Multiple platform build/check report for BioC 3.21 - CHECK results for HTSeqGenie on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4824
merida1	macOS 12.7.5 Monterey	x86_64	4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"	4604
kjohnson1	macOS 13.6.6 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4545
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4579
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 HTSeqGenie on nebbiolo1

To the developers/maintainers of the HTSeqGenie package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HTSeqGenie.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: HTSeqGenie

Version: 4.38.0

Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:HTSeqGenie.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings HTSeqGenie_4.38.0.tar.gz

StartedAt: 2025-08-20 23:24:20 -0400 (Wed, 20 Aug 2025)

EndedAt: 2025-08-21 00:04:20 -0400 (Thu, 21 Aug 2025)

EllapsedTime: 2400.6 seconds

RetCode: None

Status: TIMEOUT

CheckDir: HTSeqGenie.Rcheck

Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:HTSeqGenie.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings HTSeqGenie_4.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/HTSeqGenie.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘HTSeqGenie/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HTSeqGenie’ version ‘4.38.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘HTSeqGenie’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 ... NOTE
Unexported objects imported by ':::' calls:
  ‘ShortRead:::.set_omp_threads’ ‘gmapR:::..gsnap’ ‘gmapR:::GeneGenome’
  ‘gmapR:::checkPackageInstalled’ ‘gmapR:::getDefaultGmapGenomePath’
  ‘gmapR:::getGeneRoi’ ‘gmapR:::subsetRegion’ ‘parallel:::mckill’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .Call(ShortRead:::.set_omp_threads, ...)
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
.makePreprocessAlignPlots: no visible binding for global variable
  ‘data’
.plot.in.out.min.max.readlength: no visible global function definition
  for ‘median’
FastQStreamer.init: no visible binding for '<<-' assignment to
  ‘FastQStreamer.lfqs’
FastQStreamer.init: no visible binding for '<<-' assignment to
  ‘FastQStreamer.chunkid’
FastQStreamer.init: no visible binding for '<<-' assignment to
  ‘FastQStreamer.subsampling_filter’
FastQStreamer.init: no visible binding for '<<-' assignment to
  ‘FastQStreamer.max_nbchunks’
addHandler: no visible binding for '<<-' assignment to
  ‘logging.handlers’
addHandler: no visible binding for global variable ‘logging.handlers’
addHandler: no visible binding for '<<-' assignment to ‘logging.file’
buildAnyFastaGenome: no visible global function definition for ‘getSeq’
buildGenomicFeaturesFromTxDb: no visible global function definition for
  ‘gaps’
buildGenomicFeaturesFromTxDb: no visible global function definition for
  ‘ranges’
buildTP53FastaGenome: no visible global function definition for
  ‘getSeq’
buildTallyParam: no visible global function definition for ‘seqinfo’
computeCoverage: no visible global function definition for ‘resize’
computeCoverage: no visible global function definition for ‘coverage’
estimateCutoffs : <anonymous>: no visible binding for global variable
  ‘quantile’
getGenomeSegments: no visible global function definition for ‘seqinfo’
hashVariants: no visible global function definition for ‘ranges’
isAboveQualityThresh: no visible global function definition for ‘Views’
isAboveQualityThresh: no visible global function definition for
  ‘viewMeans’
listIterator.init: no visible binding for '<<-' assignment to
  ‘listIterator.n’
listIterator.init: no visible binding for '<<-' assignment to
  ‘listIterator.x’
logReset: no visible binding for '<<-' assignment to ‘logging.handlers’
logReset: no visible binding for '<<-' assignment to ‘logging.loglevel’
logReset: no visible binding for '<<-' assignment to ‘logging.file’
loglevel: no visible binding for global variable ‘logging.loglevel’
loglevel: no visible binding for global variable ‘logging.handlers’
processChunks : tracefun: no visible binding for global variable
  ‘sjobs’
processChunks : tracefun: no visible binding for global variable
  ‘chunkid’
setLevel: no visible binding for '<<-' assignment to ‘logging.loglevel’
statCountFeatures: no visible global function definition for ‘quantile’
truncateReads: no visible global function definition for ‘subseq’
vcfStat: no visible global function definition for ‘quantile’
writeToFile: no visible binding for global variable ‘logging.file’
Undefined global functions or variables:
  Views chunkid coverage data gaps getSeq logging.file logging.handlers
  logging.loglevel median quantile ranges resize seqinfo sjobs subseq
  viewMeans
Consider adding
  importFrom("stats", "median", "quantile")
  importFrom("utils", "data")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) calculateTargetLengths.Rd:17: Lost braces; missing escapes or markup?
    17 | Target length table and writes two files in {save_dir}/reports/images/TargetLenghts.[pdf|png]"
       |                                             ^
checkRd: (-1) initLog.Rd:18: Lost braces; missing escapes or markup?
    18 | Setup logging file in {save_dir}/progress.log
       |                       ^
* 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 ... NOTE
Documented arguments not in \usage in Rd file 'findVariantFile.Rd':
  ‘dir_path’

Documented arguments not in \usage in Rd file 'logdebug.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'logerror.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'loginfo.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'logwarn.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘doRUnit.R’

Installation output

HTSeqGenie.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL HTSeqGenie
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘HTSeqGenie’ ...
** this is package ‘HTSeqGenie’ version ‘4.38.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in fun(libname, pkgname) :
  Package 'HTSeqGenie' is deprecated and will be removed from
  Bioconductor version 3.22
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'HTSeqGenie' is deprecated and will be removed from
  Bioconductor version 3.22
** testing if installed package keeps a record of temporary installation path
* DONE (HTSeqGenie)

Tests output

HTSeqGenie.Rcheck/tests/doRUnit.Rout


R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 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("HTSeqGenie")
Loading required package: gmapR
Loading required package: GenomeInfoDb
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: GenomicRanges
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: ShortRead
Loading required package: BiocParallel
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians

Loading required package: VariantAnnotation

Attaching package: 'VariantAnnotation'

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

    tabulate

Warning message:
In fun(libname, pkgname) :
  Package 'HTSeqGenie' is deprecated and will be removed from
  Bioconductor version 3.22
> 
> source(getPackageFile("unitTests/runTests.R"))
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
did not source anything in dirname= ./R 


