Multiple platform build/check report for BioC 3.20 - CHECK results for HTSeqGenie on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4769
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4504
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4527
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4480
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4416
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 nebbiolo2

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: 4.36.0

Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:HTSeqGenie.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings HTSeqGenie_4.36.0.tar.gz

StartedAt: 2025-03-03 23:03:35 -0500 (Mon, 03 Mar 2025)

EndedAt: 2025-03-03 23:43:36 -0500 (Mon, 03 Mar 2025)

EllapsedTime: 2400.8 seconds

RetCode: None

Status: TIMEOUT

CheckDir: HTSeqGenie.Rcheck

Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:HTSeqGenie.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings HTSeqGenie_4.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/HTSeqGenie.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘HTSeqGenie/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HTSeqGenie’ version ‘4.36.0’
* 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-3.20-bioc/R/bin/R CMD INSTALL HTSeqGenie
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘HTSeqGenie’ ...
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (HTSeqGenie)

Tests output

HTSeqGenie.Rcheck/tests/doRUnit.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
    tapply, union, 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

> 
> 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= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-03 23:09:07.556703 INFO::preprocessReads.R/preprocessReads: starting...
2025-03-03 23:09:07.565475 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-03-03 23:09:07.569087 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-03-03 23:09:07.571341 DEBUG::tools.R/processChunks: starting...
2025-03-03 23:09:10.635899 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-03 23:09:10.637405 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.alignReads.2fa2d33b13adb4/chunks/chunk_000001/logs/progress.log
2025-03-03 23:09:13.442135 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.047 minutes
2025-03-03 23:09:13.443661 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.alignReads.2fa2d33b13adb4/chunks/chunk_000002/logs/progress.log
2025-03-03 23:09:16.177921 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.046 minutes
2025-03-03 23:09:16.179327 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.alignReads.2fa2d33b13adb4/chunks/chunk_000003/logs/progress.log
2025-03-03 23:09:18.888055 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.045 minutes
2025-03-03 23:09:18.912074 DEBUG::tools.R/processChunks: done
2025-03-03 23:09:18.915554 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-03-03 23:09:18.917642 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.alignReads.2fa2d33b13adb4/results/test_pe.adapter_contaminated_1.RData
2025-03-03 23:09:18.920348 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-03-03 23:09:18.92191 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.alignReads.2fa2d33b13adb4/results/test_pe.adapter_contaminated_2.RData
2025-03-03 23:09:18.930289 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
2025-03-03 23:09:18.932357 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.alignReads.2fa2d33b13adb4/results/test_pe.summary_preprocess.tab
2025-03-03 23:09:18.93531 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.alignReads.2fa2d33b13adb4/bams/processed.aligner_input_1.fastq ...
2025-03-03 23:09:18.939776 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.alignReads.2fa2d33b13adb4/bams/processed.aligner_input_2.fastq ...
2025-03-03 23:09:18.943585 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.alignReads.2fa2d33b13adb4/reports/shortReadReport_1 ...
2025-03-03 23:09:20.261211 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.alignReads.2fa2d33b13adb4/reports/shortReadReport_2 ...
2025-03-03 23:09:21.329513 INFO::preprocessReads.R/preprocessReads: done
2025-03-03 23:09:21.46627 INFO::alignReads.R/alignReads: starting alignment...
2025-03-03 23:09:21.47321 DEBUG::tools.R/processChunks: starting...
2025-03-03 23:09:24.408245 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-03 23:09:24.409952 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.alignReads.2fa2d33b13adb4/chunks/chunk_000001/logs/progress.log
2025-03-03 23:09:27.30091 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.048 minutes
2025-03-03 23:09:27.302531 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.alignReads.2fa2d33b13adb4/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.
2025-03-03 23:09:29.958125 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.044 minutes
2025-03-03 23:09:29.960569 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.alignReads.2fa2d33b13adb4/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.
2025-03-03 23:09:32.657479 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.045 minutes
2025-03-03 23:09:32.660639 DEBUG::tools.R/processChunks: done
2025-03-03 23:09:32.662619 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.
2025-03-03 23:09:32.885059 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-03-03 23:09:32.893693 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.alignReads.2fa2d33b13adb4/results/test_pe.summary_alignment.tab
2025-03-03 23:09:32.900968 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.alignReads.2fa2d33b13adb4/results/test_pe.summary_analyzed_bamstats.tab
2025-03-03 23:09:32.9027 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-03-03 23:09:33.141418 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.alignReads.2fa2d33b13adb4/results/test_pe.summary_target_lengths.tab
2025-03-03 23:09:33.187862 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-03-03 23:09:33.188924 INFO::alignReads.R/alignReads: done
 done successfully.



