] After building!!
SUCCESS [2026-05-16 04:05:20] #############################################################
SUCCESS [2026-05-16 04:05:20] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-16 04:05:20] #############################################################
INFO [2026-05-16 04:05:20]   >> 4 contigs detected from 'regular expression'.
INFO [2026-05-16 04:05:20]       >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-16 04:05:20]           >> 1 forward reads.
INFO [2026-05-16 04:05:20]           >> 1 reverse reads.
INFO [2026-05-16 04:05:20]       >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-16 04:05:20]           >> 1 forward reads.
INFO [2026-05-16 04:05:20]           >> 1 reverse reads.
INFO [2026-05-16 04:05:20]       >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-16 04:05:20]           >> 1 forward reads.
INFO [2026-05-16 04:05:20]           >> 1 reverse reads.
INFO [2026-05-16 04:05:20]       >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-16 04:05:20]           >> 1 forward reads.
INFO [2026-05-16 04:05:20]           >> 1 reverse reads.
INFO [2026-05-16 04:05:20]   >> 8 reads created from ABIF file.
INFO [2026-05-16 04:05:20]   >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:05:20]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:05:20]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-16 04:05:20] #################################################
INFO [2026-05-16 04:05:20] #### Start creating SangerAlignment instance ####
INFO [2026-05-16 04:05:20] #################################################
INFO [2026-05-16 04:05:20]   >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-16 04:05:20] ========================================================
INFO [2026-05-16 04:05:20] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:05:20] ========================================================
INFO [2026-05-16 04:05:20]   >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-16 04:05:20] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:20] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:20] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:20]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:05:21] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:21] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:21] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:21]    >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:05:21]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:05:21] ==========================================================
SUCCESS [2026-05-16 04:05:21] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:05:21] ==========================================================
INFO [2026-05-16 04:05:21]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:05:21]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:05:21]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:05:21] ========================================================
INFO [2026-05-16 04:05:21] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:05:21] ========================================================
INFO [2026-05-16 04:05:21]   >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-16 04:05:21] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:21] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:21] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:21]    >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:05:21] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:21] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:21] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:21]    >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:05:21]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:05:22] ==========================================================
SUCCESS [2026-05-16 04:05:22] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:05:22] ==========================================================
INFO [2026-05-16 04:05:22]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:05:22]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:05:22]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:05:22] ========================================================
INFO [2026-05-16 04:05:22] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:05:22] ========================================================
INFO [2026-05-16 04:05:22]   >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-16 04:05:22] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:22] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:22] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:22]    >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:05:22] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:22] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:22] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:22]    >> 'Achl_ACHLO040-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:05:22]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:05:22] ==========================================================
SUCCESS [2026-05-16 04:05:22] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:05:22] ==========================================================
INFO [2026-05-16 04:05:22]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:05:22]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:05:22]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:05:22] ========================================================
INFO [2026-05-16 04:05:22] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:05:22] ========================================================
INFO [2026-05-16 04:05:22]   >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-16 04:05:23] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:23] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:23] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:23]    >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:05:23] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:23] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:23] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:23]    >> 'Achl_ACHLO041-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:05:23]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:05:23] ==========================================================
SUCCESS [2026-05-16 04:05:23] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:05:23] ==========================================================
INFO [2026-05-16 04:05:23]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:05:23]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:05:23]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:05:23] Aligning consensus reads ... 
INFO [2026-05-16 04:05:23] Before building!!
INFO [2026-05-16 04:05:23] After building!!
SUCCESS [2026-05-16 04:05:23] #############################################################
SUCCESS [2026-05-16 04:05:23] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-16 04:05:23] #############################################################
INFO [2026-05-16 04:05:23]   >> 4 contigs detected from 'regular expression'.
INFO [2026-05-16 04:05:23]       >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-16 04:05:23]           >> 1 forward reads.
INFO [2026-05-16 04:05:23]           >> 1 reverse reads.
INFO [2026-05-16 04:05:23]       >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-16 04:05:23]           >> 1 forward reads.
INFO [2026-05-16 04:05:23]           >> 1 reverse reads.
INFO [2026-05-16 04:05:23]       >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-16 04:05:23]           >> 1 forward reads.
INFO [2026-05-16 04:05:23]           >> 1 reverse reads.
INFO [2026-05-16 04:05:23]       >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-16 04:05:23]           >> 1 forward reads.
INFO [2026-05-16 04:05:23]           >> 1 reverse reads.
INFO [2026-05-16 04:05:23]   >> 8 reads created from ABIF file.
INFO [2026-05-16 04:05:23]   >> Reads are trimmed by 'M2 - sliding window method'.
DEBUG [2026-05-16 04:05:23]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:05:23]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-16 04:05:23] #################################################
INFO [2026-05-16 04:05:23] #### Start creating SangerAlignment instance ####
INFO [2026-05-16 04:05:23] #################################################
INFO [2026-05-16 04:05:23] **** You are using CSV Name Conversion Method to group AB1 files!
INFO [2026-05-16 04:05:23] **** Contig number in your Csv file is 4
INFO [2026-05-16 04:05:23] ========================================================
INFO [2026-05-16 04:05:23] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:05:23] ========================================================
INFO [2026-05-16 04:05:23]   >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-16 04:05:23] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:23] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:23] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:23]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:05:24] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:24] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:24] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:24]    >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:05:24]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:05:24] ==========================================================
SUCCESS [2026-05-16 04:05:24] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:05:24] ==========================================================
INFO [2026-05-16 04:05:24]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:05:24]      >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-16 04:05:24]      >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-16 04:05:24] ========================================================
INFO [2026-05-16 04:05:24] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:05:24] ========================================================
INFO [2026-05-16 04:05:24]   >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-16 04:05:24] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:24] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:24] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:24]    >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:05:24] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:24] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:24] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:24]    >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:05:24]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:05:24] ==========================================================
SUCCESS [2026-05-16 04:05:24] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:05:24] ==========================================================
INFO [2026-05-16 04:05:24]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:05:24]      >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-16 04:05:24]      >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-16 04:05:24] ========================================================
INFO [2026-05-16 04:05:24] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:05:24] ========================================================
INFO [2026-05-16 04:05:24]   >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-16 04:05:25] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:25] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:25] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:25]    >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:05:25] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:25] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:25] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:25]    >> 'Achl_ACHLO040-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:05:25]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:05:25] ==========================================================
SUCCESS [2026-05-16 04:05:25] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:05:25] ==========================================================
INFO [2026-05-16 04:05:25]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:05:25]      >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-16 04:05:25]      >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-16 04:05:25] ========================================================
INFO [2026-05-16 04:05:25] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:05:25] ========================================================
INFO [2026-05-16 04:05:25]   >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-16 04:05:25] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:25] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:25] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:25]    >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:05:25] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:25] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:25] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:25]    >> 'Achl_ACHLO041-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:05:25]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:05:26] ==========================================================
SUCCESS [2026-05-16 04:05:26] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:05:26] ==========================================================
INFO [2026-05-16 04:05:26]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:05:26]      >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-16 04:05:26]      >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-16 04:05:26] Aligning consensus reads ... 
INFO [2026-05-16 04:05:26] Before building!!
INFO [2026-05-16 04:05:26] After building!!
SUCCESS [2026-05-16 04:05:26] #############################################################
SUCCESS [2026-05-16 04:05:26] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-16 04:05:26] #############################################################
INFO [2026-05-16 04:05:26]   >> 4 contigs detected from 'csv file'.
INFO [2026-05-16 04:05:26]       >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-16 04:05:26]           >> 1 forward reads.
INFO [2026-05-16 04:05:26]           >> 1 reverse reads.
INFO [2026-05-16 04:05:26]       >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-16 04:05:26]           >> 1 forward reads.
INFO [2026-05-16 04:05:26]           >> 1 reverse reads.
INFO [2026-05-16 04:05:26]       >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-16 04:05:26]           >> 1 forward reads.
INFO [2026-05-16 04:05:26]           >> 1 reverse reads.
INFO [2026-05-16 04:05:26]       >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-16 04:05:26]           >> 1 forward reads.
INFO [2026-05-16 04:05:26]           >> 1 reverse reads.
INFO [2026-05-16 04:05:26]   >> 8 reads created from ABIF file.
INFO [2026-05-16 04:05:26]   >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:05:26]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:05:26]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-16 04:05:26] #################################################
INFO [2026-05-16 04:05:26] #### Start creating SangerAlignment instance ####
INFO [2026-05-16 04:05:26] #################################################
INFO [2026-05-16 04:05:26] **** You are using CSV Name Conversion Method to group AB1 files!
INFO [2026-05-16 04:05:26] **** Contig number in your Csv file is 4
INFO [2026-05-16 04:05:26] ========================================================
INFO [2026-05-16 04:05:26] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:05:26] ========================================================
INFO [2026-05-16 04:05:26]   >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-16 04:05:26] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:26] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:26] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:26]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:05:26] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:26] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:26] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:26]    >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:05:26]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:05:27] ==========================================================
SUCCESS [2026-05-16 04:05:27] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:05:27] ==========================================================
INFO [2026-05-16 04:05:27]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:05:27]      >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-16 04:05:27]      >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-16 04:05:27] ========================================================
INFO [2026-05-16 04:05:27] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:05:27] ========================================================
INFO [2026-05-16 04:05:27]   >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-16 04:05:27] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:27] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:27] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:27]    >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:05:27] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:27] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:27] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:27]    >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:05:27]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:05:27] ==========================================================
SUCCESS [2026-05-16 04:05:27] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:05:27] ==========================================================
INFO [2026-05-16 04:05:27]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:05:27]      >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-16 04:05:27]      >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-16 04:05:27] ========================================================
INFO [2026-05-16 04:05:27] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:05:27] ========================================================
INFO [2026-05-16 04:05:27]   >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-16 04:05:27] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:27] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:27] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:27]    >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:05:27] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:27] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:27] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:27]    >> 'Achl_ACHLO040-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:05:27]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:05:28] ==========================================================
SUCCESS [2026-05-16 04:05:28] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:05:28] ==========================================================
INFO [2026-05-16 04:05:28]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:05:28]      >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-16 04:05:28]      >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-16 04:05:28] ========================================================
INFO [2026-05-16 04:05:28] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:05:28] ========================================================
INFO [2026-05-16 04:05:28]   >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-16 04:05:28] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:28] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:28] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:28]    >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:05:28] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:28] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:28] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:28]    >> 'Achl_ACHLO041-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:05:28]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:05:28] ==========================================================
SUCCESS [2026-05-16 04:05:28] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:05:28] ==========================================================
INFO [2026-05-16 04:05:28]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:05:28]      >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-16 04:05:28]      >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-16 04:05:28] Aligning consensus reads ... 
INFO [2026-05-16 04:05:28] Before building!!
INFO [2026-05-16 04:05:28] After building!!
SUCCESS [2026-05-16 04:05:28] #############################################################
SUCCESS [2026-05-16 04:05:28] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-16 04:05:28] #############################################################
INFO [2026-05-16 04:05:28]   >> 4 contigs detected from 'csv file'.
INFO [2026-05-16 04:05:28]       >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-16 04:05:28]           >> 1 forward reads.
INFO [2026-05-16 04:05:28]           >> 1 reverse reads.
INFO [2026-05-16 04:05:28]       >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-16 04:05:28]           >> 1 forward reads.
INFO [2026-05-16 04:05:28]           >> 1 reverse reads.
INFO [2026-05-16 04:05:28]       >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-16 04:05:28]           >> 1 forward reads.
INFO [2026-05-16 04:05:28]           >> 1 reverse reads.
INFO [2026-05-16 04:05:28]       >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-16 04:05:28]           >> 1 forward reads.
INFO [2026-05-16 04:05:28]           >> 1 reverse reads.
INFO [2026-05-16 04:05:28]   >> 8 reads created from ABIF file.
INFO [2026-05-16 04:05:28]   >> Reads are trimmed by 'M2 - sliding window method'.
DEBUG [2026-05-16 04:05:28]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:05:28]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-16 04:05:28] #################################################
INFO [2026-05-16 04:05:28] #### Start creating SangerAlignment instance ####
INFO [2026-05-16 04:05:28] #################################################
INFO [2026-05-16 04:05:28] **** You are using Regular Expression Method to group reads in FASTA file (No CSV file)!
INFO [2026-05-16 04:05:28] ========================================================
INFO [2026-05-16 04:05:28] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:05:28] ========================================================
INFO [2026-05-16 04:05:28]   >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-16 04:05:28] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:28] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:28] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:28]    >> 'Achl_ACHLO006-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-16 04:05:28] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:28] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:28] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:28]    >> 'Achl_ACHLO006-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-16 04:05:28]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:05:29] ==========================================================
SUCCESS [2026-05-16 04:05:29] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:05:29] ==========================================================
INFO [2026-05-16 04:05:29]    >> 2 read(s) created from FASTA file.
INFO [2026-05-16 04:05:29]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:05:29]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:05:29] ========================================================
INFO [2026-05-16 04:05:29] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:05:29] ========================================================
INFO [2026-05-16 04:05:29]   >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-16 04:05:29] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:29] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:29] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:29]    >> 'Achl_ACHLO007-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-16 04:05:29] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:29] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:29] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:29]    >> 'Achl_ACHLO007-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-16 04:05:29]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:05:29] ==========================================================
SUCCESS [2026-05-16 04:05:29] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:05:29] ==========================================================
INFO [2026-05-16 04:05:29]    >> 2 read(s) created from FASTA file.
INFO [2026-05-16 04:05:29]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:05:29]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:05:29] ========================================================
INFO [2026-05-16 04:05:29] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:05:29] ========================================================
INFO [2026-05-16 04:05:29]   >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-16 04:05:29] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:29] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:29] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:29]    >> 'Achl_ACHLO040-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-16 04:05:29] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:29] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:29] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:29]    >> 'Achl_ACHLO040-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-16 04:05:29]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:05:29] ==========================================================
SUCCESS [2026-05-16 04:05:29] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:05:29] ==========================================================
INFO [2026-05-16 04:05:29]    >> 2 read(s) created from FASTA file.
INFO [2026-05-16 04:05:29]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:05:29]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:05:29] ========================================================
INFO [2026-05-16 04:05:29] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:05:29] ========================================================
INFO [2026-05-16 04:05:29]   >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-16 04:05:29] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:29] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:29] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:29]    >> 'Achl_ACHLO041-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-16 04:05:29] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:29] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:29] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:29]    >> 'Achl_ACHLO041-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-16 04:05:29]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:05:30] ==========================================================
SUCCESS [2026-05-16 04:05:30] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:05:30] ==========================================================
INFO [2026-05-16 04:05:30]    >> 2 read(s) created from FASTA file.
INFO [2026-05-16 04:05:30]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:05:30]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:05:30] Aligning consensus reads ... 
INFO [2026-05-16 04:05:30] Before building!!
INFO [2026-05-16 04:05:30] After building!!