Executing test function test.alignReads  ... checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmpsc5RME/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-08-20 23:29:55.132385 INFO::preprocessReads.R/preprocessReads: starting...
2025-08-20 23:29:55.141511 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-08-20 23:29:55.145525 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-08-20 23:29:55.147825 DEBUG::tools.R/processChunks: starting...
2025-08-20 23:29:58.575796 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-08-20 23:29:58.577604 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /tmp/Rtmpsc5RME/test.alignReads.2e759a7444caa3/chunks/chunk_000001/logs/progress.log
2025-08-20 23:30:01.330411 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.046 minutes
2025-08-20 23:30:01.332602 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /tmp/Rtmpsc5RME/test.alignReads.2e759a7444caa3/chunks/chunk_000002/logs/progress.log
2025-08-20 23:30:04.080564 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.046 minutes
2025-08-20 23:30:04.082084 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /tmp/Rtmpsc5RME/test.alignReads.2e759a7444caa3/chunks/chunk_000003/logs/progress.log
2025-08-20 23:30:06.860556 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.046 minutes
2025-08-20 23:30:06.895257 DEBUG::tools.R/processChunks: done
2025-08-20 23:30:06.89934 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-08-20 23:30:06.90175 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.alignReads.2e759a7444caa3/results/test_pe.adapter_contaminated_1.RData
2025-08-20 23:30:06.90453 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-08-20 23:30:06.906197 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.alignReads.2e759a7444caa3/results/test_pe.adapter_contaminated_2.RData
2025-08-20 23:30:06.915455 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=26 highqual_reads=25 adapter_contam=1 read_length=75 rRNA_contam_reads=0 processed_reads=25 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-08-20 23:30:06.917849 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.alignReads.2e759a7444caa3/results/test_pe.summary_preprocess.tab
2025-08-20 23:30:06.921238 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/Rtmpsc5RME/test.alignReads.2e759a7444caa3/bams/processed.aligner_input_1.fastq ...
2025-08-20 23:30:06.925468 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/Rtmpsc5RME/test.alignReads.2e759a7444caa3/bams/processed.aligner_input_2.fastq ...
2025-08-20 23:30:06.928654 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/Rtmpsc5RME/test.alignReads.2e759a7444caa3/reports/shortReadReport_1 ...
2025-08-20 23:30:08.369632 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/Rtmpsc5RME/test.alignReads.2e759a7444caa3/reports/shortReadReport_2 ...
2025-08-20 23:30:11.742076 INFO::preprocessReads.R/preprocessReads: done
2025-08-20 23:30:11.813042 INFO::alignReads.R/alignReads: starting alignment...
2025-08-20 23:30:11.818487 DEBUG::tools.R/processChunks: starting...
2025-08-20 23:30:14.656606 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-08-20 23:30:14.658247 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /tmp/Rtmpsc5RME/test.alignReads.2e759a7444caa3/chunks/chunk_000001/logs/progress.log
2025-08-20 23:30:17.451463 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.047 minutes
2025-08-20 23:30:17.453833 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /tmp/Rtmpsc5RME/test.alignReads.2e759a7444caa3/chunks/chunk_000002/logs/progress.log
[bam_translate] PG tag "A" on read "highqualPEsInManyTxsOfMultiTxGene:1:1:1:16#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1MicrobialPE2MultimappingIntergenic:1:1:1:19#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInOneTxOfMultiTxGene:1:1:1:15#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1UniqueUtrPE2MultimappingIntergenic:1:1:1:18#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-08-20 23:30:20.134699 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.045 minutes
2025-08-20 23:30:20.136443 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /tmp/Rtmpsc5RME/test.alignReads.2e759a7444caa3/chunks/chunk_000003/logs/progress.log
[bam_translate] PG tag "A" on read "highqualPE1GeneFusionMidExonDiffChrPE2MultimappingIntergenic:1:1:1:25#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-08-20 23:30:22.877037 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.046 minutes
2025-08-20 23:30:22.879873 DEBUG::tools.R/processChunks: done
2025-08-20 23:30:22.881458 INFO::alignReads.R/mergeBAMsAcrossDirs: starting...
[bam_translate] PG tag "A" on read "highqualAdapterContamIn3PrimeEnd:1:1:1:7#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInManyTxsOfMultiTxGene:1:1:1:16#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1MicrobialPE2MultimappingIntergenic:1:1:1:19#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1GeneFusionMidExonDiffChrPE2MultimappingIntergenic:1:1:1:25#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1UniqueUtrPE2MultimappingIntergenic:1:1:1:18#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInOneTxOfMultiTxGene:1:1:1:15#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-08-20 23:30:23.146699 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-08-20 23:30:23.157438 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.alignReads.2e759a7444caa3/results/test_pe.summary_alignment.tab
2025-08-20 23:30:23.166173 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.alignReads.2e759a7444caa3/results/test_pe.summary_analyzed_bamstats.tab
2025-08-20 23:30:23.168356 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-08-20 23:30:23.434021 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.alignReads.2e759a7444caa3/results/test_pe.summary_target_lengths.tab
2025-08-20 23:30:23.48819 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-08-20 23:30:23.489841 INFO::alignReads.R/alignReads: done
 done successfully.



Executing test function test.alignReads.sparsechunks  ... checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmpsc5RME/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-08-20 23:30:23.828829 INFO::preprocessReads.R/preprocessReads: starting...
2025-08-20 23:30:23.832821 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-08-20 23:30:23.960804 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 2 , totnbreads= 26 )
2025-08-20 23:30:23.96667 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-08-20 23:30:23.970315 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-08-20 23:30:23.972735 DEBUG::tools.R/processChunks: starting...
2025-08-20 23:30:27.130463 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-08-20 23:30:27.132013 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /tmp/Rtmpsc5RME/test.alignReads.sparsechunks.2e759a6cd2ce39/chunks/chunk_000001/logs/progress.log
2025-08-20 23:30:29.843717 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.045 minutes
2025-08-20 23:30:29.845147 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /tmp/Rtmpsc5RME/test.alignReads.sparsechunks.2e759a6cd2ce39/chunks/chunk_000002/logs/progress.log
2025-08-20 23:30:32.546346 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.045 minutes
2025-08-20 23:30:32.547767 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /tmp/Rtmpsc5RME/test.alignReads.sparsechunks.2e759a6cd2ce39/chunks/chunk_000003/logs/progress.log
2025-08-20 23:30:35.313338 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.046 minutes
2025-08-20 23:30:35.314853 DEBUG::tools.R/processChunks: starting chunkid= 4 ; see logfile= /tmp/Rtmpsc5RME/test.alignReads.sparsechunks.2e759a6cd2ce39/chunks/chunk_000004/logs/progress.log
2025-08-20 23:30:38.01255 DEBUG::tools.R/processChunks: done with chunkid= 4 ; elapsed.time= 0.045 minutes
2025-08-20 23:30:38.066122 DEBUG::tools.R/processChunks: done
2025-08-20 23:30:38.070923 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-08-20 23:30:38.074484 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.alignReads.sparsechunks.2e759a6cd2ce39/results/test_pe.adapter_contaminated_1.RData
2025-08-20 23:30:38.079019 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-08-20 23:30:38.081851 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.alignReads.sparsechunks.2e759a6cd2ce39/results/test_pe.adapter_contaminated_2.RData
2025-08-20 23:30:38.096682 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=2 highqual_reads=1 adapter_contam=0 read_length=75 rRNA_contam_reads=0 processed_reads=1 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-08-20 23:30:38.099909 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.alignReads.sparsechunks.2e759a6cd2ce39/results/test_pe.summary_preprocess.tab
2025-08-20 23:30:38.104918 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/Rtmpsc5RME/test.alignReads.sparsechunks.2e759a6cd2ce39/bams/processed.aligner_input_1.fastq ...
2025-08-20 23:30:38.109531 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/Rtmpsc5RME/test.alignReads.sparsechunks.2e759a6cd2ce39/bams/processed.aligner_input_2.fastq ...
2025-08-20 23:30:38.112473 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/Rtmpsc5RME/test.alignReads.sparsechunks.2e759a6cd2ce39/reports/shortReadReport_1 ...
2025-08-20 23:30:39.403218 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/Rtmpsc5RME/test.alignReads.sparsechunks.2e759a6cd2ce39/reports/shortReadReport_2 ...
2025-08-20 23:30:41.956773 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