Executing test function test.alignReads.sparsechunks  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-03 23:09:33.443879 INFO::preprocessReads.R/preprocessReads: starting...
2025-03-03 23:09:33.447601 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-03-03 23:09:33.527217 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 2 , totnbreads= 26 )
2025-03-03 23:09:33.532865 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-03-03 23:09:33.536476 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-03-03 23:09:33.538707 DEBUG::tools.R/processChunks: starting...
2025-03-03 23:09:36.614575 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-03 23:09:36.616156 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.alignReads.sparsechunks.2fa2d394256e9/chunks/chunk_000001/logs/progress.log
2025-03-03 23:09:39.322143 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.045 minutes
2025-03-03 23:09:39.323531 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.alignReads.sparsechunks.2fa2d394256e9/chunks/chunk_000002/logs/progress.log
2025-03-03 23:09:42.039211 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.045 minutes
2025-03-03 23:09:42.040573 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.alignReads.sparsechunks.2fa2d394256e9/chunks/chunk_000003/logs/progress.log
2025-03-03 23:09:44.768085 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.045 minutes
2025-03-03 23:09:44.769533 DEBUG::tools.R/processChunks: starting chunkid= 4 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.alignReads.sparsechunks.2fa2d394256e9/chunks/chunk_000004/logs/progress.log
2025-03-03 23:09:47.470037 DEBUG::tools.R/processChunks: done with chunkid= 4 ; elapsed.time= 0.045 minutes
2025-03-03 23:09:47.519408 DEBUG::tools.R/processChunks: done
2025-03-03 23:09:47.524318 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-03-03 23:09:47.527756 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.alignReads.sparsechunks.2fa2d394256e9/results/test_pe.adapter_contaminated_1.RData
2025-03-03 23:09:47.532231 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-03-03 23:09:47.534754 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.alignReads.sparsechunks.2fa2d394256e9/results/test_pe.adapter_contaminated_2.RData
2025-03-03 23:09:47.550903 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
2025-03-03 23:09:47.554345 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.alignReads.sparsechunks.2fa2d394256e9/results/test_pe.summary_preprocess.tab
2025-03-03 23:09:47.559591 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.alignReads.sparsechunks.2fa2d394256e9/bams/processed.aligner_input_1.fastq ...
2025-03-03 23:09:47.565347 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.alignReads.sparsechunks.2fa2d394256e9/bams/processed.aligner_input_2.fastq ...
2025-03-03 23:09:47.569582 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.alignReads.sparsechunks.2fa2d394256e9/reports/shortReadReport_1 ...
2025-03-03 23:09:48.973699 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.alignReads.sparsechunks.2fa2d394256e9/reports/shortReadReport_2 ...
2025-03-03 23:09:50.125905 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



Executing test function test.alignReadsOneSingleEnd  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-03 23:09:50.308957 INFO::alignReads.R/alignReadsChunk: running gsnap...
2025-03-03 23:09:50.313661 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 /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.alignReadsOneSingleEnd.2fa2d36c610ed2/bams/test.alignReads /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq 2>&1
2025-03-03 23:09:50.517172 INFO::alignReads.R/createSummaryAlignment: counting unique bam reads...
2025-03-03 23:09:50.612206 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.alignReadsOneSingleEnd.2fa2d36c610ed2/results/test.alignReads.summary_alignment.tab
2025-03-03 23:09:50.653737 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.alignReadsOneSingleEnd.2fa2d36c610ed2/results/test.alignReads.summary_analyzed_bamstats.tab
2025-03-03 23:09:50.655248 INFO::alignReads.R/alignReadsChunk: done
 done successfully.



Executing test function test.annotateVariants  ... Timing stopped at: 0.002 0 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= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-03 23:09:50.949049 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.genotype.2fa2d3196155d0/results/test_pe.coverage.RData
2025-03-03 23:09:50.950831 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.genotype.2fa2d3196155d0/results/test_pe.coverage.bw
2025-03-03 23:09:51.066623 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.genotype.2fa2d3196155d0/results/test_pe.summary_coverage.tab
2025-03-03 23:09:51.068388 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-03-03 23:10:01.192165 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-03-03 23:10:01.282205 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-03-03 23:10:01.299452 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-03-03 23:10:01.300971 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.genotype.2fa2d3196155d0/results/test_pe.raw_variants.RData
2025-03-03 23:10:01.303469 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.genotype.2fa2d3196155d0/results/test_pe.filtered_variants.RData
2025-03-03 23:10:01.30486 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-03-03 23:10:01.30602 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-03-03 23:10:01.70445 INFO::analyzeVariants.R/writeVCF: ...done
2025-03-03 23:10:01.705767 INFO::analyzeVariants.R/.callGenotypes: calling genotypes...
2025-03-03 23:10:57.711074 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-03-03 23:10:58.143962 INFO::analyzeVariants.R/writeVCF: ...done
2025-03-03 23:10:58.144836 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= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-03 23:10:58.578442 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-03-03 23:11:08.855519 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-03-03 23:11:08.951726 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-03-03 23:11:08.973 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-03-03 23:11:08.974799 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.wrap.callVariants.2fa2d348b89d9e/results/test_pe.raw_variants.RData
2025-03-03 23:11:08.977943 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.wrap.callVariants.2fa2d348b89d9e/results/test_pe.filtered_variants.RData
2025-03-03 23:11:08.979561 INFO::analyzeVariants.R/wrap.callVariants: ...done
 done successfully.