SUCCESS [2026-05-16 04:05:30] #############################################################
SUCCESS [2026-05-16 04:05:30] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-16 04:05:30] #############################################################
INFO [2026-05-16 04:05:30]   >> 4 contigs detected from 'regular expression'.
INFO [2026-05-16 04:05:30]       >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-16 04:05:30]           >> 1 forward reads.
INFO [2026-05-16 04:05:30]           >> 1 reverse reads.
INFO [2026-05-16 04:05:30]       >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-16 04:05:30]           >> 1 forward reads.
INFO [2026-05-16 04:05:30]           >> 1 reverse reads.
INFO [2026-05-16 04:05:30]       >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-16 04:05:30]           >> 1 forward reads.
INFO [2026-05-16 04:05:30]           >> 1 reverse reads.
INFO [2026-05-16 04:05:30]       >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-16 04:05:30]           >> 1 forward reads.
INFO [2026-05-16 04:05:30]           >> 1 reverse reads.
INFO [2026-05-16 04:05:30]   >> 8 reads created from FASTA file.
DEBUG [2026-05-16 04:05:30]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:05:30]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-16 04:05:30] #################################################
INFO [2026-05-16 04:05:30] #### Start creating SangerAlignment instance ####
INFO [2026-05-16 04:05:30] #################################################
INFO [2026-05-16 04:05:30] **** You are using CSV Name Conversion Method to group reads in FASTA file (with Csv file)!
INFO [2026-05-16 04:05:30] ========================================================
INFO [2026-05-16 04:05:30] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:05:30] ========================================================
INFO [2026-05-16 04:05:30]   >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-16 04:05:30] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:30] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:30] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:30]    >> 'Achl_ACHLO006-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-16 04:05:30] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:30] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:30] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:30]    >> 'Achl_ACHLO006-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-16 04:05:30]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:05:30] ==========================================================
SUCCESS [2026-05-16 04:05:30] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:05:30] ==========================================================
INFO [2026-05-16 04:05:30]    >> 2 read(s) created from FASTA file.
INFO [2026-05-16 04:05:30]      >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-16 04:05:30]      >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-16 04:05:30] ========================================================
INFO [2026-05-16 04:05:30] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:05:30] ========================================================
INFO [2026-05-16 04:05:30]   >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-16 04:05:30] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:30] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:30] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:30]    >> 'Achl_ACHLO007-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-16 04:05:30] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:30] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:30] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:30]    >> 'Achl_ACHLO007-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-16 04:05:30]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:05:30] ==========================================================
SUCCESS [2026-05-16 04:05:30] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:05:30] ==========================================================
INFO [2026-05-16 04:05:30]    >> 2 read(s) created from FASTA file.
INFO [2026-05-16 04:05:30]      >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-16 04:05:30]      >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-16 04:05:30] ========================================================
INFO [2026-05-16 04:05:30] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:05:30] ========================================================
INFO [2026-05-16 04:05:30]   >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-16 04:05:30] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:30] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:30] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:30]    >> 'Achl_ACHLO040-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-16 04:05:30] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:30] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:30] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:30]    >> 'Achl_ACHLO040-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-16 04:05:30]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:05:31] ==========================================================
SUCCESS [2026-05-16 04:05:31] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:05:31] ==========================================================
INFO [2026-05-16 04:05:31]    >> 2 read(s) created from FASTA file.
INFO [2026-05-16 04:05:31]      >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-16 04:05:31]      >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-16 04:05:31] ========================================================
INFO [2026-05-16 04:05:31] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:05:31] ========================================================
INFO [2026-05-16 04:05:31]   >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-16 04:05:31] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:31] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:31] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:31]    >> 'Achl_ACHLO041-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-16 04:05:31] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:31] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:31] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:31]    >> 'Achl_ACHLO041-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-16 04:05:31]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:05:31] ==========================================================
SUCCESS [2026-05-16 04:05:31] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:05:31] ==========================================================
INFO [2026-05-16 04:05:31]    >> 2 read(s) created from FASTA file.
INFO [2026-05-16 04:05:31]      >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-16 04:05:31]      >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-16 04:05:31] Aligning consensus reads ... 
INFO [2026-05-16 04:05:31] Before building!!
INFO [2026-05-16 04:05:31] After building!!
SUCCESS [2026-05-16 04:05:31] #############################################################
SUCCESS [2026-05-16 04:05:31] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-16 04:05:31] #############################################################
INFO [2026-05-16 04:05:31]   >> 4 contigs detected from 'csv file'.
INFO [2026-05-16 04:05:31]       >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-16 04:05:31]           >> 1 forward reads.
INFO [2026-05-16 04:05:31]           >> 1 reverse reads.
INFO [2026-05-16 04:05:31]       >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-16 04:05:31]           >> 1 forward reads.
INFO [2026-05-16 04:05:31]           >> 1 reverse reads.
INFO [2026-05-16 04:05:31]       >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-16 04:05:31]           >> 1 forward reads.
INFO [2026-05-16 04:05:31]           >> 1 reverse reads.
INFO [2026-05-16 04:05:31]       >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-16 04:05:31]           >> 1 forward reads.
INFO [2026-05-16 04:05:31]           >> 1 reverse reads.
INFO [2026-05-16 04:05:31]   >> 8 reads created from FASTA file.
DEBUG [2026-05-16 04:05:31]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:05:31]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
SUCCESS [2026-05-16 04:05:31] 'Achl_ACHLO006-09_1_F.ab1' is successfully created!
SUCCESS [2026-05-16 04:05:31] 'Achl_ACHLO006-09' is successfully created!
SUCCESS [2026-05-16 04:05:31] 'SangerAlignment' is successfully created!
ERROR [2026-05-16 04:05:31] FILE_NOT_EXIST_ERROR
'/no/such/path.ab1' file does not exist.
DEBUG [2026-05-16 04:05:31]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:05:31]    >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
ERROR [2026-05-16 04:05:31] FILE_NOT_EXIST_ERROR
'/no/such/path.ab1' file does not exist.
INFO [2026-05-16 04:05:31] ------------------------------------------------
INFO [2026-05-16 04:05:31] -------- Creating 'SangerRead' instance --------
INFO [2026-05-16 04:05:31] ------------------------------------------------
INFO [2026-05-16 04:05:31] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-16 04:05:31]     >> Creating Forward Read raw abif ...
INFO [2026-05-16 04:05:31]     >> Creating Forward Read raw sangerseq ...
INFO [2026-05-16 04:05:31]           * Making basecall !!
INFO [2026-05-16 04:05:31]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-16 04:05:31] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:31] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:31] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:32]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-16 04:05:32]    >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:05:32]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:05:32]    >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
SUCCESS [2026-05-16 04:05:32] 'Achl_ACHLO006-09_1_F.ab1' is successfully created!
INFO [2026-05-16 04:05:32] ------------------------------------------------
INFO [2026-05-16 04:05:32] -------- Creating 'SangerRead' instance --------
INFO [2026-05-16 04:05:32] ------------------------------------------------
INFO [2026-05-16 04:05:32] Forward Read: Creating SangerRead from FASTA ...
SUCCESS [2026-05-16 04:05:32] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:32] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:32] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:32]    >> 'Achl_ACHLO006-09_1_F' is created (Forward Read; FASTA).
INFO [2026-05-16 04:05:32]    >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:05:32]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:05:32]    >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
SUCCESS [2026-05-16 04:05:32] 'Achl_ACHLO006-09_1_F.fa' is successfully created!
ERROR [2026-05-16 04:05:32] 'object' must be S4 instance!
ERROR [2026-05-16 04:05:32] 'object' must be 'SangerAlignment' or 'SangerContig' S4 instance!
INFO [2026-05-16 04:05:32] Your input is 'SangerRead' S4 instance
INFO [2026-05-16 04:05:32] >>> outputDir : /tmp/RtmpeZL3QC/file113f96192364ba
INFO [2026-05-16 04:05:32] Start writing '/Library/Frameworks/R.framework/Versions/4.1/Resources/library/sangeranalyseR/extdata//Allolobophora_chlorotica/ACHLO/Achl_ACHLO006-09_1_F.ab1' to FASTA format ...
INFO [2026-05-16 04:05:32] >> '/tmp/RtmpeZL3QC/file113f96192364ba/Achl_ACHLO006-09_1_F.fa' is written
INFO [2026-05-16 04:05:32] Your input is 'SangerContig' S4 instance
INFO [2026-05-16 04:05:32] >>> outputDir : /tmp/RtmpeZL3QC/file113f96192364ba
INFO [2026-05-16 04:05:32] Start to write 'Achl_ACHLO006-09' to FASTA format ...
INFO [2026-05-16 04:05:32] >> Writing alignment to FASTA ...
INFO [2026-05-16 04:05:32] >> Writing all single reads to FASTA ...
INFO [2026-05-16 04:05:32] >> Writing consensus read to FASTA ...
INFO [2026-05-16 04:05:32] Finish writing 'Achl_ACHLO006-09' to FASTA format
INFO [2026-05-16 04:05:32] Your input is 'SangerAlignment' S4 instance
INFO [2026-05-16 04:05:32] >>> outputDir : /tmp/RtmpeZL3QC/file113f96192364ba
INFO [2026-05-16 04:05:32] Start to write 'SangerAlignment' to FASTA format ...
INFO [2026-05-16 04:05:32] >> Writing 'alignment' to FASTA ...
INFO [2026-05-16 04:05:32] >> Writing 'contigs' to FASTA ...
INFO [2026-05-16 04:05:32] >> Writing all single reads to FASTA ...
INFO [2026-05-16 04:05:32] Finish writing 'SangerAlignment' to FASTA format
ERROR [2026-05-16 04:05:32] 'object' must be S4 instance!
ERROR [2026-05-16 04:05:32] 'object' must be S4 instance!
INFO [2026-05-16 04:05:34]           * Making basecall !!
INFO [2026-05-16 04:05:34]           * Updating slots in 'SangerRead' instance !!
INFO [2026-05-16 04:05:35] #################################################
INFO [2026-05-16 04:05:35] #### Start creating SangerAlignment instance ####
INFO [2026-05-16 04:05:35] #################################################
INFO [2026-05-16 04:05:35]   >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-16 04:05:35] ========================================================
INFO [2026-05-16 04:05:35] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:05:35] ========================================================
INFO [2026-05-16 04:05:35]   >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-16 04:05:35] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:35] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:35] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:35]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:05:35] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:35] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:35] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:35]    >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:05:35]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:05:35] ==========================================================
SUCCESS [2026-05-16 04:05:35] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:05:35] ==========================================================
INFO [2026-05-16 04:05:35]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:05:35]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:05:35]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:05:35] ========================================================
INFO [2026-05-16 04:05:35] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:05:35] ========================================================
INFO [2026-05-16 04:05:35]   >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-16 04:05:35] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:35] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:35] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:35]    >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:05:35] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:35] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:35] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:36]    >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:05:36]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:05:36] ==========================================================
SUCCESS [2026-05-16 04:05:36] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:05:36] ==========================================================
INFO [2026-05-16 04:05:36]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:05:36]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:05:36]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:05:36] ========================================================
INFO [2026-05-16 04:05:36] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:05:36] ========================================================
INFO [2026-05-16 04:05:36]   >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-16 04:05:36] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:36] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:36] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:36]    >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:05:36] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:36] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:36] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:36]    >> 'Achl_ACHLO040-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:05:36]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:05:36] ==========================================================
SUCCESS [2026-05-16 04:05:36] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:05:36] ==========================================================
INFO [2026-05-16 04:05:36]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:05:36]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:05:36]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:05:36] ========================================================
INFO [2026-05-16 04:05:36] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:05:36] ========================================================
INFO [2026-05-16 04:05:36]   >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-16 04:05:36] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:36] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:36] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:36]    >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:05:37] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:37] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:37] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:37]    >> 'Achl_ACHLO041-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:05:37]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:05:37] ==========================================================
SUCCESS [2026-05-16 04:05:37] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:05:37] ==========================================================
INFO [2026-05-16 04:05:37]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:05:37]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:05:37]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:05:37] Aligning consensus reads ... 
INFO [2026-05-16 04:05:37] Before building!!
INFO [2026-05-16 04:05:37] After building!!
SUCCESS [2026-05-16 04:05:37] #############################################################
SUCCESS [2026-05-16 04:05:37] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-16 04:05:37] #############################################################
INFO [2026-05-16 04:05:37]   >> 4 contigs detected from 'regular expression'.
INFO [2026-05-16 04:05:37]       >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-16 04:05:37]           >> 1 forward reads.
INFO [2026-05-16 04:05:37]           >> 1 reverse reads.
INFO [2026-05-16 04:05:37]       >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-16 04:05:37]           >> 1 forward reads.
INFO [2026-05-16 04:05:37]           >> 1 reverse reads.
INFO [2026-05-16 04:05:37]       >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-16 04:05:37]           >> 1 forward reads.
INFO [2026-05-16 04:05:37]           >> 1 reverse reads.
INFO [2026-05-16 04:05:37]       >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-16 04:05:37]           >> 1 forward reads.
INFO [2026-05-16 04:05:37]           >> 1 reverse reads.
INFO [2026-05-16 04:05:37]   >> 8 reads created from ABIF file.
INFO [2026-05-16 04:05:37]   >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:05:37]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:05:37]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-16 04:05:42] Aligning consensus reads ... 
INFO [2026-05-16 04:05:42] Before building!!
INFO [2026-05-16 04:05:42] After building!!
INFO [2026-05-16 04:05:52] Aligning consensus reads ... 
INFO [2026-05-16 04:05:52] Before building!!
INFO [2026-05-16 04:05:52] After building!!
INFO [2026-05-16 04:05:53] #################################################
INFO [2026-05-16 04:05:53] #### Start creating SangerAlignment instance ####
INFO [2026-05-16 04:05:53] #################################################
INFO [2026-05-16 04:05:53] **** You are using Regular Expression Method to group reads in FASTA file (No CSV file)!
INFO [2026-05-16 04:05:53] ========================================================
INFO [2026-05-16 04:05:53] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:05:53] ========================================================
INFO [2026-05-16 04:05:53]   >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-16 04:05:53] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:53] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:53] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:53]    >> 'Achl_ACHLO006-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-16 04:05:53] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:53] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:53] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:53]    >> 'Achl_ACHLO006-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-16 04:05:53]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:05:54] ==========================================================
SUCCESS [2026-05-16 04:05:54] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:05:54] ==========================================================
INFO [2026-05-16 04:05:54]    >> 2 read(s) created from FASTA file.
INFO [2026-05-16 04:05:54]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:05:54]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:05:54] ========================================================
INFO [2026-05-16 04:05:54] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:05:54] ========================================================
INFO [2026-05-16 04:05:54]   >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-16 04:05:54] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:54] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:54] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:54]    >> 'Achl_ACHLO007-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-16 04:05:54] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:54] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:54] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:54]    >> 'Achl_ACHLO007-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-16 04:05:54]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:05:55] ==========================================================
SUCCESS [2026-05-16 04:05:55] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:05:55] ==========================================================
INFO [2026-05-16 04:05:55]    >> 2 read(s) created from FASTA file.