Executing test function test.alignReadsOneSingleEnd  ... checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmpsc5RME/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-08-20 23:30:42.126477 INFO::alignReads.R/alignReadsChunk: running gsnap...
2025-08-20 23:30:42.131022 INFO::alignReads.R/alignReadsChunk: calling gsnap (from gmapR) with args= -D /home/biocbuild/.local/share/gmap -t 1 -d TP53_demo_3.2.2 --quality-protocol=illumina  -A sam --read-group-id=test_se -m 0 --split-output /tmp/Rtmpsc5RME/test.alignReadsOneSingleEnd.2e759a3387bd7b/bams/test.alignReads /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq 2>&1
2025-08-20 23:30:42.355042 INFO::alignReads.R/createSummaryAlignment: counting unique bam reads...
2025-08-20 23:30:42.457083 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.alignReadsOneSingleEnd.2e759a3387bd7b/results/test.alignReads.summary_alignment.tab
2025-08-20 23:30:42.509206 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.alignReadsOneSingleEnd.2e759a3387bd7b/results/test.alignReads.summary_analyzed_bamstats.tab
2025-08-20 23:30:42.510779 INFO::alignReads.R/alignReadsChunk: done
 done successfully.



Executing test function test.annotateVariants  ... Timing stopped at: 0.001 0.002 0.002
Error in DEACTIVATED("Skipped annotateVariants() test") : 
  Skipped annotateVariants() test
In addition: There were 11 warnings (use warnings() to see them)
 done successfully.



Executing test function test.callVariantsVariantTools.genotype  ... checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmpsc5RME/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-08-20 23:30:42.820607 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.genotype.2e759a50e68df8/results/test_pe.coverage.RData
2025-08-20 23:30:42.822526 INFO::coverage.R/saveCoverage: saving file= /tmp/Rtmpsc5RME/test.genotype.2e759a50e68df8/results/test_pe.coverage.bw
2025-08-20 23:30:42.942026 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.genotype.2e759a50e68df8/results/test_pe.summary_coverage.tab
2025-08-20 23:30:42.943779 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-08-20 23:30:53.068955 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-08-20 23:30:53.185515 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-08-20 23:30:53.208862 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-08-20 23:30:53.210804 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.genotype.2e759a50e68df8/results/test_pe.raw_variants.RData
2025-08-20 23:30:53.213899 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.genotype.2e759a50e68df8/results/test_pe.filtered_variants.RData
2025-08-20 23:30:53.215834 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-08-20 23:30:53.217427 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-08-20 23:30:53.748882 INFO::analyzeVariants.R/writeVCF: ...done
2025-08-20 23:30:53.75044 INFO::analyzeVariants.R/.callGenotypes: calling genotypes...
2025-08-20 23:31:58.310172 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-08-20 23:31:58.704573 INFO::analyzeVariants.R/writeVCF: ...done
2025-08-20 23:31:58.705539 INFO::analyzeVariants.R/.callGenotypes: done
[W::bcf_hdr_check_sanity] PL should be declared as Number=G
 done successfully.



Executing test function test.wrap.callVariants  ... checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmpsc5RME/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-08-20 23:31:59.152408 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-08-20 23:32:09.056395 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-08-20 23:32:09.138563 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-08-20 23:32:09.156521 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-08-20 23:32:09.158077 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.wrap.callVariants.2e759a2e6de83d/results/test_pe.raw_variants.RData
2025-08-20 23:32:09.160737 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.wrap.callVariants.2e759a2e6de83d/results/test_pe.filtered_variants.RData
2025-08-20 23:32:09.16224 INFO::analyzeVariants.R/wrap.callVariants: ...done
 done successfully.



Executing test function test.wrap.callVariants.filters  ... checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmpsc5RME/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-08-20 23:32:09.343829 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-08-20 23:32:18.618592 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-08-20 23:32:18.681809 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-08-20 23:32:18.700552 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-08-20 23:32:18.702201 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.wrap.callVariants.filters.2e759ac4a5e81/results/test_pe.raw_variants.RData
2025-08-20 23:32:18.704902 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.wrap.callVariants.filters.2e759ac4a5e81/results/test_pe.filtered_variants.RData
2025-08-20 23:32:18.706312 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-08-20 23:32:18.708084 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-08-20 23:32:29.366679 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-08-20 23:32:29.420175 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-08-20 23:32:29.443398 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-08-20 23:32:29.445316 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.wrap.callVariants.filters.2e759ac4a5e81/results/test_pe.raw_variants.RData
2025-08-20 23:32:29.448539 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.wrap.callVariants.filters.2e759ac4a5e81/results/test_pe.filtered_variants.RData
2025-08-20 23:32:29.450989 INFO::analyzeVariants.R/wrap.callVariants: ...done
 done successfully.



Executing test function test.wrap.callVariants.which  ... checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmpsc5RME/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-08-20 23:32:29.803341 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-08-20 23:32:29.805204 INFO::analyzeVariants.R/buildTallyParam: restricting variant calls using 'which'
2025-08-20 23:32:32.954492 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-08-20 23:32:33.030804 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-08-20 23:32:33.047334 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-08-20 23:32:33.048761 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.wrap.callVariants.which.2e759aa56a173/results/test_pe.raw_variants.RData
2025-08-20 23:32:33.050415 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.wrap.callVariants.which.2e759aa56a173/results/test_pe.filtered_variants.RData
2025-08-20 23:32:33.051733 INFO::analyzeVariants.R/wrap.callVariants: ...done
 done successfully.



Executing test function test.writeVCF.NULL  ... checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmpsc5RME/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-08-20 23:32:33.214925 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-08-20 23:32:33.216192 INFO::analyzeVariants.R/writeVCF: ...done
 done successfully.



Executing test function test.writeVCF.vcfStat  ... checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmpsc5RME/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-08-20 23:32:33.406432 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-08-20 23:32:33.634778 INFO::analyzeVariants.R/writeVCF: ...done
 done successfully.



Executing test function test.isFirstFragment  ...  done successfully.



Executing test function test.buildCountsGRangesList  ...   403 genes were dropped because they have exons located on both strands of the
  same reference sequence or on more than one reference sequence, so cannot be
  represented by a single genomic range.
  Use 'single.strand.genes.only=FALSE' to get all the genes in a GRangesList
  object, or use suppressMessages() to suppress this message.
 done successfully.



Executing test function test.generateSingleGeneDERs  ...  done successfully.



Executing test function test.computeCoverage  ...  done successfully.