Executing test function test.wrap.callVariants.filters  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-03 23:11:09.207445 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-03-03 23:11:19.856365 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-03-03 23:11:19.914292 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-03-03 23:11:19.930825 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-03-03 23:11:19.932259 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.wrap.callVariants.filters.2fa2d3feb18a5/results/test_pe.raw_variants.RData
2025-03-03 23:11:19.934702 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.wrap.callVariants.filters.2fa2d3feb18a5/results/test_pe.filtered_variants.RData
2025-03-03 23:11:19.936212 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-03-03 23:11:19.937818 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-03-03 23:11:30.133379 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-03-03 23:11:30.186922 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-03-03 23:11:30.21031 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-03-03 23:11:30.212228 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.wrap.callVariants.filters.2fa2d3feb18a5/results/test_pe.raw_variants.RData
2025-03-03 23:11:30.215317 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.wrap.callVariants.filters.2fa2d3feb18a5/results/test_pe.filtered_variants.RData
2025-03-03 23:11:30.217606 INFO::analyzeVariants.R/wrap.callVariants: ...done
 done successfully.



Executing test function test.wrap.callVariants.which  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-03 23:11:32.977093 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-03-03 23:11:32.978643 INFO::analyzeVariants.R/buildTallyParam: restricting variant calls using 'which'
2025-03-03 23:11:35.608472 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-03-03 23:11:35.674412 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-03-03 23:11:35.688831 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-03-03 23:11:35.690033 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.wrap.callVariants.which.2fa2d313a6e275/results/test_pe.raw_variants.RData
2025-03-03 23:11:35.691946 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.wrap.callVariants.which.2fa2d313a6e275/results/test_pe.filtered_variants.RData
2025-03-03 23:11:35.693098 INFO::analyzeVariants.R/wrap.callVariants: ...done
 done successfully.



Executing test function test.writeVCF.NULL  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-03 23:11:35.818152 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-03-03 23:11:35.819244 INFO::analyzeVariants.R/writeVCF: ...done
 done successfully.



Executing test function test.writeVCF.vcfStat  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-03 23:11:35.987962 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-03-03 23:11:36.175519 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  ... 2025-03-03 23:12:26.926005 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/lonjcxhz/merged/results/bla.coverage.RData
2025-03-03 23:12:26.928507 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/lonjcxhz/merged/results/bla.coverage.bw
2025-03-03 23:12:27.007466 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/lonjcxhz/merged/results/bla.summary_coverage.tab
 done successfully.



Executing test function test.mergeCoverage.sparse  ... 2025-03-03 23:12:28.032745 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/vogmjuzw/merged/results/bla.coverage.RData
2025-03-03 23:12:28.034415 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/vogmjuzw/merged/results/bla.coverage.bw
2025-03-03 23:12:28.045224 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/vogmjuzw/merged/results/bla.summary_coverage.tab
 done successfully.



Executing test function test.checkConfig.analyzeVariants  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-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= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
 done successfully.



Executing test function test.checkConfig.alignReads  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-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= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-03 23:12:29.222328 INFO::detectRRNA.R/detectRRNA: searching for rRNA contamination...
2025-03-03 23:12:29.2234 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.detectRRNA.2fa2d34319fcc9/bams/rRNA_contam/input1.fastq
2025-03-03 23:12:29.226485 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 /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.detectRRNA.2fa2d34319fcc9/bams/rRNA_contam/test_se /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.detectRRNA.2fa2d34319fcc9/bams/rRNA_contam/input1.fastq 2>&1
2025-03-03 23:12:29.357875 INFO::detectRRNA.R/detectRRNA: contaminated fraction= 1
2025-03-03 23:12:29.358821 INFO::detectRRNA.R/detectRRNA: done
 done successfully.