INFO [2026-05-16 04:05:55]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:05:55]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:05:55] ========================================================
INFO [2026-05-16 04:05:55] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:05:55] ========================================================
INFO [2026-05-16 04:05:55]   >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-16 04:05:55] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:55] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:55] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:55]    >> 'Achl_ACHLO040-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-16 04:05:55] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:55] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:55] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:55]    >> 'Achl_ACHLO040-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-16 04:05:55]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:05:56] ==========================================================
SUCCESS [2026-05-16 04:05:56] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:05:56] ==========================================================
INFO [2026-05-16 04:05:56]    >> 2 read(s) created from FASTA file.
INFO [2026-05-16 04:05:56]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:05:56]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:05:56] ========================================================
INFO [2026-05-16 04:05:56] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:05:56] ========================================================
INFO [2026-05-16 04:05:56]   >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-16 04:05:56] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:56] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:56] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:56]    >> 'Achl_ACHLO041-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-16 04:05:56] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:56] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:05:56] --------------------------------------------------------
SUCCESS [2026-05-16 04:05:56]    >> 'Achl_ACHLO041-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-16 04:05:56]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:05:59] ==========================================================
SUCCESS [2026-05-16 04:05:59] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:05:59] ==========================================================
INFO [2026-05-16 04:05:59]    >> 2 read(s) created from FASTA file.
INFO [2026-05-16 04:05:59]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:05:59]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:05:59] Aligning consensus reads ... 
INFO [2026-05-16 04:05:59] Before building!!
INFO [2026-05-16 04:05:59] After building!!
SUCCESS [2026-05-16 04:05:59] #############################################################
SUCCESS [2026-05-16 04:05:59] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-16 04:05:59] #############################################################
INFO [2026-05-16 04:05:59]   >> 4 contigs detected from 'regular expression'.
INFO [2026-05-16 04:05:59]       >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-16 04:05:59]           >> 1 forward reads.
INFO [2026-05-16 04:05:59]           >> 1 reverse reads.
INFO [2026-05-16 04:05:59]       >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-16 04:05:59]           >> 1 forward reads.
INFO [2026-05-16 04:05:59]           >> 1 reverse reads.
INFO [2026-05-16 04:05:59]       >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-16 04:05:59]           >> 1 forward reads.
INFO [2026-05-16 04:05:59]           >> 1 reverse reads.
INFO [2026-05-16 04:05:59]       >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-16 04:05:59]           >> 1 forward reads.
INFO [2026-05-16 04:05:59]           >> 1 reverse reads.
INFO [2026-05-16 04:05:59]   >> 8 reads created from FASTA file.
DEBUG [2026-05-16 04:05:59]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:05:59]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-16 04:05:59] SangerAlignment with 'FASTA' inputSource cannot update quality parameters
ERROR [2026-05-16 04:06:00] PARAMETER_VALUE_ERROR'TrimmingMethod' must be 'M1' or 'M2'.
ERROR [2026-05-16 04:06:00] PARAMETER_VALUE_ERROR'TrimmingMethod' must be 'M1' or 'M2'.
INFO [2026-05-16 04:06:00] >>> outputDir : /tmp/RtmpeZL3QC/file113f9648eb51b1
INFO [2026-05-16 04:06:02]           * Making basecall !!
INFO [2026-05-16 04:06:02]           * Updating slots in 'SangerRead' instance !!
INFO [2026-05-16 04:06:05] Chromatogram saved to /tmp/RtmpeZL3QC/file113f9648eb51b1/Achl_ACHLO006-09_1_F/Chromatogram.pdf in the current working directory
/usr/bin/pandoc +RTS -K512m -RTS SangerRead_Report_ab1.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpeZL3QC/file113f9648eb51b1/Achl_ACHLO006-09_1_F/SangerRead_Report_ab1.html --lua-filter /home/biocbuild/bbs-3.24-bioc/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.24-bioc/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /home/biocbuild/bbs-3.24-bioc/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpeZL3QC/rmarkdown-str113f96758c2fa0.html 
INFO [2026-05-16 04:06:18] ------------------------------------------------
INFO [2026-05-16 04:06:18] -------- Creating 'SangerRead' instance --------
INFO [2026-05-16 04:06:18] ------------------------------------------------
INFO [2026-05-16 04:06:18] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-16 04:06:18]     >> Creating Forward Read raw abif ...
INFO [2026-05-16 04:06:18]     >> Creating Forward Read raw sangerseq ...
INFO [2026-05-16 04:06:18]           * Making basecall !!
INFO [2026-05-16 04:06:18]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-16 04:06:18] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:18] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:18] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:18]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-16 04:06:18]    >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:06:18]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:06:18]    >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-16 04:06:18] ------------------------------------------------
INFO [2026-05-16 04:06:18] -------- Creating 'SangerRead' instance --------
INFO [2026-05-16 04:06:18] ------------------------------------------------
INFO [2026-05-16 04:06:18] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-16 04:06:18]     >> Creating Forward Read raw abif ...
INFO [2026-05-16 04:06:18]     >> Creating Forward Read raw sangerseq ...
INFO [2026-05-16 04:06:18]           * Making basecall !!
INFO [2026-05-16 04:06:18]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-16 04:06:18] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:18] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:18] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:18]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-16 04:06:18]    >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:06:18]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:06:18]    >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-16 04:06:18] ========================================================
INFO [2026-05-16 04:06:18] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:06:18] ========================================================
INFO [2026-05-16 04:06:18]   >> Contig Name: 'Achl_ACHLO006-09'
INFO [2026-05-16 04:06:18]   >> You are using Regular Expression Method to group reads in FASTA file (No CSV file)!
INFO [2026-05-16 04:06:18] >> Your contig name is Achl_ACHLO006-09
SUCCESS [2026-05-16 04:06:19] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:19] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:19] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:19]    >> 'Achl_ACHLO006-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-16 04:06:19] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:19] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:19] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:19]    >> 'Achl_ACHLO006-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-16 04:06:19]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:06:19] ==========================================================
SUCCESS [2026-05-16 04:06:19] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:06:19] ==========================================================
INFO [2026-05-16 04:06:19]    >> 2 read(s) created from FASTA file.
INFO [2026-05-16 04:06:19]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:06:19]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
DEBUG [2026-05-16 04:06:19]    >> For more information, please run 'object'
DEBUG [2026-05-16 04:06:19]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-16 04:06:19] ========================================================
INFO [2026-05-16 04:06:19] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:06:19] ========================================================
INFO [2026-05-16 04:06:19]   >> Contig Name: 'Achl_ACHLO006-09'
INFO [2026-05-16 04:06:19]   >> You are using CSV Name Conversion Method to group reads in FASTA file (with Csv file)!
INFO [2026-05-16 04:06:19] >> Your contig name is Achl_ACHLO006-09
SUCCESS [2026-05-16 04:06:19] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:19] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:19] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:19]    >> 'Achl_ACHLO006-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-16 04:06:19] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:19] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:19] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:19]    >> 'Achl_ACHLO006-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-16 04:06:19]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:06:19] ==========================================================
SUCCESS [2026-05-16 04:06:19] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:06:19] ==========================================================
INFO [2026-05-16 04:06:19]    >> 2 read(s) created from FASTA file.
INFO [2026-05-16 04:06:19]      >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-16 04:06:19]      >> 1 reads assigned to 'reverse reads' according to 'csv file'.
DEBUG [2026-05-16 04:06:19]    >> For more information, please run 'object'
DEBUG [2026-05-16 04:06:19]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-16 04:06:19] #################################################
INFO [2026-05-16 04:06:19] #### Start creating SangerAlignment instance ####
INFO [2026-05-16 04:06:19] #################################################
INFO [2026-05-16 04:06:19] **** You are using CSV Name Conversion Method to group AB1 files!
INFO [2026-05-16 04:06:19] **** Contig number in your Csv file is 2
INFO [2026-05-16 04:06:19] ========================================================
INFO [2026-05-16 04:06:19] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:06:19] ========================================================
INFO [2026-05-16 04:06:19]   >> Contig Name: 'rbcL2'
SUCCESS [2026-05-16 04:06:19] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:19] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:19] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:19]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:06:19] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:19] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:19] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:19]    >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:06:20] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:20] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:20] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:20]    >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
SUCCESS [2026-05-16 04:06:20] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:20] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:20] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:20]    >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:06:20]    >> The number of reads detected: 4
SUCCESS [2026-05-16 04:06:20] ==========================================================
SUCCESS [2026-05-16 04:06:20] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:06:20] ==========================================================
INFO [2026-05-16 04:06:20]    >> 4 read(s) created from ABIF file.
INFO [2026-05-16 04:06:20]      >> 2 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-16 04:06:20]      >> 2 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-16 04:06:20] ========================================================
INFO [2026-05-16 04:06:20] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:06:20] ========================================================
INFO [2026-05-16 04:06:20]   >> Contig Name: 'ITS5'
SUCCESS [2026-05-16 04:06:20] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:20] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:20] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:20]    >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:06:20] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:20] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:20] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:20]    >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:06:20] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:20] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:20] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:20]    >> 'Achl_ACHLO040-09_2_R.ab1' is created (Reverse Read; ABIF).
SUCCESS [2026-05-16 04:06:21] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:21] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:21] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:21]    >> 'Achl_ACHLO041-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:06:21]    >> The number of reads detected: 4
SUCCESS [2026-05-16 04:06:21] ==========================================================
SUCCESS [2026-05-16 04:06:21] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:06:21] ==========================================================
INFO [2026-05-16 04:06:21]    >> 4 read(s) created from ABIF file.
INFO [2026-05-16 04:06:21]      >> 2 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-16 04:06:21]      >> 2 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-16 04:06:21] Aligning consensus reads ... 
INFO [2026-05-16 04:06:21] Before building!!
INFO [2026-05-16 04:06:21] After building!!
INFO [2026-05-16 04:06:21] The number of contigs is less than 3 or quality of reads are too low. 'Contigs Tree' cannot be created.
SUCCESS [2026-05-16 04:06:21] #############################################################
SUCCESS [2026-05-16 04:06:21] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-16 04:06:21] #############################################################
INFO [2026-05-16 04:06:21]   >> 2 contigs detected from 'csv file'.
INFO [2026-05-16 04:06:21]       >> Contig 'rbcL2':
INFO [2026-05-16 04:06:21]           >> 2 forward reads.
INFO [2026-05-16 04:06:21]           >> 2 reverse reads.
INFO [2026-05-16 04:06:21]       >> Contig 'ITS5':
INFO [2026-05-16 04:06:21]           >> 2 forward reads.
INFO [2026-05-16 04:06:21]           >> 2 reverse reads.
INFO [2026-05-16 04:06:21]   >> 8 reads created from ABIF file.
INFO [2026-05-16 04:06:21]   >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:06:21]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:06:21]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
WARN [2026-05-16 04:06:21] 'Achl_ACHLO040-09_1_F.ab1' is not in the csv file (/tmp/RtmpeZL3QC/file113f965f4cfc4d/names_conversion.csv)
WARN [2026-05-16 04:06:21] 'Achl_ACHLO040-09_2_R.ab1' is not in the csv file (/tmp/RtmpeZL3QC/file113f965f4cfc4d/names_conversion.csv)
WARN [2026-05-16 04:06:21] 'Achl_ACHLO041-09_1_F.ab1' is not in the csv file (/tmp/RtmpeZL3QC/file113f965f4cfc4d/names_conversion.csv)
WARN [2026-05-16 04:06:21] 'Achl_ACHLO041-09_2_R.ab1' is not in the csv file (/tmp/RtmpeZL3QC/file113f965f4cfc4d/names_conversion.csv)
WARN [2026-05-16 04:06:21] 'NONEXISTENT_F.ab1' is not in the parent directory.
WARN [2026-05-16 04:06:21] 'NONEXISTENT_R.ab1' is not in the parent directory.
INFO [2026-05-16 04:06:21] #################################################
INFO [2026-05-16 04:06:21] #### Start creating SangerAlignment instance ####
INFO [2026-05-16 04:06:21] #################################################
INFO [2026-05-16 04:06:21] **** You are using CSV Name Conversion Method to group AB1 files!
INFO [2026-05-16 04:06:21] **** Contig number in your Csv file is 2
WARN [2026-05-16 04:06:21]   >> Contig 'ghost' has no reads matching any file under ABIF_Directory; skipping.
INFO [2026-05-16 04:06:21] ========================================================
INFO [2026-05-16 04:06:21] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:06:21] ========================================================
INFO [2026-05-16 04:06:21]   >> Contig Name: 'good'
SUCCESS [2026-05-16 04:06:21] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:21] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:21] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:21]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:06:21] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:21] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:21] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:21]    >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:06:21] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:21] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:21] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:21]    >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
SUCCESS [2026-05-16 04:06:22] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:22] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:22] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:22]    >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:06:22]    >> The number of reads detected: 4
SUCCESS [2026-05-16 04:06:22] ==========================================================
SUCCESS [2026-05-16 04:06:22] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:06:22] ==========================================================
INFO [2026-05-16 04:06:22]    >> 4 read(s) created from ABIF file.
INFO [2026-05-16 04:06:22]      >> 2 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-16 04:06:22]      >> 2 reads assigned to 'reverse reads' according to 'csv file'.
SUCCESS [2026-05-16 04:06:22] #############################################################
SUCCESS [2026-05-16 04:06:22] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-16 04:06:22] #############################################################
INFO [2026-05-16 04:06:22]   >> 1 contigs detected from 'csv file'.
INFO [2026-05-16 04:06:22]       >> Contig 'good':
INFO [2026-05-16 04:06:22]           >> 2 forward reads.
INFO [2026-05-16 04:06:22]           >> 2 reverse reads.
INFO [2026-05-16 04:06:22]   >> 4 reads created from ABIF file.
INFO [2026-05-16 04:06:22]   >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:06:22]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:06:22]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
WARN [2026-05-16 04:06:22] >> No 'REGEX_SuffixReverse' supplied; treating as forward-only run.
INFO [2026-05-16 04:06:22] #################################################
INFO [2026-05-16 04:06:22] #### Start creating SangerAlignment instance ####
INFO [2026-05-16 04:06:22] #################################################
INFO [2026-05-16 04:06:22]   >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-16 04:06:22] ========================================================
INFO [2026-05-16 04:06:22] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:06:22] ========================================================
INFO [2026-05-16 04:06:22]   >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-16 04:06:22] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:22] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:22] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:22]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-16 04:06:22]    >> The number of reads detected: 1
SUCCESS [2026-05-16 04:06:22] ==========================================================
SUCCESS [2026-05-16 04:06:22] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:06:22] ==========================================================
INFO [2026-05-16 04:06:22]    >> 1 read(s) created from ABIF file.
INFO [2026-05-16 04:06:22]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:06:22]      >> 0 reads assigned to 'reverse reads' according to 'regular expression'.
WARN [2026-05-16 04:06:22]   >> No 'reverse read' is detected!
WARN [2026-05-16 04:06:22]    >> There is only one read in your SangerContig.