Executing test function test.isSparse  ...  done successfully.



Executing test function test.mergeCoverage  ... 2025-08-20 23:33:26.618574 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/qlmuxvtj/merged/results/bla.coverage.RData
2025-08-20 23:33:26.622317 INFO::coverage.R/saveCoverage: saving file= /tmp/Rtmpsc5RME/qlmuxvtj/merged/results/bla.coverage.bw
2025-08-20 23:33:26.701518 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/qlmuxvtj/merged/results/bla.summary_coverage.tab
 done successfully.



Executing test function test.mergeCoverage.sparse  ... 2025-08-20 23:33:27.812995 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/szfqoirt/merged/results/bla.coverage.RData
2025-08-20 23:33:27.814475 INFO::coverage.R/saveCoverage: saving file= /tmp/Rtmpsc5RME/szfqoirt/merged/results/bla.coverage.bw
2025-08-20 23:33:27.8257 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/szfqoirt/merged/results/bla.summary_coverage.tab
 done successfully.



Executing test function test.checkConfig.analyzeVariants  ... checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmpsc5RME/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
 done successfully.



Executing test function test.findTemplate  ...  done successfully.



Executing test function test.checkConfig  ... checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmpsc5RME/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmpsc5RME/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmpsc5RME/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmpsc5RME/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
 done successfully.



Executing test function test.checkConfig.alignReads  ... checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmpsc5RME/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmpsc5RME/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmpsc5RME/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmpsc5RME/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
 done successfully.



Executing test function test.getConfig  ...  done successfully.



Executing test function test.loadConfig  ...  done successfully.



Executing test function test.parseDCF  ...  done successfully.



Executing test function test.updateConfig  ...  done successfully.



Executing test function test.getAdapterSeqs  ...  done successfully.



Executing test function test.isAdapter  ...  done successfully.



Executing test function test.isAdapter3.primeEnd  ...  done successfully.



Executing test function test.detectRRNA  ... checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmpsc5RME/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-08-20 23:33:29.027343 INFO::detectRRNA.R/detectRRNA: searching for rRNA contamination...
2025-08-20 23:33:29.028494 INFO::io.R/writeFastQFiles: writing filename= /tmp/Rtmpsc5RME/test.detectRRNA.2e759a3d668ae1/bams/rRNA_contam/input1.fastq
2025-08-20 23:33:29.031688 INFO::alignReads.R/alignReadsChunk: calling gsnap (from gmapR) with args= -t 0 -D /home/biocbuild/.local/share/gmap -n 1 -d TP53_demo_3.2.2 -A sam -B 2 --pairmax-rna=200000 --split-output /tmp/Rtmpsc5RME/test.detectRRNA.2e759a3d668ae1/bams/rRNA_contam/test_se /tmp/Rtmpsc5RME/test.detectRRNA.2e759a3d668ae1/bams/rRNA_contam/input1.fastq 2>&1
2025-08-20 23:33:29.207881 INFO::detectRRNA.R/detectRRNA: contaminated fraction= 1
2025-08-20 23:33:29.208967 INFO::detectRRNA.R/detectRRNA: done
 done successfully.



Executing test function test.detectRRNA.paired_end  ... checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmpsc5RME/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-08-20 23:33:29.365309 INFO::detectRRNA.R/detectRRNA: searching for rRNA contamination...
2025-08-20 23:33:29.36633 INFO::io.R/writeFastQFiles: writing filename= /tmp/Rtmpsc5RME/test.detectRRNA.paired_end.2e759a1a98e82c/bams/rRNA_contam/input1.fastq
2025-08-20 23:33:29.367812 INFO::io.R/writeFastQFiles: writing filename= /tmp/Rtmpsc5RME/test.detectRRNA.paired_end.2e759a1a98e82c/bams/rRNA_contam/input2.fastq
2025-08-20 23:33:29.369992 INFO::alignReads.R/alignReadsChunk: calling gsnap (from gmapR) with args= -t 0 -D /home/biocbuild/.local/share/gmap -n 1 -d TP53_demo_3.2.2 -A sam -B 2 --pairmax-rna=200000 --split-output /tmp/Rtmpsc5RME/test.detectRRNA.paired_end.2e759a1a98e82c/bams/rRNA_contam/test_pe /tmp/Rtmpsc5RME/test.detectRRNA.paired_end.2e759a1a98e82c/bams/rRNA_contam/input1.fastq -a paired /tmp/Rtmpsc5RME/test.detectRRNA.paired_end.2e759a1a98e82c/bams/rRNA_contam/input2.fastq 2>&1
2025-08-20 23:33:29.616298 INFO::detectRRNA.R/detectRRNA: contaminated fraction= 1
2025-08-20 23:33:29.617363 INFO::detectRRNA.R/detectRRNA: done
 done successfully.



Executing test function test.getRRNAIds  ... 2025-08-20 23:33:29.637817 INFO::alignReads.R/alignReadsChunk: calling gsnap (from gmapR) with args= -t 0 -D /home/biocbuild/.local/share/gmap -n 1 -d TP53_demo_3.2.2 -A sam -B 2 --pairmax-rna=200000 --split-output /tmp/Rtmpsc5RME/test_get_rRNA_idsujxklfbt/test_pe /tmp/Rtmpsc5RME/test_get_rRNA_idsujxklfbt/1.fastq -a paired /tmp/Rtmpsc5RME/test_get_rRNA_idsujxklfbt/2.fastq 2>&1
 done successfully.



Executing test function test.getRRNAIds_random  ... 2025-08-20 23:33:29.895001 INFO::alignReads.R/alignReadsChunk: calling gsnap (from gmapR) with args= -t 0 -D /home/biocbuild/.local/share/gmap -n 1 -d TP53_demo_3.2.2 -A sam -B 2 --pairmax-rna=200000 --split-output /tmp/Rtmpsc5RME/test_get_rRNAIds_randombenokimh/test_pe /tmp/Rtmpsc5RME/test_get_rRNAIds_randombenokimh/1.fastq 2>&1
 done successfully.



Executing test function test.filterByLength  ... 2025-08-20 23:33:30.154601 INFO::filterQuality.R/filterQuality: filterByLength...
2025-08-20 23:33:30.156037 INFO::filterQuality.R/filterByLength: fraction of filtered short reads= 0.5
2025-08-20 23:33:30.156912 INFO::filterQuality.R/filterByLength: done
2025-08-20 23:33:30.201925 INFO::filterQuality.R/filterQuality: filterByLength...
2025-08-20 23:33:30.202844 INFO::filterQuality.R/filterByLength: fraction of filtered short reads= 1
2025-08-20 23:33:30.203686 INFO::filterQuality.R/filterByLength: done
 done successfully.



Executing test function test.isAboveQualityThresh  ...  done successfully.



Executing test function test.trimTailsByQuality  ... 2025-08-20 23:33:30.253267 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-08-20 23:33:30.26192 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-08-20 23:33:30.263003 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-08-20 23:33:30.267312 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-08-20 23:33:30.268303 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-08-20 23:33:30.272592 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-08-20 23:33:30.273544 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-08-20 23:33:30.277833 INFO::preprocessReads.R/preprocessReadsChunk: done
 done successfully.