Executing test function test.detectRRNA.paired_end  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-03 23:12:29.499247 INFO::detectRRNA.R/detectRRNA: searching for rRNA contamination...
2025-03-03 23:12:29.500119 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.detectRRNA.paired_end.2fa2d3e4c4a4d/bams/rRNA_contam/input1.fastq
2025-03-03 23:12:29.501464 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.detectRRNA.paired_end.2fa2d3e4c4a4d/bams/rRNA_contam/input2.fastq
2025-03-03 23:12:29.503469 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 /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.detectRRNA.paired_end.2fa2d3e4c4a4d/bams/rRNA_contam/test_pe /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.detectRRNA.paired_end.2fa2d3e4c4a4d/bams/rRNA_contam/input1.fastq -a paired /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.detectRRNA.paired_end.2fa2d3e4c4a4d/bams/rRNA_contam/input2.fastq 2>&1
2025-03-03 23:12:29.716933 INFO::detectRRNA.R/detectRRNA: contaminated fraction= 1
2025-03-03 23:12:29.71784 INFO::detectRRNA.R/detectRRNA: done
 done successfully.



Executing test function test.getRRNAIds  ... 2025-03-03 23:12:29.73598 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 /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test_get_rRNA_idslfruejim/test_pe /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test_get_rRNA_idslfruejim/1.fastq -a paired /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test_get_rRNA_idslfruejim/2.fastq 2>&1
 done successfully.



Executing test function test.getRRNAIds_random  ... 2025-03-03 23:12:29.968153 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 /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test_get_rRNAIds_randomsciwuvth/test_pe /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test_get_rRNAIds_randomsciwuvth/1.fastq 2>&1
 done successfully.



Executing test function test.filterByLength  ... 2025-03-03 23:12:30.163026 INFO::filterQuality.R/filterQuality: filterByLength...
2025-03-03 23:12:30.164344 INFO::filterQuality.R/filterByLength: fraction of filtered short reads= 0.5
2025-03-03 23:12:30.165144 INFO::filterQuality.R/filterByLength: done
2025-03-03 23:12:30.208961 INFO::filterQuality.R/filterQuality: filterByLength...
2025-03-03 23:12:30.209883 INFO::filterQuality.R/filterByLength: fraction of filtered short reads= 1
2025-03-03 23:12:30.210666 INFO::filterQuality.R/filterByLength: done
 done successfully.



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



Executing test function test.trimTailsByQuality  ... 2025-03-03 23:12:30.257461 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-03-03 23:12:30.265793 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-03-03 23:12:30.26678 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-03-03 23:12:30.271178 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-03-03 23:12:30.272082 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-03-03 23:12:30.27618 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-03-03 23:12:30.277072 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-03-03 23:12:30.281131 INFO::preprocessReads.R/preprocessReadsChunk: done
 done successfully.



Executing test function test.callVariantsGATK  ... Timing stopped at: 0.001 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= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-03 23:12:30.547496 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-03-03 23:12:30.549541 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-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= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-03 23:12:30.725542 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-03-03 23:12:30.831153 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-03-03 23:12:30.833813 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-03-03 23:12:30.835926 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-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= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-03 23:12:31.067464 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-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= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-03 23:12:31.20425 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-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= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-03 23:12:31.358634 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-03-03 23:12:31.426595 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-03-03 23:12:31.428917 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-03-03 23:12:31.430951 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-03 23:12:31.627438 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-03-03 23:12:31.673762 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-03-03 23:12:31.67616 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-03-03 23:12:31.678258 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-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= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
 done successfully.