WARN [2026-05-16 04:06:22] REGEX_MATCH_WARN
Your 'contigName' and 'REGEX_SuffixReverse' regular expression parameters can not match any reverse reads.
INFO [2026-05-16 04:06:22] ========================================================
INFO [2026-05-16 04:06:22] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:06:22] ========================================================
INFO [2026-05-16 04:06:22]   >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-16 04:06:22] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:22] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:22] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:22]    >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-16 04:06:22]    >> The number of reads detected: 1
SUCCESS [2026-05-16 04:06:22] ==========================================================
SUCCESS [2026-05-16 04:06:22] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:06:22] ==========================================================
INFO [2026-05-16 04:06:22]    >> 1 read(s) created from ABIF file.
INFO [2026-05-16 04:06:22]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:06:22]      >> 0 reads assigned to 'reverse reads' according to 'regular expression'.
WARN [2026-05-16 04:06:22]   >> No 'reverse read' is detected!
WARN [2026-05-16 04:06:22]    >> There is only one read in your SangerContig.
WARN [2026-05-16 04:06:22] REGEX_MATCH_WARN
Your 'contigName' and 'REGEX_SuffixReverse' regular expression parameters can not match any reverse reads.
INFO [2026-05-16 04:06:22] ========================================================
INFO [2026-05-16 04:06:22] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:06:22] ========================================================
INFO [2026-05-16 04:06:22]   >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-16 04:06:22] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:22] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:22] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:22]    >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-16 04:06:22]    >> The number of reads detected: 1
SUCCESS [2026-05-16 04:06:22] ==========================================================
SUCCESS [2026-05-16 04:06:22] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:06:22] ==========================================================
INFO [2026-05-16 04:06:22]    >> 1 read(s) created from ABIF file.
INFO [2026-05-16 04:06:22]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:06:22]      >> 0 reads assigned to 'reverse reads' according to 'regular expression'.
WARN [2026-05-16 04:06:22]   >> No 'reverse read' is detected!
WARN [2026-05-16 04:06:22]    >> There is only one read in your SangerContig.
WARN [2026-05-16 04:06:22] REGEX_MATCH_WARN
Your 'contigName' and 'REGEX_SuffixReverse' regular expression parameters can not match any reverse reads.
INFO [2026-05-16 04:06:22] ========================================================
INFO [2026-05-16 04:06:22] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:06:22] ========================================================
INFO [2026-05-16 04:06:22]   >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-16 04:06:23] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:23] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:23] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:23]    >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-16 04:06:23]    >> The number of reads detected: 1
SUCCESS [2026-05-16 04:06:23] ==========================================================
SUCCESS [2026-05-16 04:06:23] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:06:23] ==========================================================
INFO [2026-05-16 04:06:23]    >> 1 read(s) created from ABIF file.
INFO [2026-05-16 04:06:23]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:06:23]      >> 0 reads assigned to 'reverse reads' according to 'regular expression'.
WARN [2026-05-16 04:06:23]   >> No 'reverse read' is detected!
WARN [2026-05-16 04:06:23]    >> There is only one read in your SangerContig.
WARN [2026-05-16 04:06:23] REGEX_MATCH_WARN
Your 'contigName' and 'REGEX_SuffixReverse' regular expression parameters can not match any reverse reads.
INFO [2026-05-16 04:06:23] Aligning consensus reads ... 
INFO [2026-05-16 04:06:23] Before building!!
INFO [2026-05-16 04:06:23] After building!!
SUCCESS [2026-05-16 04:06:23] #############################################################
SUCCESS [2026-05-16 04:06:23] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-16 04:06:23] #############################################################
INFO [2026-05-16 04:06:23]   >> 4 contigs detected from 'regular expression'.
INFO [2026-05-16 04:06:23]       >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-16 04:06:23]           >> 1 forward reads.
INFO [2026-05-16 04:06:23]           >> 0 reverse reads.
INFO [2026-05-16 04:06:23]       >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-16 04:06:23]           >> 1 forward reads.
INFO [2026-05-16 04:06:23]           >> 0 reverse reads.
INFO [2026-05-16 04:06:23]       >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-16 04:06:23]           >> 1 forward reads.
INFO [2026-05-16 04:06:23]           >> 0 reverse reads.
INFO [2026-05-16 04:06:23]       >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-16 04:06:23]           >> 1 forward reads.
INFO [2026-05-16 04:06:23]           >> 0 reverse reads.
INFO [2026-05-16 04:06:23]   >> 4 reads created from ABIF file.
INFO [2026-05-16 04:06:23]   >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:06:23]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:06:23]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
WARN [2026-05-16 04:06:23] >> No 'REGEX_SuffixReverse' supplied; treating as forward-only run.
INFO [2026-05-16 04:06:23] #################################################
INFO [2026-05-16 04:06:23] #### Start creating SangerAlignment instance ####
INFO [2026-05-16 04:06:23] #################################################
INFO [2026-05-16 04:06:23]   >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-16 04:06:23] ========================================================
INFO [2026-05-16 04:06:23] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:06:23] ========================================================
INFO [2026-05-16 04:06:23]   >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-16 04:06:23] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:23] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:23] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:23]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-16 04:06:23]    >> The number of reads detected: 1
SUCCESS [2026-05-16 04:06:23] ==========================================================
SUCCESS [2026-05-16 04:06:23] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:06:23] ==========================================================
INFO [2026-05-16 04:06:23]    >> 1 read(s) created from ABIF file.
INFO [2026-05-16 04:06:23]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:06:23]      >> 0 reads assigned to 'reverse reads' according to 'regular expression'.
WARN [2026-05-16 04:06:23]   >> No 'reverse read' is detected!
WARN [2026-05-16 04:06:23]    >> There is only one read in your SangerContig.
WARN [2026-05-16 04:06:23] REGEX_MATCH_WARN
Your 'contigName' and 'REGEX_SuffixReverse' regular expression parameters can not match any reverse reads.
INFO [2026-05-16 04:06:23] ========================================================
INFO [2026-05-16 04:06:23] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:06:23] ========================================================
INFO [2026-05-16 04:06:23]   >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-16 04:06:23] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:23] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:23] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:23]    >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-16 04:06:23]    >> The number of reads detected: 1
SUCCESS [2026-05-16 04:06:23] ==========================================================
SUCCESS [2026-05-16 04:06:23] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:06:23] ==========================================================
INFO [2026-05-16 04:06:23]    >> 1 read(s) created from ABIF file.
INFO [2026-05-16 04:06:23]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:06:23]      >> 0 reads assigned to 'reverse reads' according to 'regular expression'.
WARN [2026-05-16 04:06:23]   >> No 'reverse read' is detected!
WARN [2026-05-16 04:06:23]    >> There is only one read in your SangerContig.
WARN [2026-05-16 04:06:23] REGEX_MATCH_WARN
Your 'contigName' and 'REGEX_SuffixReverse' regular expression parameters can not match any reverse reads.
INFO [2026-05-16 04:06:23] ========================================================
INFO [2026-05-16 04:06:23] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:06:23] ========================================================
INFO [2026-05-16 04:06:23]   >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-16 04:06:23] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:23] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:23] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:23]    >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-16 04:06:23]    >> The number of reads detected: 1
SUCCESS [2026-05-16 04:06:23] ==========================================================
SUCCESS [2026-05-16 04:06:23] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:06:23] ==========================================================
INFO [2026-05-16 04:06:23]    >> 1 read(s) created from ABIF file.
INFO [2026-05-16 04:06:23]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:06:23]      >> 0 reads assigned to 'reverse reads' according to 'regular expression'.
WARN [2026-05-16 04:06:23]   >> No 'reverse read' is detected!
WARN [2026-05-16 04:06:23]    >> There is only one read in your SangerContig.
WARN [2026-05-16 04:06:23] REGEX_MATCH_WARN
Your 'contigName' and 'REGEX_SuffixReverse' regular expression parameters can not match any reverse reads.
INFO [2026-05-16 04:06:23] ========================================================
INFO [2026-05-16 04:06:23] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:06:23] ========================================================
INFO [2026-05-16 04:06:23]   >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-16 04:06:24] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:24] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:24] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:24]    >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-16 04:06:24]    >> The number of reads detected: 1
SUCCESS [2026-05-16 04:06:24] ==========================================================
SUCCESS [2026-05-16 04:06:24] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:06:24] ==========================================================
INFO [2026-05-16 04:06:24]    >> 1 read(s) created from ABIF file.
INFO [2026-05-16 04:06:24]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:06:24]      >> 0 reads assigned to 'reverse reads' according to 'regular expression'.
WARN [2026-05-16 04:06:24]   >> No 'reverse read' is detected!
WARN [2026-05-16 04:06:24]    >> There is only one read in your SangerContig.
WARN [2026-05-16 04:06:24] REGEX_MATCH_WARN
Your 'contigName' and 'REGEX_SuffixReverse' regular expression parameters can not match any reverse reads.
INFO [2026-05-16 04:06:24] Aligning consensus reads ... 
INFO [2026-05-16 04:06:24] Before building!!
INFO [2026-05-16 04:06:24] After building!!
SUCCESS [2026-05-16 04:06:24] #############################################################
SUCCESS [2026-05-16 04:06:24] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-16 04:06:24] #############################################################
INFO [2026-05-16 04:06:24]   >> 4 contigs detected from 'regular expression'.
INFO [2026-05-16 04:06:24]       >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-16 04:06:24]           >> 1 forward reads.
INFO [2026-05-16 04:06:24]           >> 0 reverse reads.
INFO [2026-05-16 04:06:24]       >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-16 04:06:24]           >> 1 forward reads.
INFO [2026-05-16 04:06:24]           >> 0 reverse reads.
INFO [2026-05-16 04:06:24]       >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-16 04:06:24]           >> 1 forward reads.
INFO [2026-05-16 04:06:24]           >> 0 reverse reads.
INFO [2026-05-16 04:06:24]       >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-16 04:06:24]           >> 1 forward reads.
INFO [2026-05-16 04:06:24]           >> 0 reverse reads.
INFO [2026-05-16 04:06:24]   >> 4 reads created from ABIF file.
INFO [2026-05-16 04:06:24]   >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:06:24]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:06:24]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
WARN [2026-05-16 04:06:24] >> No 'REGEX_SuffixReverse' supplied; treating as forward-only contig.
INFO [2026-05-16 04:06:24] ========================================================
INFO [2026-05-16 04:06:24] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:06:24] ========================================================
INFO [2026-05-16 04:06:24]   >> Contig Name: 'Achl_ACHLO006-09'
INFO [2026-05-16 04:06:24]   >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-16 04:06:24] >> Your contig name is Achl_ACHLO006-09
SUCCESS [2026-05-16 04:06:24] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:24] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:24] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:24]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-16 04:06:24]    >> The number of reads detected: 1
SUCCESS [2026-05-16 04:06:24] ==========================================================
SUCCESS [2026-05-16 04:06:24] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:06:24] ==========================================================
INFO [2026-05-16 04:06:24]    >> 1 read(s) created from ABIF file.
INFO [2026-05-16 04:06:24]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:06:24]      >> 0 reads assigned to 'reverse reads' according to 'regular expression'.
WARN [2026-05-16 04:06:24]   >> No 'reverse read' is detected!
WARN [2026-05-16 04:06:24]    >> There is only one read in your SangerContig.
INFO [2026-05-16 04:06:24]    >> Trimmed by 'M1 - Mott's trimming algorithm'.
WARN [2026-05-16 04:06:24] REGEX_MATCH_WARN
Your 'contigName' and 'REGEX_SuffixReverse' regular expression parameters can not match any reverse reads.
DEBUG [2026-05-16 04:06:24]    >> For more information, please run 'object'
DEBUG [2026-05-16 04:06:24]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-16 04:06:24] ------------------------------------------------
INFO [2026-05-16 04:06:24] -------- Creating 'SangerRead' instance --------
INFO [2026-05-16 04:06:24] ------------------------------------------------
INFO [2026-05-16 04:06:24] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-16 04:06:24]     >> Creating Forward Read raw abif ...
INFO [2026-05-16 04:06:24]     >> Creating Forward Read raw sangerseq ...
WARN [2026-05-16 04:06:24] >> ABIF 'Achl_ACHLO006-09_1_F.ab1' has no PCON.2 quality block; synthesising flat Phred 30 (MISSING_QUALITY_SCORES_WARN).
INFO [2026-05-16 04:06:24]           * Making basecall !!
INFO [2026-05-16 04:06:24]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-16 04:06:24] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:24] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:24] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:24]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-16 04:06:24]    >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:06:24]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:06:24]    >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-16 04:06:24] ------------------------------------------------
INFO [2026-05-16 04:06:24] -------- Creating 'SangerRead' instance --------
INFO [2026-05-16 04:06:24] ------------------------------------------------
INFO [2026-05-16 04:06:24] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-16 04:06:24]     >> Creating Forward Read raw abif ...
INFO [2026-05-16 04:06:24]     >> Creating Forward Read raw sangerseq ...
INFO [2026-05-16 04:06:24]           * Making basecall !!
INFO [2026-05-16 04:06:24]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-16 04:06:24] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:24] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:24] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:24]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-16 04:06:24]    >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:06:24]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:06:24]    >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
WARN [2026-05-16 04:06:24] >> No 'REGEX_SuffixReverse' supplied; treating as forward-only contig.
INFO [2026-05-16 04:06:24] ========================================================
INFO [2026-05-16 04:06:24] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:06:24] ========================================================
INFO [2026-05-16 04:06:24]   >> Contig Name: 'Achl_ACHLO006-09'
INFO [2026-05-16 04:06:24]   >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-16 04:06:24] >> Your contig name is Achl_ACHLO006-09
SUCCESS [2026-05-16 04:06:24] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:24] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:24] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:24]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-16 04:06:24]    >> The number of reads detected: 1
SUCCESS [2026-05-16 04:06:24] ==========================================================
SUCCESS [2026-05-16 04:06:24] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:06:24] ==========================================================
INFO [2026-05-16 04:06:24]    >> 1 read(s) created from ABIF file.
INFO [2026-05-16 04:06:24]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:06:24]      >> 0 reads assigned to 'reverse reads' according to 'regular expression'.
WARN [2026-05-16 04:06:24]   >> No 'reverse read' is detected!
WARN [2026-05-16 04:06:24]    >> There is only one read in your SangerContig.
INFO [2026-05-16 04:06:24]    >> Trimmed by 'M1 - Mott's trimming algorithm'.
WARN [2026-05-16 04:06:24] REGEX_MATCH_WARN
Your 'contigName' and 'REGEX_SuffixReverse' regular expression parameters can not match any reverse reads.
DEBUG [2026-05-16 04:06:24]    >> For more information, please run 'object'
DEBUG [2026-05-16 04:06:24]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-16 04:06:24] >>> outputDir : /tmp/RtmpeZL3QC/file113f96762ab0dd
INFO [2026-05-16 04:06:24] Start to write 'Achl_ACHLO006-09' to FASTA format ...