Executing test function test.callVariantsGATK  ... Timing stopped at: 0 0 0
Error in DEACTIVATED("callVariantsGATK() tests need gatk.path option set") : 
  callVariantsGATK() tests need gatk.path option set
In addition: There were 50 or more warnings (use warnings() to see the first 50)
 done successfully.



Executing test function test.callVariantsGATK.withFiltering  ... Timing stopped at: 0 0 0
Error in DEACTIVATED("callVariantsGATK() tests need gatk.path option set") : 
  callVariantsGATK() tests need gatk.path option set
 done successfully.



Executing test function test.checkGATKJar  ... Timing stopped at: 0 0 0
Error in DEACTIVATED("checkGATKJar() test needs gatk.path option set") : 
  checkGATKJar() test needs gatk.path option set
 done successfully.



Executing test function test.excludeVariantsByRegion  ...  done successfully.



Executing test function test.gatk  ... Timing stopped at: 0 0 0
Error in DEACTIVATED("gatk() tests need gatk.path option set") : 
  gatk() tests need gatk.path option set
 done successfully.



Executing test function test.realignIndels  ... Timing stopped at: 0 0 0
Error in DEACTIVATED("test.realignIndels() tests need gatk.path option set") : 
  test.realignIndels() tests need gatk.path option set
 done successfully.



Executing test function test.realignIndelsGATK  ... Timing stopped at: 0 0 0
Error in DEACTIVATED("realignIndelsGATK() tests need gatk.path option set") : 
  realignIndelsGATK() tests need gatk.path option set
 done successfully.



Executing test function test.realignIndelsGATK.parallel  ... Timing stopped at: 0 0 0
Error in DEACTIVATED("realignIndelsGATK() tests need gatk.path option set") : 
  realignIndelsGATK() tests need gatk.path option set
 done successfully.



Executing test function test_zipUp  ...  done successfully.



Executing test function test.FastQStreamer.getReads.pefq  ... checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmpsc5RME/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-08-20 23:33:30.542927 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-08-20 23:33:30.545305 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
 done successfully.



Executing test function test.FastQStreamer.getReads.pefq.subsample  ... checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmpsc5RME/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-08-20 23:33:30.723655 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-08-20 23:33:30.794734 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-08-20 23:33:30.797495 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-08-20 23:33:30.799749 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
 done successfully.



Executing test function test.FastQStreamer.getReads.segz  ... checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmpsc5RME/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-08-20 23:33:30.999636 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/reads.fastq.gz
 done successfully.



Executing test function test.FastQStreamer.getReads.truncated  ... checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmpsc5RME/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-08-20 23:33:31.146297 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/truncated.fastq.gz
 done successfully.



Executing test function test.FastQStreamer.subsampler.isdeterministic  ... checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmpsc5RME/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-08-20 23:33:31.280805 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-08-20 23:33:31.325769 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-08-20 23:33:31.328209 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-08-20 23:33:31.330458 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmpsc5RME/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-08-20 23:33:31.540956 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-08-20 23:33:31.556056 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-08-20 23:33:31.558424 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-08-20 23:33:31.560583 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
 done successfully.



Executing test function test.createTmpDir  ...  done successfully.



Executing test function test.detectQualityInFASTQFile  ...  done successfully.



Executing test function test.getObjectFilename  ...  done successfully.



Executing test function test.safeUnlink  ...  done successfully.



Executing test function test.writeAudit  ... checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmpsc5RME/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
 done successfully.