Executing test function test.mergeLanes  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-03 23:12:32.406316 INFO::preprocessReads.R/preprocessReads: starting...
2025-03-03 23:12:32.41175 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-03-03 23:12:32.414921 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-03-03 23:12:32.417054 DEBUG::tools.R/processChunks: starting...
2025-03-03 23:12:35.346673 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-03 23:12:35.34805 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/chunks/chunk_000001/logs/progress.log
2025-03-03 23:12:37.953691 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.043 minutes
2025-03-03 23:12:37.955607 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/chunks/chunk_000002/logs/progress.log
2025-03-03 23:12:40.666132 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.045 minutes
2025-03-03 23:12:40.667603 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/chunks/chunk_000003/logs/progress.log
2025-03-03 23:12:43.367362 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.045 minutes
2025-03-03 23:12:43.407273 DEBUG::tools.R/processChunks: done
2025-03-03 23:12:43.410234 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-03-03 23:12:43.411966 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/results/test_pe.adapter_contaminated_1.RData
2025-03-03 23:12:43.414133 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-03-03 23:12:43.415679 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/results/test_pe.adapter_contaminated_2.RData
2025-03-03 23:12:43.423713 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
2025-03-03 23:12:43.425418 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/results/test_pe.summary_preprocess.tab
2025-03-03 23:12:43.427703 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/bams/processed.aligner_input_1.fastq ...
2025-03-03 23:12:43.431655 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/bams/processed.aligner_input_2.fastq ...
2025-03-03 23:12:43.43466 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/reports/shortReadReport_1 ...
2025-03-03 23:12:44.762424 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/reports/shortReadReport_2 ...
2025-03-03 23:12:45.7975 INFO::preprocessReads.R/preprocessReads: done
2025-03-03 23:12:45.878577 INFO::alignReads.R/alignReads: starting alignment...
2025-03-03 23:12:45.882928 DEBUG::tools.R/processChunks: starting...
2025-03-03 23:12:48.913809 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-03 23:12:48.915535 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/chunks/chunk_000001/logs/progress.log
2025-03-03 23:12:51.529179 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.044 minutes
2025-03-03 23:12:51.530964 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/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.
2025-03-03 23:12:54.121629 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.043 minutes
2025-03-03 23:12:54.123304 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/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.
2025-03-03 23:12:56.733695 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.043 minutes
2025-03-03 23:12:56.736053 DEBUG::tools.R/processChunks: done
2025-03-03 23:12:56.737463 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.
2025-03-03 23:12:56.916498 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-03-03 23:12:56.923331 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/results/test_pe.summary_alignment.tab
2025-03-03 23:12:56.929658 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/results/test_pe.summary_analyzed_bamstats.tab
2025-03-03 23:12:56.931284 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-03-03 23:12:57.181128 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/results/test_pe.summary_target_lengths.tab
2025-03-03 23:12:57.23826 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-03-03 23:12:57.23932 INFO::alignReads.R/alignReads: done
2025-03-03 23:12:57.363121 INFO::countGenomicFeatures.R/countGenomicFeatures: starting...
2025-03-03 23:12:57.385627 DEBUG::tools.R/processChunks: starting...
2025-03-03 23:13:00.856822 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-03 23:13:00.858688 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/chunks/chunk_000001/logs/progress.log
2025-03-03 23:13:03.32746 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.041 minutes
2025-03-03 23:13:03.330531 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/chunks/chunk_000002/logs/progress.log
2025-03-03 23:13:05.857026 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.042 minutes
2025-03-03 23:13:05.858543 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/chunks/chunk_000003/logs/progress.log
2025-03-03 23:13:08.328148 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.041 minutes
2025-03-03 23:13:08.332364 DEBUG::tools.R/processChunks: done
2025-03-03 23:13:08.334717 INFO::countGenomicFeatures.R/mergeCounts: starting...
2025-03-03 23:13:08.350234 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/results/test_pe.counts_exon.tab
2025-03-03 23:13:08.361621 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/results/test_pe.counts_exon_disjoint.tab
2025-03-03 23:13:08.368416 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/results/test_pe.counts_gene.tab
2025-03-03 23:13:08.37378 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/results/test_pe.counts_gene_coding.tab
2025-03-03 23:13:08.378995 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/results/test_pe.counts_gene_exonic.tab
2025-03-03 23:13:08.384147 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/results/test_pe.counts_intergenic.tab
2025-03-03 23:13:08.393152 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/results/test_pe.counts_intron.tab
2025-03-03 23:13:08.395704 INFO::countGenomicFeatures.R/mergeCounts: done
2025-03-03 23:13:08.401292 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/results/test_pe.summary_counts.tab
2025-03-03 23:13:08.402929 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2025-03-03 23:13:08.711012 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2025-03-03 23:13:08.711975 INFO::countGenomicFeatures.R/countGenomicFeatures: done...
2025-03-03 23:13:08.827658 INFO::coverage.R/calculateCoverage: starting...
2025-03-03 23:13:08.831881 DEBUG::tools.R/processChunks: starting...
2025-03-03 23:13:11.956124 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-03 23:13:11.958083 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/chunks/chunk_000001/logs/progress.log
2025-03-03 23:13:14.115796 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.036 minutes
2025-03-03 23:13:14.11737 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/chunks/chunk_000002/logs/progress.log
2025-03-03 23:13:16.280317 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.036 minutes
2025-03-03 23:13:16.281849 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/chunks/chunk_000003/logs/progress.log
2025-03-03 23:13:18.450968 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.036 minutes
2025-03-03 23:13:18.454293 DEBUG::tools.R/processChunks: done
2025-03-03 23:13:19.795122 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/results/test_pe.coverage.RData
2025-03-03 23:13:19.796562 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/results/test_pe.coverage.bw
2025-03-03 23:13:19.807498 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/results/test_pe.summary_coverage.tab
2025-03-03 23:13:19.808677 INFO::coverage.R/calculateCoverage: done
2025-03-03 23:13:19.81125 INFO::analyzeVariants/analyzeVariants: starting ...
2025-03-03 23:13:19.920076 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-03-03 23:13:22.817143 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-03-03 23:13:22.885122 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-03-03 23:13:22.9004 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-03-03 23:13:22.9017 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/results/test_pe.raw_variants.RData
2025-03-03 23:13:22.903192 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/results/test_pe.filtered_variants.RData
2025-03-03 23:13:22.904362 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-03-03 23:13:22.905288 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-03-03 23:13:23.11034 INFO::analyzeVariants.R/writeVCF: ...done
2025-03-03 23:13:23.203699 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/results/test_pe.summary_variants.tab
2025-03-03 23:13:23.205552 INFO::analyzeVariants/analyzeVariants: done
2025-03-03 23:13:23.208652 INFO::Pipeline run successful.
2025-03-03 23:13:23.370868 INFO::mergeLanes.R/doMergeLanes: starting...
2025-03-03 23:13:23.375556 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-03-03 23:13:23.377662 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/merged/results/merged.adapter_contaminated_1.RData
2025-03-03 23:13:23.380379 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-03-03 23:13:23.382231 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/merged/results/merged.adapter_contaminated_2.RData
2025-03-03 23:13:23.393711 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
2025-03-03 23:13:23.395989 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/merged/results/merged.summary_preprocess.tab
2025-03-03 23:13:23.398213 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.
2025-03-03 23:13:23.635613 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-03-03 23:13:23.642938 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/merged/results/merged.summary_alignment.tab
2025-03-03 23:13:23.650843 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/merged/results/merged.summary_analyzed_bamstats.tab
2025-03-03 23:13:23.652925 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-03-03 23:13:23.889634 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/merged/results/merged.summary_target_lengths.tab
2025-03-03 23:13:23.938855 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-03-03 23:13:23.983244 INFO::countGenomicFeatures.R/mergeCounts: starting...
2025-03-03 23:13:24.003082 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/merged/results/merged.counts_exon.tab
2025-03-03 23:13:24.014547 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/merged/results/merged.counts_exon_disjoint.tab
2025-03-03 23:13:24.020903 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/merged/results/merged.counts_gene.tab
2025-03-03 23:13:24.026066 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/merged/results/merged.counts_gene_coding.tab
2025-03-03 23:13:24.031213 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/merged/results/merged.counts_gene_exonic.tab
2025-03-03 23:13:24.036708 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/merged/results/merged.counts_intergenic.tab
2025-03-03 23:13:24.048127 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/merged/results/merged.counts_intron.tab
2025-03-03 23:13:24.050761 INFO::countGenomicFeatures.R/mergeCounts: done
2025-03-03 23:13:24.056773 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/merged/results/merged.summary_counts.tab
2025-03-03 23:13:24.058547 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2025-03-03 23:13:24.293148 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2025-03-03 23:13:26.22598 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/merged/results/merged.coverage.RData
2025-03-03 23:13:26.228556 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/merged/results/merged.coverage.bw
2025-03-03 23:13:26.239657 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/merged/results/merged.summary_coverage.tab
2025-03-03 23:13:26.283201 INFO::analyzeVariants/analyzeVariants: starting ...
2025-03-03 23:13:26.385376 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-03-03 23:13:30.284882 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-03-03 23:13:30.456724 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-03-03 23:13:30.500775 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-03-03 23:13:30.503991 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/merged/results/merged.raw_variants.RData
2025-03-03 23:13:30.508118 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/merged/results/merged.filtered_variants.RData
2025-03-03 23:13:30.511172 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-03-03 23:13:30.513149 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-03-03 23:13:30.991229 INFO::analyzeVariants.R/writeVCF: ...done
2025-03-03 23:13:31.266929 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.mergeLanes.2fa2d3665ee249/merged/results/merged.summary_variants.tab
2025-03-03 23:13:31.272378 INFO::analyzeVariants/analyzeVariants: done
2025-03-03 23:13:31.283571 INFO::mergeLanes.R/doMergeLanes: merge lanes successful.
 done successfully.