INFO [2026-05-16 04:06:24] >> Writing alignment to FASTA ...
INFO [2026-05-16 04:06:24] >> Writing all single reads to FASTA ...
INFO [2026-05-16 04:06:24] >> Writing consensus read to FASTA ...
INFO [2026-05-16 04:06:24] Finish writing 'Achl_ACHLO006-09' to FASTA format
WARN [2026-05-16 04:06:24] >> No 'REGEX_SuffixReverse' supplied; treating as forward-only contig.
INFO [2026-05-16 04:06:24] ========================================================
INFO [2026-05-16 04:06:24] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:06:24] ========================================================
INFO [2026-05-16 04:06:24]   >> Contig Name: 'Achl_ACHLO006-09'
INFO [2026-05-16 04:06:24]   >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-16 04:06:24] >> Your contig name is Achl_ACHLO006-09
SUCCESS [2026-05-16 04:06:25] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:25] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:25] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:25]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-16 04:06:25]    >> The number of reads detected: 1
SUCCESS [2026-05-16 04:06:25] ==========================================================
SUCCESS [2026-05-16 04:06:25] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:06:25] ==========================================================
INFO [2026-05-16 04:06:25]    >> 1 read(s) created from ABIF file.
INFO [2026-05-16 04:06:25]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:06:25]      >> 0 reads assigned to 'reverse reads' according to 'regular expression'.
WARN [2026-05-16 04:06:25]   >> No 'reverse read' is detected!
WARN [2026-05-16 04:06:25]    >> There is only one read in your SangerContig.
INFO [2026-05-16 04:06:25]    >> Trimmed by 'M1 - Mott's trimming algorithm'.
WARN [2026-05-16 04:06:25] REGEX_MATCH_WARN
Your 'contigName' and 'REGEX_SuffixReverse' regular expression parameters can not match any reverse reads.
DEBUG [2026-05-16 04:06:25]    >> For more information, please run 'object'
DEBUG [2026-05-16 04:06:25]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-16 04:06:25] Your input is 'SangerContig' S4 instance
INFO [2026-05-16 04:06:25] >>> outputDir : /tmp/RtmpeZL3QC/file113f9658f970e3
INFO [2026-05-16 04:06:25] Start to write 'Achl_ACHLO006-09' to FASTA format ...
INFO [2026-05-16 04:06:25] >> Writing alignment to FASTA ...
INFO [2026-05-16 04:06:25] >> Writing all single reads to FASTA ...
INFO [2026-05-16 04:06:25] >> Writing consensus read to FASTA ...
INFO [2026-05-16 04:06:25] Finish writing 'Achl_ACHLO006-09' to FASTA format
WARN [2026-05-16 04:06:25] >> Dropping 1 read(s) with trimmed length < 2 bp (MIN_READ_LENGTH_DEFENSIVE_DROP).
WARN [2026-05-16 04:06:25] >> Fewer than 2 usable reads after defensive filter; returning empty consensus.
INFO [2026-05-16 04:06:25] ------------------------------------------------
INFO [2026-05-16 04:06:25] -------- Creating 'SangerRead' instance --------
INFO [2026-05-16 04:06:25] ------------------------------------------------
INFO [2026-05-16 04:06:25] Forward Read: Creating SangerRead from FASTA ...
SUCCESS [2026-05-16 04:06:25] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:25] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:25] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:25]    >> 'Achl_ACHLO006-09_1_F' is created (Forward Read; FASTA).
INFO [2026-05-16 04:06:25]    >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:06:25]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:06:25]    >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-16 04:06:25] ------------------------------------------------
INFO [2026-05-16 04:06:25] -------- Creating 'SangerRead' instance --------
INFO [2026-05-16 04:06:25] ------------------------------------------------
INFO [2026-05-16 04:06:25] Reverse Read: Creating SangerRead from FASTA ...
SUCCESS [2026-05-16 04:06:25] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:25] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:25] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:25]    >> 'Achl_ACHLO006-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-16 04:06:25]    >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:06:25]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:06:25]    >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-16 04:06:25] ========================================================
INFO [2026-05-16 04:06:25] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:06:25] ========================================================
INFO [2026-05-16 04:06:25]   >> Contig Name: 'Achl_ACHLO006-09'
INFO [2026-05-16 04:06:25]   >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-16 04:06:25] >> Your contig name is Achl_ACHLO006-09
SUCCESS [2026-05-16 04:06:25] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:25] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:25] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:25]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:06:26] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:26] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:26] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:26]    >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:06:26]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:06:26] ==========================================================
SUCCESS [2026-05-16 04:06:26] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:06:26] ==========================================================
INFO [2026-05-16 04:06:26]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:06:26]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:06:26]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:06:26]    >> Trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:06:26]    >> For more information, please run 'object'
DEBUG [2026-05-16 04:06:26]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
WARN [2026-05-16 04:06:26] Read(s) assigned to >1 distinct contig in CSV: 'Achl_ACHLO006-09_1_F.ab1'. Each read must belong to exactly one contig.
WARN [2026-05-16 04:06:26] 'Achl_ACHLO007-09_1_F.ab1' is not in the csv file (/tmp/RtmpeZL3QC/file113f96749d68fe/names_conversion.csv)
WARN [2026-05-16 04:06:26] 'Achl_ACHLO040-09_1_F.ab1' is not in the csv file (/tmp/RtmpeZL3QC/file113f96749d68fe/names_conversion.csv)
WARN [2026-05-16 04:06:26] 'Achl_ACHLO040-09_2_R.ab1' is not in the csv file (/tmp/RtmpeZL3QC/file113f96749d68fe/names_conversion.csv)
WARN [2026-05-16 04:06:26] 'Achl_ACHLO041-09_1_F.ab1' is not in the csv file (/tmp/RtmpeZL3QC/file113f96749d68fe/names_conversion.csv)
WARN [2026-05-16 04:06:26] 'Achl_ACHLO041-09_2_R.ab1' is not in the csv file (/tmp/RtmpeZL3QC/file113f96749d68fe/names_conversion.csv)
WARN [2026-05-16 04:06:26] Read(s) assigned to >1 distinct contig in CSV: 'Achl_ACHLO006-09_1_F.ab1'. Each read must belong to exactly one contig. (READ_ASSIGNED_MULTIPLE_CONTIGS_WARN)
[[1]]
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INFO [2026-05-16 04:06:26] ========================================================
INFO [2026-05-16 04:06:26] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:06:26] ========================================================
INFO [2026-05-16 04:06:26]   >> Contig Name: 'Achl_ACHLO006-09'
INFO [2026-05-16 04:06:26]   >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-16 04:06:26] >> Your contig name is Achl_ACHLO006-09
SUCCESS [2026-05-16 04:06:26] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:26] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:26] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:26]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:06:27] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:27] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:27] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:27]    >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:06:27]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:06:27] ==========================================================
SUCCESS [2026-05-16 04:06:27] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:06:27] ==========================================================
INFO [2026-05-16 04:06:27]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:06:27]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:06:27]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:06:27]    >> Trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:06:27]    >> For more information, please run 'object'
DEBUG [2026-05-16 04:06:27]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-16 04:06:27] ========================================================
INFO [2026-05-16 04:06:27] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:06:27] ========================================================
INFO [2026-05-16 04:06:27]   >> Contig Name: 'Achl_ACHLO006-09'
INFO [2026-05-16 04:06:27]   >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-16 04:06:27] >> Your contig name is Achl_ACHLO006-09
SUCCESS [2026-05-16 04:06:27] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:27] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:27] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:27]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:06:27] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:27] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:27] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:27]    >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:06:27]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:06:28] ==========================================================
SUCCESS [2026-05-16 04:06:28] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:06:28] ==========================================================
INFO [2026-05-16 04:06:28]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:06:28]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:06:28]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:06:28]    >> Trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:06:28]    >> For more information, please run 'object'
DEBUG [2026-05-16 04:06:28]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-16 04:06:28] ========================================================
INFO [2026-05-16 04:06:28] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:06:28] ========================================================
INFO [2026-05-16 04:06:28]   >> Contig Name: 'Achl_ACHLO006-09'
INFO [2026-05-16 04:06:28]   >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-16 04:06:28] >> Your contig name is Achl_ACHLO006-09
SUCCESS [2026-05-16 04:06:28] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:28] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:28] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:28]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:06:28] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:28] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:28] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:28]    >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:06:28]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:06:28] ==========================================================
SUCCESS [2026-05-16 04:06:28] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:06:28] ==========================================================
INFO [2026-05-16 04:06:28]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:06:28]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:06:28]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:06:28]    >> Trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:06:28]    >> For more information, please run 'object'
DEBUG [2026-05-16 04:06:28]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-16 04:06:28] ========================================================
INFO [2026-05-16 04:06:28] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:06:28] ========================================================
INFO [2026-05-16 04:06:28]   >> Contig Name: 'Achl_ACHLO006-09'
INFO [2026-05-16 04:06:28]   >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-16 04:06:28] >> Your contig name is Achl_ACHLO006-09
SUCCESS [2026-05-16 04:06:28] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:28] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:28] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:28]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:06:29] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:29] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:29] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:29]    >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:06:29]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:06:29] ==========================================================
SUCCESS [2026-05-16 04:06:29] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:06:29] ==========================================================
INFO [2026-05-16 04:06:29]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:06:29]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:06:29]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:06:29]    >> Trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:06:29]    >> For more information, please run 'object'
DEBUG [2026-05-16 04:06:29]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-16 04:06:29] #################################################
INFO [2026-05-16 04:06:29] #### Start creating SangerAlignment instance ####
INFO [2026-05-16 04:06:29] #################################################
INFO [2026-05-16 04:06:29]   >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-16 04:06:29] ========================================================
INFO [2026-05-16 04:06:29] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:06:29] ========================================================
INFO [2026-05-16 04:06:29]   >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-16 04:06:29] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:29] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:29] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:29]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:06:30] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:30] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:30] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:30]    >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:06:30]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:06:30] ==========================================================
SUCCESS [2026-05-16 04:06:30] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:06:30] ==========================================================
INFO [2026-05-16 04:06:30]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:06:30]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:06:30]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:06:30] ========================================================
INFO [2026-05-16 04:06:30] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:06:30] ========================================================
INFO [2026-05-16 04:06:30]   >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-16 04:06:30] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:30] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:30] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:30]    >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:06:30] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:30] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:30] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:30]    >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:06:30]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:06:31] ==========================================================
SUCCESS [2026-05-16 04:06:31] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:06:31] ==========================================================
INFO [2026-05-16 04:06:31]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:06:31]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:06:31]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:06:31] ========================================================
INFO [2026-05-16 04:06:31] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:06:31] ========================================================
INFO [2026-05-16 04:06:31]   >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-16 04:06:31] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:31] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:31] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:31]    >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:06:31] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:31] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:31] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:31]    >> 'Achl_ACHLO040-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:06:31]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:06:31] ==========================================================
SUCCESS [2026-05-16 04:06:31] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:06:31] ==========================================================
INFO [2026-05-16 04:06:31]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:06:31]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:06:31]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:06:31] ========================================================
INFO [2026-05-16 04:06:31] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:06:31] ========================================================
INFO [2026-05-16 04:06:31]   >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-16 04:06:31] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:31] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:31] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:31]    >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:06:32] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:32] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:32] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:32]    >> 'Achl_ACHLO041-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:06:32]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:06:32] ==========================================================
SUCCESS [2026-05-16 04:06:32] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:06:32] ==========================================================
INFO [2026-05-16 04:06:32]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:06:32]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:06:32]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:06:32] Aligning consensus reads ... 
INFO [2026-05-16 04:06:32] Before building!!
INFO [2026-05-16 04:06:32] After building!!
SUCCESS [2026-05-16 04:06:32] #############################################################
SUCCESS [2026-05-16 04:06:32] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-16 04:06:32] #############################################################
INFO [2026-05-16 04:06:32]   >> 4 contigs detected from 'regular expression'.
INFO [2026-05-16 04:06:32]       >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-16 04:06:32]           >> 1 forward reads.
INFO [2026-05-16 04:06:32]           >> 1 reverse reads.
INFO [2026-05-16 04:06:32]       >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-16 04:06:32]           >> 1 forward reads.
INFO [2026-05-16 04:06:32]           >> 1 reverse reads.
INFO [2026-05-16 04:06:32]       >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-16 04:06:32]           >> 1 forward reads.
INFO [2026-05-16 04:06:32]           >> 1 reverse reads.
INFO [2026-05-16 04:06:32]       >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-16 04:06:32]           >> 1 forward reads.
INFO [2026-05-16 04:06:32]           >> 1 reverse reads.
INFO [2026-05-16 04:06:32]   >> 8 reads created from ABIF file.
INFO [2026-05-16 04:06:32]   >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:06:32]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:06:32]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-16 04:06:32] #################################################
INFO [2026-05-16 04:06:32] #### Start creating SangerAlignment instance ####
INFO [2026-05-16 04:06:32] #################################################
INFO [2026-05-16 04:06:32] **** You are using Regular Expression Method to group reads in FASTA file (No CSV file)!
INFO [2026-05-16 04:06:32] ========================================================
INFO [2026-05-16 04:06:32] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:06:32] ========================================================
INFO [2026-05-16 04:06:32]   >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-16 04:06:32] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:32] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:32] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:32]    >> 'Achl_ACHLO006-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-16 04:06:32] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:32] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:32] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:32]    >> 'Achl_ACHLO006-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-16 04:06:32]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:06:32] ==========================================================
SUCCESS [2026-05-16 04:06:32] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:06:32] ==========================================================
INFO [2026-05-16 04:06:32]    >> 2 read(s) created from FASTA file.
INFO [2026-05-16 04:06:32]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:06:32]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:06:32] ========================================================
INFO [2026-05-16 04:06:32] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:06:32] ========================================================
INFO [2026-05-16 04:06:32]   >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-16 04:06:32] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:32] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:32] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:32]    >> 'Achl_ACHLO007-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-16 04:06:32] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:32] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:32] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:32]    >> 'Achl_ACHLO007-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-16 04:06:32]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:06:33] ==========================================================
SUCCESS [2026-05-16 04:06:33] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:06:33] ==========================================================
INFO [2026-05-16 04:06:33]    >> 2 read(s) created from FASTA file.
INFO [2026-05-16 04:06:33]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:06:33]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:06:33] ========================================================
INFO [2026-05-16 04:06:33] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:06:33] ========================================================
INFO [2026-05-16 04:06:33]   >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-16 04:06:33] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:33] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:33] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:33]    >> 'Achl_ACHLO040-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-16 04:06:33] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:33] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:33] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:33]    >> 'Achl_ACHLO040-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-16 04:06:33]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:06:33] ==========================================================
SUCCESS [2026-05-16 04:06:33] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:06:33] ==========================================================
INFO [2026-05-16 04:06:33]    >> 2 read(s) created from FASTA file.