Executing test function test.mergeLanes  ... checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmpsc5RME/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-08-20 23:33:32.295985 INFO::preprocessReads.R/preprocessReads: starting...
2025-08-20 23:33:32.30203 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-08-20 23:33:32.305561 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-08-20 23:33:32.307986 DEBUG::tools.R/processChunks: starting...
2025-08-20 23:33:35.447843 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-08-20 23:33:35.449341 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/chunks/chunk_000001/logs/progress.log
2025-08-20 23:33:38.038573 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.043 minutes
2025-08-20 23:33:38.039934 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/chunks/chunk_000002/logs/progress.log
2025-08-20 23:33:40.636814 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.043 minutes
2025-08-20 23:33:40.638324 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/chunks/chunk_000003/logs/progress.log
2025-08-20 23:33:43.284695 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.044 minutes
2025-08-20 23:33:43.332081 DEBUG::tools.R/processChunks: done
2025-08-20 23:33:43.334774 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-08-20 23:33:43.336386 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/results/test_pe.adapter_contaminated_1.RData
2025-08-20 23:33:43.338414 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-08-20 23:33:43.339909 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/results/test_pe.adapter_contaminated_2.RData
2025-08-20 23:33:43.34796 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=26 highqual_reads=25 adapter_contam=1 read_length=75 rRNA_contam_reads=0 processed_reads=25 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-08-20 23:33:43.349738 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/results/test_pe.summary_preprocess.tab
2025-08-20 23:33:43.352106 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/bams/processed.aligner_input_1.fastq ...
2025-08-20 23:33:43.356113 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/bams/processed.aligner_input_2.fastq ...
2025-08-20 23:33:43.359235 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/reports/shortReadReport_1 ...
2025-08-20 23:33:44.657739 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/reports/shortReadReport_2 ...
2025-08-20 23:33:45.717266 INFO::preprocessReads.R/preprocessReads: done
2025-08-20 23:33:45.824491 INFO::alignReads.R/alignReads: starting alignment...
2025-08-20 23:33:45.82905 DEBUG::tools.R/processChunks: starting...
2025-08-20 23:33:48.801696 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-08-20 23:33:48.803533 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/chunks/chunk_000001/logs/progress.log
2025-08-20 23:33:51.397649 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.043 minutes
2025-08-20 23:33:51.399149 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/chunks/chunk_000002/logs/progress.log
[bam_translate] PG tag "A" on read "highqualPEsInManyTxsOfMultiTxGene:1:1:1:16#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1MicrobialPE2MultimappingIntergenic:1:1:1:19#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInOneTxOfMultiTxGene:1:1:1:15#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1UniqueUtrPE2MultimappingIntergenic:1:1:1:18#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-08-20 23:33:53.999914 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.043 minutes
2025-08-20 23:33:54.001817 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/chunks/chunk_000003/logs/progress.log
[bam_translate] PG tag "A" on read "highqualPE1GeneFusionMidExonDiffChrPE2MultimappingIntergenic:1:1:1:25#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-08-20 23:33:56.60399 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.043 minutes
2025-08-20 23:33:56.607216 DEBUG::tools.R/processChunks: done
2025-08-20 23:33:56.609193 INFO::alignReads.R/mergeBAMsAcrossDirs: starting...
[bam_translate] PG tag "A" on read "highqualAdapterContamIn3PrimeEnd:1:1:1:7#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInManyTxsOfMultiTxGene:1:1:1:16#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1MicrobialPE2MultimappingIntergenic:1:1:1:19#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1GeneFusionMidExonDiffChrPE2MultimappingIntergenic:1:1:1:25#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1UniqueUtrPE2MultimappingIntergenic:1:1:1:18#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInOneTxOfMultiTxGene:1:1:1:15#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-08-20 23:33:56.80809 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-08-20 23:33:56.815035 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/results/test_pe.summary_alignment.tab
2025-08-20 23:33:56.821444 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/results/test_pe.summary_analyzed_bamstats.tab
2025-08-20 23:33:56.823164 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-08-20 23:33:57.041002 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/results/test_pe.summary_target_lengths.tab
2025-08-20 23:33:57.087415 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-08-20 23:33:57.08857 INFO::alignReads.R/alignReads: done
2025-08-20 23:33:57.201968 INFO::countGenomicFeatures.R/countGenomicFeatures: starting...
2025-08-20 23:33:57.223552 DEBUG::tools.R/processChunks: starting...
2025-08-20 23:34:00.261425 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-08-20 23:34:00.263229 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/chunks/chunk_000001/logs/progress.log
2025-08-20 23:34:02.734369 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.041 minutes
2025-08-20 23:34:02.736191 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/chunks/chunk_000002/logs/progress.log
2025-08-20 23:34:05.219082 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.041 minutes
2025-08-20 23:34:05.220809 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/chunks/chunk_000003/logs/progress.log
2025-08-20 23:34:07.674196 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.041 minutes
2025-08-20 23:34:07.677763 DEBUG::tools.R/processChunks: done
2025-08-20 23:34:07.68009 INFO::countGenomicFeatures.R/mergeCounts: starting...
2025-08-20 23:34:07.701048 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/results/test_pe.counts_exon.tab
2025-08-20 23:34:07.71752 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/results/test_pe.counts_exon_disjoint.tab
2025-08-20 23:34:07.727581 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/results/test_pe.counts_gene.tab
2025-08-20 23:34:07.734331 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/results/test_pe.counts_gene_coding.tab
2025-08-20 23:34:07.741211 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/results/test_pe.counts_gene_exonic.tab
2025-08-20 23:34:07.748158 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/results/test_pe.counts_intergenic.tab
2025-08-20 23:34:07.761517 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/results/test_pe.counts_intron.tab
2025-08-20 23:34:07.76545 INFO::countGenomicFeatures.R/mergeCounts: done
2025-08-20 23:34:07.773008 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/results/test_pe.summary_counts.tab
2025-08-20 23:34:07.775273 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2025-08-20 23:34:08.073819 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2025-08-20 23:34:08.074752 INFO::countGenomicFeatures.R/countGenomicFeatures: done...
2025-08-20 23:34:08.169244 INFO::coverage.R/calculateCoverage: starting...
2025-08-20 23:34:08.17371 DEBUG::tools.R/processChunks: starting...
2025-08-20 23:34:11.247204 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-08-20 23:34:11.248935 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/chunks/chunk_000001/logs/progress.log
2025-08-20 23:34:13.417583 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.036 minutes
2025-08-20 23:34:13.419059 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/chunks/chunk_000002/logs/progress.log
2025-08-20 23:34:15.592386 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.036 minutes
2025-08-20 23:34:15.593964 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/chunks/chunk_000003/logs/progress.log
2025-08-20 23:34:17.770268 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.036 minutes
2025-08-20 23:34:17.77301 DEBUG::tools.R/processChunks: done
2025-08-20 23:34:20.200409 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/results/test_pe.coverage.RData
2025-08-20 23:34:20.203085 INFO::coverage.R/saveCoverage: saving file= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/results/test_pe.coverage.bw
2025-08-20 23:34:20.232486 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/results/test_pe.summary_coverage.tab
2025-08-20 23:34:20.23407 INFO::coverage.R/calculateCoverage: done
2025-08-20 23:34:20.236322 INFO::analyzeVariants/analyzeVariants: starting ...
2025-08-20 23:34:20.343642 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-08-20 23:34:23.379364 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-08-20 23:34:23.451955 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-08-20 23:34:23.468118 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-08-20 23:34:23.469419 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/results/test_pe.raw_variants.RData
2025-08-20 23:34:23.471006 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/results/test_pe.filtered_variants.RData
2025-08-20 23:34:23.47222 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-08-20 23:34:23.473158 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-08-20 23:34:23.682277 INFO::analyzeVariants.R/writeVCF: ...done
2025-08-20 23:34:23.77829 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/results/test_pe.summary_variants.tab
2025-08-20 23:34:23.780505 INFO::analyzeVariants/analyzeVariants: done
2025-08-20 23:34:23.785496 INFO::Pipeline run successful.
2025-08-20 23:34:23.962364 INFO::mergeLanes.R/doMergeLanes: starting...
2025-08-20 23:34:23.967264 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-08-20 23:34:23.9696 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/merged/results/merged.adapter_contaminated_1.RData
2025-08-20 23:34:23.972773 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-08-20 23:34:23.974794 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/merged/results/merged.adapter_contaminated_2.RData
2025-08-20 23:34:23.986816 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=26 highqual_reads=25 adapter_contam=1 read_length=75 rRNA_contam_reads=0 processed_reads=25 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-08-20 23:34:23.989291 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/merged/results/merged.summary_preprocess.tab
2025-08-20 23:34:23.991642 INFO::alignReads.R/mergeBAMsAcrossDirs: starting...
[bam_translate] PG tag "A" on read "highqualAdapterContamIn3PrimeEnd:1:1:1:7#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInManyTxsOfMultiTxGene:1:1:1:16#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1MicrobialPE2MultimappingIntergenic:1:1:1:19#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1GeneFusionMidExonDiffChrPE2MultimappingIntergenic:1:1:1:25#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1UniqueUtrPE2MultimappingIntergenic:1:1:1:18#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInOneTxOfMultiTxGene:1:1:1:15#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-08-20 23:34:24.249316 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-08-20 23:34:24.257366 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/merged/results/merged.summary_alignment.tab
2025-08-20 23:34:24.265934 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/merged/results/merged.summary_analyzed_bamstats.tab
2025-08-20 23:34:24.268523 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-08-20 23:34:24.513245 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/merged/results/merged.summary_target_lengths.tab
2025-08-20 23:34:24.565125 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-08-20 23:34:24.627069 INFO::countGenomicFeatures.R/mergeCounts: starting...
2025-08-20 23:34:24.648881 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/merged/results/merged.counts_exon.tab
2025-08-20 23:34:24.661481 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/merged/results/merged.counts_exon_disjoint.tab
2025-08-20 23:34:24.668751 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/merged/results/merged.counts_gene.tab
2025-08-20 23:34:24.6746 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/merged/results/merged.counts_gene_coding.tab
2025-08-20 23:34:24.680235 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/merged/results/merged.counts_gene_exonic.tab
2025-08-20 23:34:24.686116 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/merged/results/merged.counts_intergenic.tab
2025-08-20 23:34:24.697515 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/merged/results/merged.counts_intron.tab
2025-08-20 23:34:24.700252 INFO::countGenomicFeatures.R/mergeCounts: done
2025-08-20 23:34:24.706403 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/merged/results/merged.summary_counts.tab
2025-08-20 23:34:24.708228 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2025-08-20 23:34:24.945851 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2025-08-20 23:34:27.479058 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/merged/results/merged.coverage.RData
2025-08-20 23:34:27.481634 INFO::coverage.R/saveCoverage: saving file= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/merged/results/merged.coverage.bw
2025-08-20 23:34:27.493827 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/merged/results/merged.summary_coverage.tab
2025-08-20 23:34:27.582171 INFO::analyzeVariants/analyzeVariants: starting ...
2025-08-20 23:34:27.673368 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-08-20 23:34:32.467839 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-08-20 23:34:32.798819 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-08-20 23:34:32.890213 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-08-20 23:34:32.897399 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/merged/results/merged.raw_variants.RData
2025-08-20 23:34:32.90556 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/merged/results/merged.filtered_variants.RData
2025-08-20 23:34:32.911592 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-08-20 23:34:32.914047 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-08-20 23:34:33.618074 INFO::analyzeVariants.R/writeVCF: ...done
2025-08-20 23:34:34.039278 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.mergeLanes.2e759a4317371d/merged/results/merged.summary_variants.tab
2025-08-20 23:34:34.043042 INFO::analyzeVariants/analyzeVariants: done
2025-08-20 23:34:34.052963 INFO::mergeLanes.R/doMergeLanes: merge lanes successful.
 done successfully.