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



Executing test function test.preprocessReads  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-03 23:13:32.631681 INFO::preprocessReads.R/preprocessReads: starting...
2025-03-03 23:13:32.687283 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-03-03 23:13:32.712934 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-03-03 23:13:32.71707 DEBUG::tools.R/processChunks: starting...
2025-03-03 23:13:39.170542 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-03 23:13:39.173966 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.preprocessReads.2fa2d354deb1d0/chunks/chunk_000001/logs/progress.log
2025-03-03 23:13:42.746819 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.06 minutes
2025-03-03 23:13:42.949549 DEBUG::tools.R/processChunks: done
2025-03-03 23:13:42.961407 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-03-03 23:13:42.968171 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.preprocessReads.2fa2d354deb1d0/results/test_pe.adapter_contaminated_1.RData
2025-03-03 23:13:42.971808 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-03-03 23:13:42.982177 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.preprocessReads.2fa2d354deb1d0/results/test_pe.adapter_contaminated_2.RData
2025-03-03 23:13:43.013496 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
2025-03-03 23:13:43.024858 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.preprocessReads.2fa2d354deb1d0/results/test_pe.summary_preprocess.tab
2025-03-03 23:13:43.033484 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.preprocessReads.2fa2d354deb1d0/bams/processed.aligner_input_1.fastq ...
2025-03-03 23:13:43.049733 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.preprocessReads.2fa2d354deb1d0/bams/processed.aligner_input_2.fastq ...
2025-03-03 23:13:43.067863 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.preprocessReads.2fa2d354deb1d0/reports/shortReadReport_1 ...
2025-03-03 23:13:47.231679 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.preprocessReads.2fa2d354deb1d0/reports/shortReadReport_2 ...
2025-03-03 23:13:49.844179 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