INFO [2026-05-16 04:06:33]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:06:33]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:06:33] ========================================================
INFO [2026-05-16 04:06:33] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:06:33] ========================================================
INFO [2026-05-16 04:06:33]   >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-16 04:06:33] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:33] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:33] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:33]    >> 'Achl_ACHLO041-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-16 04:06:33] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:33] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:33] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:33]    >> 'Achl_ACHLO041-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-16 04:06:33]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:06:33] ==========================================================
SUCCESS [2026-05-16 04:06:33] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:06:33] ==========================================================
INFO [2026-05-16 04:06:33]    >> 2 read(s) created from FASTA file.
INFO [2026-05-16 04:06:33]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:06:33]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:06:33] Aligning consensus reads ... 
INFO [2026-05-16 04:06:33] Before building!!
INFO [2026-05-16 04:06:33] After building!!
SUCCESS [2026-05-16 04:06:33] #############################################################
SUCCESS [2026-05-16 04:06:33] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-16 04:06:33] #############################################################
INFO [2026-05-16 04:06:33]   >> 4 contigs detected from 'regular expression'.
INFO [2026-05-16 04:06:33]       >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-16 04:06:33]           >> 1 forward reads.
INFO [2026-05-16 04:06:33]           >> 1 reverse reads.
INFO [2026-05-16 04:06:33]       >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-16 04:06:33]           >> 1 forward reads.
INFO [2026-05-16 04:06:33]           >> 1 reverse reads.
INFO [2026-05-16 04:06:33]       >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-16 04:06:33]           >> 1 forward reads.
INFO [2026-05-16 04:06:33]           >> 1 reverse reads.
INFO [2026-05-16 04:06:33]       >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-16 04:06:33]           >> 1 forward reads.
INFO [2026-05-16 04:06:33]           >> 1 reverse reads.
INFO [2026-05-16 04:06:33]   >> 8 reads created from FASTA file.
DEBUG [2026-05-16 04:06:33]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:06:33]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-16 04:06:33] #################################################
INFO [2026-05-16 04:06:33] #### Start creating SangerAlignment instance ####
INFO [2026-05-16 04:06:33] #################################################
INFO [2026-05-16 04:06:33]   >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-16 04:06:33] ========================================================
INFO [2026-05-16 04:06:33] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:06:33] ========================================================
INFO [2026-05-16 04:06:33]   >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-16 04:06:34] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:34] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:34] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:34]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:06:34] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:34] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:34] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:34]    >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:06:34]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:06:34] ==========================================================
SUCCESS [2026-05-16 04:06:34] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:06:34] ==========================================================
INFO [2026-05-16 04:06:34]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:06:34]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:06:34]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:06:34] ========================================================
INFO [2026-05-16 04:06:34] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:06:34] ========================================================
INFO [2026-05-16 04:06:34]   >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-16 04:06:34] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:34] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:34] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:34]    >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:06:34] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:34] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:34] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:34]    >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:06:34]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:06:35] ==========================================================
SUCCESS [2026-05-16 04:06:35] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:06:35] ==========================================================
INFO [2026-05-16 04:06:35]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:06:35]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:06:35]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:06:35] ========================================================
INFO [2026-05-16 04:06:35] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:06:35] ========================================================
INFO [2026-05-16 04:06:35]   >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-16 04:06:35] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:35] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:35] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:35]    >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:06:35] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:35] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:35] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:35]    >> 'Achl_ACHLO040-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:06:35]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:06:35] ==========================================================
SUCCESS [2026-05-16 04:06:35] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:06:35] ==========================================================
INFO [2026-05-16 04:06:35]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:06:35]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:06:35]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:06:35] ========================================================
INFO [2026-05-16 04:06:35] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:06:35] ========================================================
INFO [2026-05-16 04:06:35]   >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-16 04:06:35] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:35] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:35] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:35]    >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:06:35] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:35] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:35] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:35]    >> 'Achl_ACHLO041-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:06:36]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:06:36] ==========================================================
SUCCESS [2026-05-16 04:06:36] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:06:36] ==========================================================
INFO [2026-05-16 04:06:36]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:06:36]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:06:36]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:06:36] Aligning consensus reads ... 
INFO [2026-05-16 04:06:36] Before building!!
INFO [2026-05-16 04:06:36] After building!!
SUCCESS [2026-05-16 04:06:36] #############################################################
SUCCESS [2026-05-16 04:06:36] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-16 04:06:36] #############################################################
INFO [2026-05-16 04:06:36]   >> 4 contigs detected from 'regular expression'.
INFO [2026-05-16 04:06:36]       >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-16 04:06:36]           >> 1 forward reads.
INFO [2026-05-16 04:06:36]           >> 1 reverse reads.
INFO [2026-05-16 04:06:36]       >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-16 04:06:36]           >> 1 forward reads.
INFO [2026-05-16 04:06:36]           >> 1 reverse reads.
INFO [2026-05-16 04:06:36]       >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-16 04:06:36]           >> 1 forward reads.
INFO [2026-05-16 04:06:36]           >> 1 reverse reads.
INFO [2026-05-16 04:06:36]       >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-16 04:06:36]           >> 1 forward reads.
INFO [2026-05-16 04:06:36]           >> 1 reverse reads.
INFO [2026-05-16 04:06:36]   >> 8 reads created from ABIF file.
INFO [2026-05-16 04:06:36]   >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:06:36]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:06:36]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-16 04:06:36] ------------------------------------------------
INFO [2026-05-16 04:06:36] -------- Creating 'SangerRead' instance --------
INFO [2026-05-16 04:06:36] ------------------------------------------------
INFO [2026-05-16 04:06:36] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-16 04:06:36]     >> Creating Forward Read raw abif ...
INFO [2026-05-16 04:06:36]     >> Creating Forward Read raw sangerseq ...
INFO [2026-05-16 04:06:36]           * Making basecall !!
INFO [2026-05-16 04:06:36]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-16 04:06:36] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:36] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:36] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:36]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-16 04:06:36]    >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:06:36]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:06:36]    >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-16 04:06:36] ------------------------------------------------
INFO [2026-05-16 04:06:36] -------- Creating 'SangerRead' instance --------
INFO [2026-05-16 04:06:36] ------------------------------------------------
INFO [2026-05-16 04:06:36] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-16 04:06:36]     >> Creating Forward Read raw abif ...
INFO [2026-05-16 04:06:36]     >> Creating Forward Read raw sangerseq ...
INFO [2026-05-16 04:06:36]           * Making basecall !!
INFO [2026-05-16 04:06:36]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-16 04:06:36] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:36] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:36] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:36]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-16 04:06:36]    >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:06:36]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:06:36]    >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-16 04:06:36] ------------------------------------------------
INFO [2026-05-16 04:06:36] -------- Creating 'SangerRead' instance --------
INFO [2026-05-16 04:06:36] ------------------------------------------------
INFO [2026-05-16 04:06:36] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-16 04:06:36]     >> Creating Forward Read raw abif ...
INFO [2026-05-16 04:06:36]     >> Creating Forward Read raw sangerseq ...
INFO [2026-05-16 04:06:36]           * Making basecall !!
INFO [2026-05-16 04:06:36]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-16 04:06:36] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:36] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:36] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:36]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-16 04:06:36]    >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:06:36]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:06:36]    >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-16 04:06:36] ------------------------------------------------
INFO [2026-05-16 04:06:36] -------- Creating 'SangerRead' instance --------
INFO [2026-05-16 04:06:36] ------------------------------------------------
INFO [2026-05-16 04:06:36] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-16 04:06:36]     >> Creating Forward Read raw abif ...
INFO [2026-05-16 04:06:37]     >> Creating Forward Read raw sangerseq ...
INFO [2026-05-16 04:06:37]           * Making basecall !!
INFO [2026-05-16 04:06:37]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-16 04:06:37] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:37] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:37] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:37]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-16 04:06:37]    >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:06:37]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:06:37]    >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-16 04:06:37] ------------------------------------------------
INFO [2026-05-16 04:06:37] -------- Creating 'SangerRead' instance --------
INFO [2026-05-16 04:06:37] ------------------------------------------------
INFO [2026-05-16 04:06:37] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-16 04:06:37]     >> Creating Forward Read raw abif ...
INFO [2026-05-16 04:06:37]     >> Creating Forward Read raw sangerseq ...
INFO [2026-05-16 04:06:37]           * Making basecall !!
INFO [2026-05-16 04:06:37]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-16 04:06:37] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:37] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:37] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:37]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-16 04:06:37]    >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:06:37]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:06:37]    >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-16 04:06:37] #################################################
INFO [2026-05-16 04:06:37] #### Start creating SangerAlignment instance ####
INFO [2026-05-16 04:06:37] #################################################
INFO [2026-05-16 04:06:37]   >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-16 04:06:37] ========================================================
INFO [2026-05-16 04:06:37] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:06:37] ========================================================
INFO [2026-05-16 04:06:37]   >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-16 04:06:37] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:37] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:37] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:37]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:06:37] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:37] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:37] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:37]    >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:06:37]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:06:37] ==========================================================
SUCCESS [2026-05-16 04:06:37] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:06:37] ==========================================================
INFO [2026-05-16 04:06:37]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:06:37]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:06:37]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:06:37] ========================================================
INFO [2026-05-16 04:06:37] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:06:37] ========================================================
INFO [2026-05-16 04:06:37]   >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-16 04:06:38] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:38] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:38] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:38]    >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:06:38] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:38] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:38] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:38]    >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:06:38]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:06:38] ==========================================================
SUCCESS [2026-05-16 04:06:38] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:06:38] ==========================================================
INFO [2026-05-16 04:06:38]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:06:38]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:06:38]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:06:38] ========================================================
INFO [2026-05-16 04:06:38] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:06:38] ========================================================
INFO [2026-05-16 04:06:38]   >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-16 04:06:38] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:38] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:38] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:38]    >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:06:38] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:38] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:38] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:38]    >> 'Achl_ACHLO040-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:06:38]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:06:39] ==========================================================
SUCCESS [2026-05-16 04:06:39] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:06:39] ==========================================================
INFO [2026-05-16 04:06:39]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:06:39]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:06:39]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:06:39] ========================================================
INFO [2026-05-16 04:06:39] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:06:39] ========================================================
INFO [2026-05-16 04:06:39]   >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-16 04:06:39] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:39] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:39] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:39]    >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:06:39] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:39] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:06:39] --------------------------------------------------------
SUCCESS [2026-05-16 04:06:39]    >> 'Achl_ACHLO041-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:06:39]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:06:39] ==========================================================
SUCCESS [2026-05-16 04:06:39] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:06:39] ==========================================================
INFO [2026-05-16 04:06:39]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:06:39]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:06:39]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:06:39] Aligning consensus reads ... 
INFO [2026-05-16 04:06:39] Before building!!
INFO [2026-05-16 04:06:39] After building!!
SUCCESS [2026-05-16 04:06:39] #############################################################
SUCCESS [2026-05-16 04:06:39] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-16 04:06:39] #############################################################
INFO [2026-05-16 04:06:39]   >> 4 contigs detected from 'regular expression'.
INFO [2026-05-16 04:06:39]       >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-16 04:06:39]           >> 1 forward reads.
INFO [2026-05-16 04:06:39]           >> 1 reverse reads.
INFO [2026-05-16 04:06:39]       >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-16 04:06:39]           >> 1 forward reads.
INFO [2026-05-16 04:06:39]           >> 1 reverse reads.
INFO [2026-05-16 04:06:39]       >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-16 04:06:39]           >> 1 forward reads.
INFO [2026-05-16 04:06:39]           >> 1 reverse reads.
INFO [2026-05-16 04:06:39]       >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-16 04:06:39]           >> 1 forward reads.
INFO [2026-05-16 04:06:39]           >> 1 reverse reads.
INFO [2026-05-16 04:06:39]   >> 8 reads created from ABIF file.
INFO [2026-05-16 04:06:39]   >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:06:39]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:06:39]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-16 04:06:45] Aligning consensus reads ... 
INFO [2026-05-16 04:06:45] Before building!!
INFO [2026-05-16 04:06:45] After building!!
INFO [2026-05-16 04:06:50] Aligning consensus reads ... 
INFO [2026-05-16 04:06:50] Before building!!
INFO [2026-05-16 04:06:50] After building!!
INFO [2026-05-16 04:06:55] Aligning consensus reads ... 
INFO [2026-05-16 04:06:55] Before building!!
INFO [2026-05-16 04:06:55] After building!!
INFO [2026-05-16 04:07:00] Aligning consensus reads ... 
INFO [2026-05-16 04:07:00] Before building!!
INFO [2026-05-16 04:07:00] After building!!
INFO [2026-05-16 04:07:05] Aligning consensus reads ... 
INFO [2026-05-16 04:07:05] Before building!!
INFO [2026-05-16 04:07:05] After building!!
INFO [2026-05-16 04:07:05] ------------------------------------------------
INFO [2026-05-16 04:07:05] -------- Creating 'SangerRead' instance --------
INFO [2026-05-16 04:07:05] ------------------------------------------------
INFO [2026-05-16 04:07:05] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-16 04:07:05]     >> Creating Forward Read raw abif ...
INFO [2026-05-16 04:07:05]     >> Creating Forward Read raw sangerseq ...
INFO [2026-05-16 04:07:05]           * Making basecall !!
INFO [2026-05-16 04:07:05]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-16 04:07:05] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:05] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:07:05] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:05]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-16 04:07:05]    >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:07:05]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:07:05]    >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-16 04:07:05] ------------------------------------------------
INFO [2026-05-16 04:07:05] -------- Creating 'SangerRead' instance --------
INFO [2026-05-16 04:07:05] ------------------------------------------------
INFO [2026-05-16 04:07:05] >> Reverse Read: Creating abif & sangerseq ...
INFO [2026-05-16 04:07:05]     >> Creating Reverse Read raw abif ...
INFO [2026-05-16 04:07:05]     >> Creating Reverse Read raw sangerseq ...
INFO [2026-05-16 04:07:05]           * Making basecall !!
INFO [2026-05-16 04:07:05]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-16 04:07:05] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:05] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:07:05] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:05]    >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:07:05]    >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:07:06]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:07:06]    >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-16 04:07:06] ------------------------------------------------
INFO [2026-05-16 04:07:06] -------- Creating 'SangerRead' instance --------
INFO [2026-05-16 04:07:06] ------------------------------------------------
INFO [2026-05-16 04:07:06] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-16 04:07:06]     >> Creating Forward Read raw abif ...
INFO [2026-05-16 04:07:06]     >> Creating Forward Read raw sangerseq ...
INFO [2026-05-16 04:07:06]           * Making basecall !!