Executing test function test.markDuplicates  ... Timing stopped at: 0.001 0 0.001
Error in DEACTIVATED("Skipped markDuplicates() test") : 
  Skipped markDuplicates() test
In addition: There were 28 warnings (use warnings() to see them)
 done successfully.



Executing test function test.markDuplicates_w_outfile  ... Timing stopped at: 0 0 0.001
Error in DEACTIVATED("Skipped markDuplicates() test") : 
  Skipped markDuplicates() test
 done successfully.



Executing test function test.preprocessReads  ... checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmpsc5RME/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-08-20 23:34:34.840877 INFO::preprocessReads.R/preprocessReads: starting...
2025-08-20 23:34:34.899137 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-08-20 23:34:34.926318 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-08-20 23:34:34.930736 DEBUG::tools.R/processChunks: starting...
2025-08-20 23:34:42.677547 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-08-20 23:34:42.689717 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /tmp/Rtmpsc5RME/test.preprocessReads.2e759a10daddcb/chunks/chunk_000001/logs/progress.log
2025-08-20 23:34:46.226656 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.059 minutes
2025-08-20 23:34:46.432215 DEBUG::tools.R/processChunks: done
2025-08-20 23:34:46.437351 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-08-20 23:34:46.440586 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.preprocessReads.2e759a10daddcb/results/test_pe.adapter_contaminated_1.RData
2025-08-20 23:34:46.444118 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-08-20 23:34:46.446732 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.preprocessReads.2e759a10daddcb/results/test_pe.adapter_contaminated_2.RData
2025-08-20 23:34:46.459935 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=26 highqual_reads=25 adapter_contam=1 read_length=75 rRNA_contam_reads=0 processed_reads=25 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-08-20 23:34:46.464054 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.preprocessReads.2e759a10daddcb/results/test_pe.summary_preprocess.tab
2025-08-20 23:34:46.468527 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/Rtmpsc5RME/test.preprocessReads.2e759a10daddcb/bams/processed.aligner_input_1.fastq ...
2025-08-20 23:34:46.484251 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/Rtmpsc5RME/test.preprocessReads.2e759a10daddcb/bams/processed.aligner_input_2.fastq ...
2025-08-20 23:34:46.501824 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/Rtmpsc5RME/test.preprocessReads.2e759a10daddcb/reports/shortReadReport_1 ...
2025-08-20 23:34:51.220907 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/Rtmpsc5RME/test.preprocessReads.2e759a10daddcb/reports/shortReadReport_2 ...
2025-08-20 23:34:53.109896 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



Executing test function test.preprocessReads.minichunks  ... checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmpsc5RME/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-08-20 23:34:53.704116 INFO::preprocessReads.R/preprocessReads: starting...
2025-08-20 23:34:53.717867 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-08-20 23:34:53.729833 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-08-20 23:34:53.736585 DEBUG::tools.R/processChunks: starting...
2025-08-20 23:34:59.076629 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-08-20 23:34:59.079868 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /tmp/Rtmpsc5RME/test.preprocessReads.minichunks.2e759a18ad95c5/chunks/chunk_000001/logs/progress.log
2025-08-20 23:35:01.953267 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.048 minutes
2025-08-20 23:35:01.955842 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /tmp/Rtmpsc5RME/test.preprocessReads.minichunks.2e759a18ad95c5/chunks/chunk_000002/logs/progress.log
2025-08-20 23:35:05.074409 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.052 minutes
2025-08-20 23:35:05.077193 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /tmp/Rtmpsc5RME/test.preprocessReads.minichunks.2e759a18ad95c5/chunks/chunk_000003/logs/progress.log
2025-08-20 23:35:08.221504 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.052 minutes
2025-08-20 23:35:08.307231 DEBUG::tools.R/processChunks: done
2025-08-20 23:35:08.312445 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-08-20 23:35:08.315687 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.preprocessReads.minichunks.2e759a18ad95c5/results/test_pe.adapter_contaminated_1.RData
2025-08-20 23:35:08.319681 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-08-20 23:35:08.32271 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.preprocessReads.minichunks.2e759a18ad95c5/results/test_pe.adapter_contaminated_2.RData
2025-08-20 23:35:08.338808 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=26 highqual_reads=25 adapter_contam=1 read_length=75 rRNA_contam_reads=0 processed_reads=25 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-08-20 23:35:08.342524 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.preprocessReads.minichunks.2e759a18ad95c5/results/test_pe.summary_preprocess.tab
2025-08-20 23:35:08.347208 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/Rtmpsc5RME/test.preprocessReads.minichunks.2e759a18ad95c5/bams/processed.aligner_input_1.fastq ...
2025-08-20 23:35:08.354983 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/Rtmpsc5RME/test.preprocessReads.minichunks.2e759a18ad95c5/bams/processed.aligner_input_2.fastq ...
2025-08-20 23:35:08.361001 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/Rtmpsc5RME/test.preprocessReads.minichunks.2e759a18ad95c5/reports/shortReadReport_1 ...
2025-08-20 23:35:10.954679 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/Rtmpsc5RME/test.preprocessReads.minichunks.2e759a18ad95c5/reports/shortReadReport_2 ...
2025-08-20 23:35:12.443815 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