Executing test function test.preprocessReads.minichunks  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-03 23:13:50.440851 INFO::preprocessReads.R/preprocessReads: starting...
2025-03-03 23:13:50.450817 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-03-03 23:13:50.456953 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-03-03 23:13:50.460804 DEBUG::tools.R/processChunks: starting...
2025-03-03 23:13:54.138043 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-03 23:13:54.139675 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.preprocessReads.minichunks.2fa2d339ee2d73/chunks/chunk_000001/logs/progress.log
2025-03-03 23:13:57.364951 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.054 minutes
2025-03-03 23:13:57.367593 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.preprocessReads.minichunks.2fa2d339ee2d73/chunks/chunk_000002/logs/progress.log
2025-03-03 23:14:00.720922 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.056 minutes
2025-03-03 23:14:00.72396 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.preprocessReads.minichunks.2fa2d339ee2d73/chunks/chunk_000003/logs/progress.log
2025-03-03 23:14:03.948106 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.054 minutes
2025-03-03 23:14:04.027864 DEBUG::tools.R/processChunks: done
2025-03-03 23:14:04.033091 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-03-03 23:14:04.036275 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.preprocessReads.minichunks.2fa2d339ee2d73/results/test_pe.adapter_contaminated_1.RData
2025-03-03 23:14:04.040325 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-03-03 23:14:04.043426 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.preprocessReads.minichunks.2fa2d339ee2d73/results/test_pe.adapter_contaminated_2.RData
2025-03-03 23:14:04.059654 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
2025-03-03 23:14:04.063327 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.preprocessReads.minichunks.2fa2d339ee2d73/results/test_pe.summary_preprocess.tab
2025-03-03 23:14:04.068472 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.preprocessReads.minichunks.2fa2d339ee2d73/bams/processed.aligner_input_1.fastq ...
2025-03-03 23:14:04.07775 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.preprocessReads.minichunks.2fa2d339ee2d73/bams/processed.aligner_input_2.fastq ...
2025-03-03 23:14:04.084732 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.preprocessReads.minichunks.2fa2d339ee2d73/reports/shortReadReport_1 ...
2025-03-03 23:14:06.885427 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.preprocessReads.minichunks.2fa2d339ee2d73/reports/shortReadReport_2 ...
2025-03-03 23:14:09.15837 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