INFO [2026-05-16 04:07:06]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-16 04:07:06] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:06] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:07:06] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:06]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-16 04:07:06]    >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:07:06]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:07:06]    >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-16 04:07:06] #################################################
INFO [2026-05-16 04:07:06] #### Start creating SangerAlignment instance ####
INFO [2026-05-16 04:07:06] #################################################
INFO [2026-05-16 04:07:06]   >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-16 04:07:06] ========================================================
INFO [2026-05-16 04:07:06] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:07:06] ========================================================
INFO [2026-05-16 04:07:06]   >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-16 04:07:06] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:06] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:07:06] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:06]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:07:06] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:06] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:07:06] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:06]    >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:07:06]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:07:07] ==========================================================
SUCCESS [2026-05-16 04:07:07] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:07:07] ==========================================================
INFO [2026-05-16 04:07:07]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:07:07]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:07:07]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:07:07] ========================================================
INFO [2026-05-16 04:07:07] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:07:07] ========================================================
INFO [2026-05-16 04:07:07]   >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-16 04:07:07] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:07] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:07:07] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:07]    >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:07:07] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:07] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:07:07] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:07]    >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:07:07]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:07:07] ==========================================================
SUCCESS [2026-05-16 04:07:07] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:07:07] ==========================================================
INFO [2026-05-16 04:07:07]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:07:07]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:07:07]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:07:07] ========================================================
INFO [2026-05-16 04:07:07] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:07:07] ========================================================
INFO [2026-05-16 04:07:07]   >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-16 04:07:07] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:07] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:07:07] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:07]    >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:07:08] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:08] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:07:08] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:08]    >> 'Achl_ACHLO040-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:07:08]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:07:08] ==========================================================
SUCCESS [2026-05-16 04:07:08] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:07:08] ==========================================================
INFO [2026-05-16 04:07:08]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:07:08]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:07:08]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:07:08] ========================================================
INFO [2026-05-16 04:07:08] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:07:08] ========================================================
INFO [2026-05-16 04:07:08]   >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-16 04:07:08] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:08] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:07:08] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:08]    >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:07:08] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:08] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:07:08] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:08]    >> 'Achl_ACHLO041-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:07:08]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:07:08] ==========================================================
SUCCESS [2026-05-16 04:07:08] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:07:08] ==========================================================
INFO [2026-05-16 04:07:08]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:07:08]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:07:08]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:07:08] Aligning consensus reads ... 
INFO [2026-05-16 04:07:08] Before building!!
INFO [2026-05-16 04:07:08] After building!!
SUCCESS [2026-05-16 04:07:08] #############################################################
SUCCESS [2026-05-16 04:07:08] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-16 04:07:08] #############################################################
INFO [2026-05-16 04:07:08]   >> 4 contigs detected from 'regular expression'.
INFO [2026-05-16 04:07:08]       >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-16 04:07:08]           >> 1 forward reads.
INFO [2026-05-16 04:07:08]           >> 1 reverse reads.
INFO [2026-05-16 04:07:08]       >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-16 04:07:08]           >> 1 forward reads.
INFO [2026-05-16 04:07:08]           >> 1 reverse reads.
INFO [2026-05-16 04:07:08]       >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-16 04:07:08]           >> 1 forward reads.
INFO [2026-05-16 04:07:08]           >> 1 reverse reads.
INFO [2026-05-16 04:07:08]       >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-16 04:07:08]           >> 1 forward reads.
INFO [2026-05-16 04:07:08]           >> 1 reverse reads.
INFO [2026-05-16 04:07:08]   >> 8 reads created from ABIF file.
INFO [2026-05-16 04:07:08]   >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:07:08]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:07:08]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-16 04:07:08] #################################################
INFO [2026-05-16 04:07:08] #### Start creating SangerAlignment instance ####
INFO [2026-05-16 04:07:08] #################################################
INFO [2026-05-16 04:07:08]   >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-16 04:07:08] ========================================================
INFO [2026-05-16 04:07:08] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:07:08] ========================================================
INFO [2026-05-16 04:07:08]   >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-16 04:07:09] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:09] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:07:09] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:09]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:07:09] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:09] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:07:09] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:09]    >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:07:09]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:07:09] ==========================================================
SUCCESS [2026-05-16 04:07:09] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:07:09] ==========================================================
INFO [2026-05-16 04:07:09]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:07:09]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:07:09]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:07:09] ========================================================
INFO [2026-05-16 04:07:09] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:07:09] ========================================================
INFO [2026-05-16 04:07:09]   >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-16 04:07:09] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:09] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:07:09] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:09]    >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:07:09] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:09] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:07:09] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:09]    >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:07:09]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:07:09] ==========================================================
SUCCESS [2026-05-16 04:07:09] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:07:09] ==========================================================
INFO [2026-05-16 04:07:09]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:07:09]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:07:09]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:07:09] ========================================================
INFO [2026-05-16 04:07:09] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:07:09] ========================================================
INFO [2026-05-16 04:07:10]   >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-16 04:07:10] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:10] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:07:10] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:10]    >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:07:10] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:10] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:07:10] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:10]    >> 'Achl_ACHLO040-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:07:10]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:07:10] ==========================================================
SUCCESS [2026-05-16 04:07:10] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:07:10] ==========================================================
INFO [2026-05-16 04:07:10]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:07:10]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:07:10]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:07:10] ========================================================
INFO [2026-05-16 04:07:10] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:07:10] ========================================================
INFO [2026-05-16 04:07:10]   >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-16 04:07:10] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:10] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:07:10] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:10]    >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:07:10] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:10] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:07:10] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:10]    >> 'Achl_ACHLO041-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:07:10]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:07:11] ==========================================================
SUCCESS [2026-05-16 04:07:11] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:07:11] ==========================================================
INFO [2026-05-16 04:07:11]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:07:11]      >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-16 04:07:11]      >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-16 04:07:11] Aligning consensus reads ... 
INFO [2026-05-16 04:07:11] Before building!!
INFO [2026-05-16 04:07:11] After building!!
SUCCESS [2026-05-16 04:07:11] #############################################################
SUCCESS [2026-05-16 04:07:11] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-16 04:07:11] #############################################################
INFO [2026-05-16 04:07:11]   >> 4 contigs detected from 'regular expression'.
INFO [2026-05-16 04:07:11]       >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-16 04:07:11]           >> 1 forward reads.
INFO [2026-05-16 04:07:11]           >> 1 reverse reads.
INFO [2026-05-16 04:07:11]       >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-16 04:07:11]           >> 1 forward reads.
INFO [2026-05-16 04:07:11]           >> 1 reverse reads.
INFO [2026-05-16 04:07:11]       >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-16 04:07:11]           >> 1 forward reads.
INFO [2026-05-16 04:07:11]           >> 1 reverse reads.
INFO [2026-05-16 04:07:11]       >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-16 04:07:11]           >> 1 forward reads.
INFO [2026-05-16 04:07:11]           >> 1 reverse reads.
INFO [2026-05-16 04:07:11]   >> 8 reads created from ABIF file.
INFO [2026-05-16 04:07:11]   >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:07:11]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:07:11]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-16 04:07:11] ------------------------------------------------
INFO [2026-05-16 04:07:11] -------- Creating 'SangerRead' instance --------
INFO [2026-05-16 04:07:11] ------------------------------------------------
INFO [2026-05-16 04:07:11] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-16 04:07:11]     >> Creating Forward Read raw abif ...
INFO [2026-05-16 04:07:11]     >> Creating Forward Read raw sangerseq ...
INFO [2026-05-16 04:07:11]           * Making basecall !!
INFO [2026-05-16 04:07:11]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-16 04:07:11] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:11] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:07:11] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:11]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-16 04:07:11]    >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:07:11]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:07:11]    >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
================================================================================

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INFO [2026-05-16 04:07:18] Aligning consensus reads ... 
================================================================================

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================================================================================

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================================================================================

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================================================================================

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INFO [2026-05-16 04:07:26] Aligning consensus reads ... 
================================================================================

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================================================================================

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INFO [2026-05-16 04:07:30]           * Making basecall !!
INFO [2026-05-16 04:07:31]           * Updating slots in 'SangerRead' instance !!
INFO [2026-05-16 04:07:31]           * Making basecall !!
INFO [2026-05-16 04:07:31]           * Updating slots in 'SangerRead' instance !!
INFO [2026-05-16 04:07:31]           * Making basecall !!
INFO [2026-05-16 04:07:31]           * Updating slots in 'SangerRead' instance !!
INFO [2026-05-16 04:07:31]           * Making basecall !!
INFO [2026-05-16 04:07:31]           * Updating slots in 'SangerRead' instance !!
INFO [2026-05-16 04:07:32]           * Making basecall !!
INFO [2026-05-16 04:07:32]           * Updating slots in 'SangerRead' instance !!
INFO [2026-05-16 04:07:34] >>> outputDir : /tmp/RtmpeZL3QC
INFO [2026-05-16 04:07:34] Start writing '/home/biocbuild/bbs-3.24-bioc/R/site-library/sangeranalyseR/extdata//Allolobophora_chlorotica/ACHLO/Achl_ACHLO006-09_1_F.ab1' to FASTA format ...
INFO [2026-05-16 04:07:34] >> '/tmp/RtmpeZL3QC/Achl_ACHLO006-09_1_F.fa' is written
INFO [2026-05-16 04:07:34] >>> outputDir : /tmp/RtmpeZL3QC
INFO [2026-05-16 04:07:34] Start writing '/home/biocbuild/bbs-3.24-bioc/R/site-library/sangeranalyseR/extdata//fasta/SangerRead/Achl_ACHLO006-09_1_F.fa' to FASTA format ...
INFO [2026-05-16 04:07:34] >> '/tmp/RtmpeZL3QC/Achl_ACHLO006-09_1_F.fa' is written
INFO [2026-05-16 04:07:34] >>> outputDir : /tmp/RtmpeZL3QC
INFO [2026-05-16 04:07:34] Start writing '/home/biocbuild/bbs-3.24-bioc/R/site-library/sangeranalyseR/extdata//fasta/SangerRead/Achl_ACHLO006-09_2_R.fa' to FASTA format ...
INFO [2026-05-16 04:07:34] >> '/tmp/RtmpeZL3QC/Achl_ACHLO006-09_2_R.fa' is written
INFO [2026-05-16 04:07:34] ------------------------------------------------
INFO [2026-05-16 04:07:34] -------- Creating 'SangerRead' instance --------
INFO [2026-05-16 04:07:34] ------------------------------------------------
INFO [2026-05-16 04:07:35] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-16 04:07:35]     >> Creating Forward Read raw abif ...
INFO [2026-05-16 04:07:35]     >> Creating Forward Read raw sangerseq ...
INFO [2026-05-16 04:07:35]           * Making basecall !!
INFO [2026-05-16 04:07:35]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-16 04:07:35] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:35] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:07:35] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:35]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-16 04:07:35]    >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:07:35]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:07:35]    >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-16 04:07:35] ------------------------------------------------
INFO [2026-05-16 04:07:35] -------- Creating 'SangerRead' instance --------
INFO [2026-05-16 04:07:35] ------------------------------------------------
INFO [2026-05-16 04:07:35] >> Reverse Read: Creating abif & sangerseq ...
INFO [2026-05-16 04:07:35]     >> Creating Reverse Read raw abif ...
INFO [2026-05-16 04:07:35]     >> Creating Reverse Read raw sangerseq ...
INFO [2026-05-16 04:07:35]           * Making basecall !!
INFO [2026-05-16 04:07:35]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-16 04:07:35] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:35] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:07:35] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:35]    >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:07:35]    >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:07:35]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:07:35]    >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-16 04:07:35] ------------------------------------------------
INFO [2026-05-16 04:07:35] -------- Creating 'SangerRead' instance --------
INFO [2026-05-16 04:07:35] ------------------------------------------------
INFO [2026-05-16 04:07:35] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-16 04:07:35]     >> Creating Forward Read raw abif ...
INFO [2026-05-16 04:07:35]     >> Creating Forward Read raw sangerseq ...
INFO [2026-05-16 04:07:35]           * Making basecall !!
INFO [2026-05-16 04:07:35]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-16 04:07:35] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:35] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:07:35] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:35]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-16 04:07:35]    >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:07:35]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:07:35]    >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-16 04:07:35] ------------------------------------------------
INFO [2026-05-16 04:07:35] -------- Creating 'SangerRead' instance --------
INFO [2026-05-16 04:07:35] ------------------------------------------------
INFO [2026-05-16 04:07:35] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-16 04:07:35]     >> Creating Forward Read raw abif ...
INFO [2026-05-16 04:07:35]     >> Creating Forward Read raw sangerseq ...
INFO [2026-05-16 04:07:35]           * Making basecall !!
INFO [2026-05-16 04:07:35]           * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-16 04:07:35] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:35] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:07:35] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:35]    >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-16 04:07:35]    >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:07:35]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:07:35]    >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
ERROR [2026-05-16 04:07:35] FILE_TYPE_ERROR
'/tmp/RtmpeZL3QC/file113f961918dd3b/Sanger_all_reads.Xfa' file extension must be '.fa' or '.fasta'.
DEBUG [2026-05-16 04:07:35]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:07:35]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
ERROR [2026-05-16 04:07:35] FILE_TYPE_ERROR
'/tmp/RtmpeZL3QC/file113f9621b73fb0/Achl_ACHLO006-09_1_F.Xab1' file extension must be '.ab1'.
DEBUG [2026-05-16 04:07:35]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:07:35]    >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
ERROR [2026-05-16 04:07:36] FILE_TYPE_ERROR
'/tmp/RtmpeZL3QC/file113f967f3f39b5/Achl_ACHLO006-09_1_F.ab2' file extension must be '.ab1'.
DEBUG [2026-05-16 04:07:36]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:07:36]    >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
ERROR [2026-05-16 04:07:36] FILE_TYPE_ERROR
'/tmp/RtmpeZL3QC/file113f96332fd580/Sanger_all_reads.fast' file extension must be '.fa' or '.fasta'.
DEBUG [2026-05-16 04:07:36]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:07:36]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
ERROR [2026-05-16 04:07:36] FILE_NOT_EXIST_ERROR
'/no/such/file_1_F.ab1' file does not exist.
DEBUG [2026-05-16 04:07:36]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:07:36]    >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-16 04:07:36] ------------------------------------------------
INFO [2026-05-16 04:07:36] -------- Creating 'SangerRead' instance --------
INFO [2026-05-16 04:07:36] ------------------------------------------------
INFO [2026-05-16 04:07:36] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-16 04:07:36]     >> Creating Forward Read raw abif ...
INFO [2026-05-16 04:07:36] ------------------------------------------------
INFO [2026-05-16 04:07:36] -------- Creating 'SangerRead' instance --------
INFO [2026-05-16 04:07:36] ------------------------------------------------
INFO [2026-05-16 04:07:36] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-16 04:07:36]     >> Creating Forward Read raw abif ...
INFO [2026-05-16 04:07:36] ------------------------------------------------
INFO [2026-05-16 04:07:36] -------- Creating 'SangerRead' instance --------
INFO [2026-05-16 04:07:36] ------------------------------------------------
INFO [2026-05-16 04:07:36] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-16 04:07:36]     >> Creating Forward Read raw abif ...
INFO [2026-05-16 04:07:36]     >> Creating Forward Read raw sangerseq ...