Executing test function test.preprocessReads_single_end  ... checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmpsc5RME/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-08-20 23:35:12.915843 INFO::preprocessReads.R/preprocessReads: starting...
2025-08-20 23:35:12.940476 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-08-20 23:35:12.943959 DEBUG::tools.R/processChunks: starting...
2025-08-20 23:35:17.265097 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-08-20 23:35:17.267162 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /tmp/Rtmpsc5RME/test.preprocessReads_single_end.2e759a5347a145/chunks/chunk_000001/logs/progress.log
2025-08-20 23:35:19.857597 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.043 minutes
2025-08-20 23:35:19.926087 DEBUG::tools.R/processChunks: done
2025-08-20 23:35:19.930331 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-08-20 23:35:19.933436 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.preprocessReads_single_end.2e759a5347a145/results/test_se.adapter_contaminated_1.RData
2025-08-20 23:35:19.945244 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=26 highqual_reads=25 adapter_contam=1 read_length=75 rRNA_contam_reads=0 processed_reads=25 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-08-20 23:35:19.948797 INFO::io.R/saveWithID: saving file= /tmp/Rtmpsc5RME/test.preprocessReads_single_end.2e759a5347a145/results/test_se.summary_preprocess.tab
2025-08-20 23:35:19.95265 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/Rtmpsc5RME/test.preprocessReads_single_end.2e759a5347a145/bams/processed.aligner_input_1.fastq ...
2025-08-20 23:35:19.958468 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/Rtmpsc5RME/test.preprocessReads_single_end.2e759a5347a145/reports/shortReadReport_1 ...
2025-08-20 23:35:21.685487 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



Executing test function test.readRNASeqEnds  ...  done successfully.



Executing test function test.readRNASeqEnds.dupmark  ...  done successfully.



Executing test function test.how_many  ...  done successfully.



Executing test function test.plotDF  ...  done successfully.



Executing test function test.relativeBarPlot  ...  done successfully.



Executing test function test.runPipeline  ... checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-08-20 23:35:22.416765 INFO::preprocessReads.R/preprocessReads: starting...
2025-08-20 23:35:22.437989 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/extdata/H1993_TP53_subset2500_1.fastq.gz
2025-08-20 23:35:22.456275 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/extdata/H1993_TP53_subset2500_2.fastq.gz
2025-08-20 23:35:22.45906 DEBUG::tools.R/processChunks: starting...
2025-08-20 23:35:25.534413 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-08-20 23:35:25.535819 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= test/chunks/chunk_000001/logs/progress.log
2025-08-20 23:35:28.364182 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.047 minutes
2025-08-20 23:35:28.410608 DEBUG::tools.R/processChunks: done
2025-08-20 23:35:28.412977 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-08-20 23:35:28.41454 INFO::io.R/saveWithID: saving file= test/results/test.adapter_contaminated_1.RData
2025-08-20 23:35:28.416245 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-08-20 23:35:28.417539 INFO::io.R/saveWithID: saving file= test/results/test.adapter_contaminated_2.RData
2025-08-20 23:35:28.424673 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=2500 highqual_reads=2500 adapter_contam=0 read_length=100 rRNA_contam_reads=0 processed_reads=2500 input_min_read_length=100 input_max_read_length=100 processed_min_read_length=71 processed_max_read_length=100
2025-08-20 23:35:28.426703 INFO::io.R/saveWithID: saving file= test/results/test.summary_preprocess.tab
2025-08-20 23:35:28.428884 INFO::preprocessReads.R/mergePreprocessedReads: merging file= test/bams/processed.aligner_input_1.fastq ...
2025-08-20 23:35:28.434408 INFO::preprocessReads.R/mergePreprocessedReads: merging file= test/bams/processed.aligner_input_2.fastq ...
2025-08-20 23:35:28.438334 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= test/reports/shortReadReport_1 ...
2025-08-20 23:36:22.438941 DEBUG::tools.R/traceMem: wired.mem=15.394017 GiB
2025-08-20 23:37:22.506021 DEBUG::tools.R/traceMem: wired.mem=23.253389 GiB
2025-08-20 23:38:22.569957 DEBUG::tools.R/traceMem: wired.mem=22.132675 GiB
2025-08-20 23:39:22.588769 DEBUG::tools.R/traceMem: wired.mem=21.978649 GiB
2025-08-20 23:40:22.655342 DEBUG::tools.R/traceMem: wired.mem=26.599322 GiB
2025-08-20 23:41:22.720965 DEBUG::tools.R/traceMem: wired.mem=20.294775 GiB
2025-08-20 23:42:22.788193 DEBUG::tools.R/traceMem: wired.mem=36.497043 GiB
2025-08-20 23:43:22.855487 DEBUG::tools.R/traceMem: wired.mem=24.113230 GiB
2025-08-20 23:44:22.920326 DEBUG::tools.R/traceMem: wired.mem=34.444251 GiB
2025-08-20 23:45:22.985158 DEBUG::tools.R/traceMem: wired.mem=22.726988 GiB
2025-08-20 23:46:23.052664 DEBUG::tools.R/traceMem: wired.mem=31.874748 GiB
2025-08-20 23:47:23.11891 DEBUG::tools.R/traceMem: wired.mem=20.880265 GiB
2025-08-20 23:48:23.185252 DEBUG::tools.R/traceMem: wired.mem=26.340930 GiB
2025-08-20 23:49:23.250937 DEBUG::tools.R/traceMem: wired.mem=26.746073 GiB
2025-08-20 23:50:23.316705 DEBUG::tools.R/traceMem: wired.mem=24.911254 GiB
2025-08-20 23:51:23.383738 DEBUG::tools.R/traceMem: wired.mem=31.495221 GiB
2025-08-20 23:52:23.449059 DEBUG::tools.R/traceMem: wired.mem=30.426608 GiB
2025-08-20 23:53:23.482955 DEBUG::tools.R/traceMem: wired.mem=17.250292 GiB
2025-08-20 23:54:23.547719 DEBUG::tools.R/traceMem: wired.mem=23.160508 GiB
2025-08-20 23:55:23.612849 DEBUG::tools.R/traceMem: wired.mem=21.866303 GiB
2025-08-20 23:56:23.677891 DEBUG::tools.R/traceMem: wired.mem=27.616055 GiB
2025-08-20 23:57:23.743995 DEBUG::tools.R/traceMem: wired.mem=31.546774 GiB
2025-08-20 23:58:23.809708 DEBUG::tools.R/traceMem: wired.mem=27.045704 GiB
2025-08-20 23:59:23.875531 DEBUG::tools.R/traceMem: wired.mem=21.052723 GiB
2025-08-21 00:00:23.940912 DEBUG::tools.R/traceMem: wired.mem=30.920585 GiB
2025-08-21 00:01:24.007359 DEBUG::tools.R/traceMem: wired.mem=36.970025 GiB
2025-08-21 00:02:24.075372 DEBUG::tools.R/traceMem: wired.mem=32.760041 GiB
2025-08-21 00:03:24.141586 DEBUG::tools.R/traceMem: wired.mem=37.011976 GiB

Example timings

HTSeqGenie.Rcheck/HTSeqGenie-Ex.timings

name	user	system	elapsed
HTSeqGenie	0.000	0.000	0.001
buildGenomicFeaturesFromTxDb	0	0	0
runPipeline	0	0	0