Executing test function test.preprocessReads_single_end  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-03 23:14:09.733225 INFO::preprocessReads.R/preprocessReads: starting...
2025-03-03 23:14:09.766035 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-03-03 23:14:09.771187 DEBUG::tools.R/processChunks: starting...
2025-03-03 23:14:14.240806 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-03 23:14:14.242436 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.preprocessReads_single_end.2fa2d34a956e7b/chunks/chunk_000001/logs/progress.log
2025-03-03 23:14:16.957954 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.045 minutes
2025-03-03 23:14:16.978158 DEBUG::tools.R/processChunks: done
2025-03-03 23:14:16.982186 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-03-03 23:14:16.985154 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.preprocessReads_single_end.2fa2d34a956e7b/results/test_se.adapter_contaminated_1.RData
2025-03-03 23:14:16.999409 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
2025-03-03 23:14:17.002974 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.preprocessReads_single_end.2fa2d34a956e7b/results/test_se.summary_preprocess.tab
2025-03-03 23:14:17.006635 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.preprocessReads_single_end.2fa2d34a956e7b/bams/processed.aligner_input_1.fastq ...
2025-03-03 23:14:17.012675 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpdjkCSv/test.preprocessReads_single_end.2fa2d34a956e7b/reports/shortReadReport_1 ...
2025-03-03 23:14:18.519262 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-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-03 23:14:19.322607 INFO::preprocessReads.R/preprocessReads: starting...
2025-03-03 23:14:19.345973 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/extdata/H1993_TP53_subset2500_1.fastq.gz
2025-03-03 23:14:19.366335 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/extdata/H1993_TP53_subset2500_2.fastq.gz
2025-03-03 23:14:19.36938 DEBUG::tools.R/processChunks: starting...
2025-03-03 23:14:23.198113 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-03 23:14:23.19953 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= test/chunks/chunk_000001/logs/progress.log
2025-03-03 23:14:26.307136 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.052 minutes
2025-03-03 23:14:26.367464 DEBUG::tools.R/processChunks: done
2025-03-03 23:14:26.370877 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-03-03 23:14:26.372639 INFO::io.R/saveWithID: saving file= test/results/test.adapter_contaminated_1.RData
2025-03-03 23:14:26.374319 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-03-03 23:14:26.375697 INFO::io.R/saveWithID: saving file= test/results/test.adapter_contaminated_2.RData
2025-03-03 23:14:26.382019 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
2025-03-03 23:14:26.383799 INFO::io.R/saveWithID: saving file= test/results/test.summary_preprocess.tab
2025-03-03 23:14:26.385726 INFO::preprocessReads.R/mergePreprocessedReads: merging file= test/bams/processed.aligner_input_1.fastq ...
2025-03-03 23:14:26.389866 INFO::preprocessReads.R/mergePreprocessedReads: merging file= test/bams/processed.aligner_input_2.fastq ...
2025-03-03 23:14:26.393445 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= test/reports/shortReadReport_1 ...
2025-03-03 23:15:19.320275 DEBUG::tools.R/traceMem: wired.mem=-80.658338 GiB
2025-03-03 23:16:19.388118 DEBUG::tools.R/traceMem: wired.mem=-75.314958 GiB
2025-03-03 23:17:19.453882 DEBUG::tools.R/traceMem: wired.mem=-74.277695 GiB
2025-03-03 23:18:19.521734 DEBUG::tools.R/traceMem: wired.mem=-70.243570 GiB
2025-03-03 23:19:19.587707 DEBUG::tools.R/traceMem: wired.mem=-71.360303 GiB
2025-03-03 23:20:19.656114 DEBUG::tools.R/traceMem: wired.mem=-66.674905 GiB
2025-03-03 23:21:19.721296 DEBUG::tools.R/traceMem: wired.mem=-68.760170 GiB
2025-03-03 23:22:19.787505 DEBUG::tools.R/traceMem: wired.mem=-70.895170 GiB
2025-03-03 23:23:19.853274 DEBUG::tools.R/traceMem: wired.mem=-65.883886 GiB
2025-03-03 23:24:19.919861 DEBUG::tools.R/traceMem: wired.mem=-74.412028 GiB
2025-03-03 23:25:19.984174 DEBUG::tools.R/traceMem: wired.mem=-71.075287 GiB
2025-03-03 23:26:20.048009 DEBUG::tools.R/traceMem: wired.mem=-71.402328 GiB
2025-03-03 23:27:20.112597 DEBUG::tools.R/traceMem: wired.mem=-77.770093 GiB
2025-03-03 23:28:20.17807 DEBUG::tools.R/traceMem: wired.mem=-71.775326 GiB
2025-03-03 23:29:20.243729 DEBUG::tools.R/traceMem: wired.mem=-64.488755 GiB
2025-03-03 23:30:20.308679 DEBUG::tools.R/traceMem: wired.mem=-64.413086 GiB
2025-03-03 23:31:20.375051 DEBUG::tools.R/traceMem: wired.mem=-76.589249 GiB
2025-03-03 23:32:20.442007 DEBUG::tools.R/traceMem: wired.mem=-69.483696 GiB
2025-03-03 23:33:20.508084 DEBUG::tools.R/traceMem: wired.mem=-72.007479 GiB
2025-03-03 23:34:20.574426 DEBUG::tools.R/traceMem: wired.mem=-82.562806 GiB
2025-03-03 23:35:20.640415 DEBUG::tools.R/traceMem: wired.mem=-75.999130 GiB
2025-03-03 23:36:20.707292 DEBUG::tools.R/traceMem: wired.mem=-63.538721 GiB
2025-03-03 23:37:20.773518 DEBUG::tools.R/traceMem: wired.mem=-74.058699 GiB
2025-03-03 23:38:20.84015 DEBUG::tools.R/traceMem: wired.mem=-83.867267 GiB
2025-03-03 23:39:20.904997 DEBUG::tools.R/traceMem: wired.mem=-71.775654 GiB
2025-03-03 23:40:20.970304 DEBUG::tools.R/traceMem: wired.mem=-65.175671 GiB
2025-03-03 23:41:21.035364 DEBUG::tools.R/traceMem: wired.mem=-69.554590 GiB
2025-03-03 23:42:21.102474 DEBUG::tools.R/traceMem: wired.mem=-70.578622 GiB
2025-03-03 23:43:21.11608 DEBUG::tools.R/traceMem: wired.mem=-76.117832 GiB

Example timings

HTSeqGenie.Rcheck/HTSeqGenie-Ex.timings

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