ERROR [2026-05-16 04:07:36] CSV_MISMATCH_ERROR
'contig' is not in the csv file (/tmp/RtmpeZL3QC/file113f964c21ab60/missing_contig.csv)
DEBUG [2026-05-16 04:07:36]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:07:36]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
ERROR [2026-05-16 04:07:36] CSV_MISMATCH_ERROR
'direction' is not in the csv file (/tmp/RtmpeZL3QC/file113f96304f255f/missing_direction.csv)
DEBUG [2026-05-16 04:07:36]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:07:36]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
ERROR [2026-05-16 04:07:36] CSV_MISMATCH_ERROR
'reads' is not in the csv file (/tmp/RtmpeZL3QC/file113f96bd19e3a/missing_reads.csv)
DEBUG [2026-05-16 04:07:36]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:07:36]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
ERROR [2026-05-16 04:07:36] CSV_VALUE_ERROR
In the 'direction' column of your CSV file, you can only have 'F' and 'R'
DEBUG [2026-05-16 04:07:36]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:07:36]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
WARN [2026-05-16 04:07:36] 'Achl_ACHLO006-09_1_F.ab1' is not in the csv file (/tmp/RtmpeZL3QC/file113f9668771d64/mismatched_names_conversion.csv)
WARN [2026-05-16 04:07:36] 'DOES_NOT_EXIST.ab1' is not in the parent directory.
INFO [2026-05-16 04:07:36] #################################################
INFO [2026-05-16 04:07:36] #### Start creating SangerAlignment instance ####
INFO [2026-05-16 04:07:36] #################################################
INFO [2026-05-16 04:07:36] **** You are using CSV Name Conversion Method to group AB1 files!
INFO [2026-05-16 04:07:36] **** Contig number in your Csv file is 4
INFO [2026-05-16 04:07:36] ========================================================
INFO [2026-05-16 04:07:36] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:07:36] ========================================================
INFO [2026-05-16 04:07:36]   >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-16 04:07:36] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:36] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:07:36] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:36]    >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:07:36]    >> The number of reads detected: 1
WARN [2026-05-16 04:07:36] CSV_MATCH_WARN
The names of forward reads in your 'CSV_NamesConversion' CSV file do not match any forward reads.
ERROR [2026-05-16 04:07:36] READ_NUMBER_ERROR
The number of your total reads is 1.
Number of total reads has to be equal or more than 2 ('minReadsNum' that you set)
INFO [2026-05-16 04:07:36] ========================================================
INFO [2026-05-16 04:07:36] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:07:36] ========================================================
INFO [2026-05-16 04:07:36]   >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-16 04:07:36] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:36] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:07:36] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:36]    >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:07:36] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:36] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:07:36] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:36]    >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:07:36]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:07:37] ==========================================================
SUCCESS [2026-05-16 04:07:37] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:07:37] ==========================================================
INFO [2026-05-16 04:07:37]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:07:37]      >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-16 04:07:37]      >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-16 04:07:37] ========================================================
INFO [2026-05-16 04:07:37] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:07:37] ========================================================
INFO [2026-05-16 04:07:37]   >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-16 04:07:37] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:37] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:07:37] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:37]    >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:07:37] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:37] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:07:37] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:37]    >> 'Achl_ACHLO040-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:07:37]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:07:37] ==========================================================
SUCCESS [2026-05-16 04:07:37] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:07:37] ==========================================================
INFO [2026-05-16 04:07:37]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:07:37]      >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-16 04:07:37]      >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-16 04:07:37] ========================================================
INFO [2026-05-16 04:07:37] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:07:37] ========================================================
INFO [2026-05-16 04:07:37]   >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-16 04:07:37] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:37] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:07:37] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:37]    >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-16 04:07:38] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:38] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:07:38] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:38]    >> 'Achl_ACHLO041-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-16 04:07:38]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:07:38] ==========================================================
SUCCESS [2026-05-16 04:07:38] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:07:38] ==========================================================
INFO [2026-05-16 04:07:38]    >> 2 read(s) created from ABIF file.
INFO [2026-05-16 04:07:38]      >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-16 04:07:38]      >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-16 04:07:38] Aligning consensus reads ... 
INFO [2026-05-16 04:07:38] Before building!!
INFO [2026-05-16 04:07:38] After building!!
SUCCESS [2026-05-16 04:07:38] #############################################################
SUCCESS [2026-05-16 04:07:38] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-16 04:07:38] #############################################################
INFO [2026-05-16 04:07:38]   >> 3 contigs detected from 'csv file'.
INFO [2026-05-16 04:07:38]       >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-16 04:07:38]           >> 1 forward reads.
INFO [2026-05-16 04:07:38]           >> 1 reverse reads.
INFO [2026-05-16 04:07:38]       >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-16 04:07:38]           >> 1 forward reads.
INFO [2026-05-16 04:07:38]           >> 1 reverse reads.
INFO [2026-05-16 04:07:38]       >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-16 04:07:38]           >> 1 forward reads.
INFO [2026-05-16 04:07:38]           >> 1 reverse reads.
INFO [2026-05-16 04:07:38]   >> 6 reads created from ABIF file.
INFO [2026-05-16 04:07:38]   >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-16 04:07:38]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:07:38]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
WARN [2026-05-16 04:07:38] 'Achl_ACHLO006-09_1_F' is not in the parent directory.
INFO [2026-05-16 04:07:38] #################################################
INFO [2026-05-16 04:07:38] #### Start creating SangerAlignment instance ####
INFO [2026-05-16 04:07:38] #################################################
INFO [2026-05-16 04:07:38] **** You are using CSV Name Conversion Method to group reads in FASTA file (with Csv file)!
INFO [2026-05-16 04:07:38] ========================================================
INFO [2026-05-16 04:07:38] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:07:38] ========================================================
INFO [2026-05-16 04:07:38]   >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-16 04:07:38] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:38] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:07:38] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:38]    >> 'Achl_ACHLO006-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-16 04:07:38]    >> The number of reads detected: 1
WARN [2026-05-16 04:07:38] CSV_MATCH_WARN
The names of forward reads in your 'CSV_NamesConversion' CSV file do not match any forward reads.
ERROR [2026-05-16 04:07:38] READ_NUMBER_ERROR
The number of your total reads is 1.
Number of total reads has to be equal or more than 2 ('minReadsNum' that you set)
INFO [2026-05-16 04:07:38] ========================================================
INFO [2026-05-16 04:07:38] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:07:38] ========================================================
INFO [2026-05-16 04:07:38]   >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-16 04:07:38] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:38] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:07:38] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:38]    >> 'Achl_ACHLO007-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-16 04:07:38] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:38] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:07:38] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:38]    >> 'Achl_ACHLO007-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-16 04:07:38]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:07:38] ==========================================================
SUCCESS [2026-05-16 04:07:38] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:07:38] ==========================================================
INFO [2026-05-16 04:07:38]    >> 2 read(s) created from FASTA file.
INFO [2026-05-16 04:07:38]      >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-16 04:07:38]      >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-16 04:07:38] ========================================================
INFO [2026-05-16 04:07:38] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:07:38] ========================================================
INFO [2026-05-16 04:07:38]   >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-16 04:07:38] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:38] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:07:38] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:38]    >> 'Achl_ACHLO040-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-16 04:07:38] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:38] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:07:38] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:38]    >> 'Achl_ACHLO040-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-16 04:07:38]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:07:39] ==========================================================
SUCCESS [2026-05-16 04:07:39] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:07:39] ==========================================================
INFO [2026-05-16 04:07:39]    >> 2 read(s) created from FASTA file.
INFO [2026-05-16 04:07:39]      >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-16 04:07:39]      >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-16 04:07:39] ========================================================
INFO [2026-05-16 04:07:39] ================ Creating 'SangerContig' ===============
INFO [2026-05-16 04:07:39] ========================================================
INFO [2026-05-16 04:07:39]   >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-16 04:07:39] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:39] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:07:39] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:39]    >> 'Achl_ACHLO041-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-16 04:07:39] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:39] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-16 04:07:39] --------------------------------------------------------
SUCCESS [2026-05-16 04:07:39]    >> 'Achl_ACHLO041-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-16 04:07:39]    >> The number of reads detected: 2
SUCCESS [2026-05-16 04:07:39] ==========================================================
SUCCESS [2026-05-16 04:07:39] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-16 04:07:39] ==========================================================
INFO [2026-05-16 04:07:39]    >> 2 read(s) created from FASTA file.
INFO [2026-05-16 04:07:39]      >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-16 04:07:39]      >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-16 04:07:39] Aligning consensus reads ... 
INFO [2026-05-16 04:07:39] Before building!!
INFO [2026-05-16 04:07:39] After building!!
SUCCESS [2026-05-16 04:07:39] #############################################################
SUCCESS [2026-05-16 04:07:39] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-16 04:07:39] #############################################################
INFO [2026-05-16 04:07:39]   >> 3 contigs detected from 'csv file'.
INFO [2026-05-16 04:07:39]       >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-16 04:07:39]           >> 1 forward reads.
INFO [2026-05-16 04:07:39]           >> 1 reverse reads.
INFO [2026-05-16 04:07:39]       >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-16 04:07:39]           >> 1 forward reads.
INFO [2026-05-16 04:07:39]           >> 1 reverse reads.
INFO [2026-05-16 04:07:39]       >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-16 04:07:39]           >> 1 forward reads.
INFO [2026-05-16 04:07:39]           >> 1 reverse reads.
INFO [2026-05-16 04:07:39]   >> 6 reads created from FASTA file.
DEBUG [2026-05-16 04:07:39]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:07:39]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
ERROR [2026-05-16 04:07:39] PARAMETER_RANGE_ERROR
'M1TrimmingCutoff' must be between 0 and 1.
DEBUG [2026-05-16 04:07:39]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:07:39]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
ERROR [2026-05-16 04:07:39] PARAMETER_VALUE_ERROR
'TrimmingMethod' must be 'M1' or 'M2'.
DEBUG [2026-05-16 04:07:39]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:07:39]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
ERROR [2026-05-16 04:07:39] PARAMETER_TYPE_ERROR
'processorsNum' must be numeric
DEBUG [2026-05-16 04:07:39]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:07:39]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
ERROR [2026-05-16 04:07:39] PARAMETER_RANGE_ERROR
'signalRatioCutoff' must be between 0 and 1.
DEBUG [2026-05-16 04:07:39]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:07:39]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
ERROR [2026-05-16 04:07:39] PARAMETER_VALUE_ERROR
'inputSource' must be one of: 'ABIF', 'FASTA'.
DEBUG [2026-05-16 04:07:39]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:07:39]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
ERROR [2026-05-16 04:07:39] PARAMETER_VALUE_ERROR
'processMethod' must be one of: 'REGEX', 'CSV'.
DEBUG [2026-05-16 04:07:39]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:07:39]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
ERROR [2026-05-16 04:07:39] PARAMETER_VALUE_ERROR
'acceptStopCodons' must be 'TRUE' or 'FALSE'
DEBUG [2026-05-16 04:07:39]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:07:39]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
ERROR [2026-05-16 04:07:39] PARAMETER_VALUE_ERROR
'readingFrame' must be 1, 2, or 3.
DEBUG [2026-05-16 04:07:39]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:07:39]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
ERROR [2026-05-16 04:07:39] PARAMETER_RANGE_ERROR
'minFractionCall' must be between 0 and 1.
DEBUG [2026-05-16 04:07:39]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:07:39]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
ERROR [2026-05-16 04:07:39] PARAMETER_VALUE_ERROR
'minReadsNum' cannot be zero.
DEBUG [2026-05-16 04:07:39]    >> For more information, please run 'object'.
DEBUG [2026-05-16 04:07:39]    >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-16 04:07:39] Aligning consensus reads ... 
================================================================================

Time difference of 0.04 secs

INFO [2026-05-16 04:07:41]           * Making basecall !!
INFO [2026-05-16 04:07:41]           * Updating slots in 'SangerRead' instance !!
INFO [2026-05-16 04:07:41]           * Making basecall !!
INFO [2026-05-16 04:07:42]           * Updating slots in 'SangerRead' instance !!
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 1447 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On CRAN (1): 'test-LazyAA-Reports.R:65:5'

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 1447 ]
> 
> proc.time()
   user  system elapsed 
187.101  12.725 207.176

Example timings

sangeranalyseR.Rcheck/sangeranalyseR-Ex.timings

name	user	system	elapsed
ChromatogramParam-class	0.003	0.001	0.005
MakeBaseCalls-methods	0.443	0.013	0.455
ObjectResults-class	0.001	0.001	0.003
QualityReport-class-qualityBasePlot	0.001	0.001	0.001
QualityReport-class-updateQualityParam	0.004	0.002	0.006
QualityReport-class	0.523	0.047	0.571
SangerAlignment-class-generateReportSA	0.109	0.007	0.115
SangerAlignment-class-launchAppSA	0.123	0.005	0.128
SangerAlignment-class-updateQualityParam	0.113	0.003	0.117
SangerAlignment-class-writeFastaSA	0.141	0.006	0.147
SangerAlignment-class	37.533	8.969	43.846
SangerAlignment	9.243	2.856	11.394
SangerContig-class-generateReportSC	0.047	0.007	0.054
SangerContig-class-launchAppSC	0.059	0.006	0.064
SangerContig-class-readTable	0.087	0.001	0.088
SangerContig-class-updateQualityParam	0.043	0.007	0.050
SangerContig-class-writeFastaSC	0.080	0.017	0.096
SangerContig-class	8.898	2.336	10.573
SangerContig	0.477	0.123	0.600
SangerRead-class-MakeBaseCalls	0.282	0.004	0.285
SangerRead-class-generateReportSR	0.034	0.003	0.037
SangerRead-class-qualityBasePlot	0.035	0.002	0.037
SangerRead-class-readTable	0.085	0.001	0.086
SangerRead-class-updateQualityParam	0.260	0.008	0.268
SangerRead-class-writeFastaSR	0.047	0.003	0.051
SangerRead-class	0.549	0.018	0.568
SangerRead	0.166	0.004	0.170
chromatogram_overwrite	0.036	0.001	0.037
chromatogram_plotly	0.037	0.001	0.038
generateReport	0.197	0.004	0.201
generateReportSA-methods	0.109	0.007	0.117
generateReportSC-methods	0.046	0.003	0.049
generateReportSR-methods	0.036	0.001	0.037
globalTrimApp	0	0	0
launchApp	0.156	0.020	0.176
launchAppSA-methods	0.110	0.007	0.117
launchAppSC-methods	0.045	0.003	0.048
primaryAASeqS1-methods	0.039	0.004	0.043
primaryAASeqS2-methods	0.037	0.001	0.038
primaryAASeqS3-methods	0.037	0.002	0.038
qualityBasePlot-methods	0.344	0.021	0.365
readTable-methods	0.080	0.009	0.088
updateQualityParam-methods	0.215	0.013	0.228
writeFasta	0.193	0.012	0.205
writeFastaSA-methods	0.134	0.003	0.137
writeFastaSC-methods	0.085	0.003	0.088
writeFastaSR-methods	0.049	0.003	0.052