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"	4753
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4501
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4524
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4476
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4407
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: 2025-02-03 23:15:15 -0500 (Mon, 03 Feb 2025)

EndedAt: 2025-02-03 23:55:16 -0500 (Mon, 03 Feb 2025)

EllapsedTime: 2400.9 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 24.04.1 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/RtmpauYpVT/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-02-03 23:21:00.025629 INFO::preprocessReads.R/preprocessReads: starting...
2025-02-03 23:21:00.034459 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
2025-02-03 23:21:00.038241 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
2025-02-03 23:21:00.040534 DEBUG::tools.R/processChunks: starting...
2025-02-03 23:21:03.015294 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-02-03 23:21:03.016671 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.alignReads.25a83171197b9b/chunks/chunk_000001/logs/progress.log
2025-02-03 23:21:05.751517 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.046 minutes
2025-02-03 23:21:05.75326 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.alignReads.25a83171197b9b/chunks/chunk_000002/logs/progress.log
2025-02-03 23:21:08.511561 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.046 minutes
2025-02-03 23:21:08.51308 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.alignReads.25a83171197b9b/chunks/chunk_000003/logs/progress.log
2025-02-03 23:21:11.28059 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.046 minutes
2025-02-03 23:21:11.312249 DEBUG::tools.R/processChunks: done
2025-02-03 23:21:11.316205 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-02-03 23:21:11.318514 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.alignReads.25a83171197b9b/results/test_pe.adapter_contaminated_1.RData
2025-02-03 23:21:11.321456 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-02-03 23:21:11.323413 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.alignReads.25a83171197b9b/results/test_pe.adapter_contaminated_2.RData
2025-02-03 23:21:11.334001 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
2025-02-03 23:21:11.336239 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.alignReads.25a83171197b9b/results/test_pe.summary_preprocess.tab
2025-02-03 23:21:11.339504 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.alignReads.25a83171197b9b/bams/processed.aligner_input_1.fastq ...
2025-02-03 23:21:11.343299 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.alignReads.25a83171197b9b/bams/processed.aligner_input_2.fastq ...
2025-02-03 23:21:11.346662 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.alignReads.25a83171197b9b/reports/shortReadReport_1 ...
2025-02-03 23:21:12.8338 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.alignReads.25a83171197b9b/reports/shortReadReport_2 ...
2025-02-03 23:21:13.987462 INFO::preprocessReads.R/preprocessReads: done
2025-02-03 23:21:14.073976 INFO::alignReads.R/alignReads: starting alignment...
2025-02-03 23:21:14.079959 DEBUG::tools.R/processChunks: starting...
2025-02-03 23:21:17.043464 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-02-03 23:21:17.044993 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.alignReads.25a83171197b9b/chunks/chunk_000001/logs/progress.log
2025-02-03 23:21:19.931471 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.048 minutes
2025-02-03 23:21:19.933204 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.alignReads.25a83171197b9b/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.
2025-02-03 23:21:22.580407 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.044 minutes
2025-02-03 23:21:22.582063 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.alignReads.25a83171197b9b/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.
2025-02-03 23:21:25.217903 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.044 minutes
2025-02-03 23:21:25.220229 DEBUG::tools.R/processChunks: done
2025-02-03 23:21:25.221608 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.
2025-02-03 23:21:25.434071 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-02-03 23:21:25.442569 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.alignReads.25a83171197b9b/results/test_pe.summary_alignment.tab
2025-02-03 23:21:25.449734 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.alignReads.25a83171197b9b/results/test_pe.summary_analyzed_bamstats.tab
2025-02-03 23:21:25.45139 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-02-03 23:21:25.689821 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.alignReads.25a83171197b9b/results/test_pe.summary_target_lengths.tab
2025-02-03 23:21:25.735755 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-02-03 23:21:25.736833 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/RtmpauYpVT/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-02-03 23:21:26.026019 INFO::preprocessReads.R/preprocessReads: starting...
2025-02-03 23:21:26.030002 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
2025-02-03 23:21:26.121683 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 2 , totnbreads= 26 )
2025-02-03 23:21:26.127485 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
2025-02-03 23:21:26.130764 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
2025-02-03 23:21:26.132985 DEBUG::tools.R/processChunks: starting...
2025-02-03 23:21:29.595313 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-02-03 23:21:29.596832 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.alignReads.sparsechunks.25a8314118edc6/chunks/chunk_000001/logs/progress.log
2025-02-03 23:21:32.330913 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.046 minutes
2025-02-03 23:21:32.332439 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.alignReads.sparsechunks.25a8314118edc6/chunks/chunk_000002/logs/progress.log
2025-02-03 23:21:35.078768 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.046 minutes
2025-02-03 23:21:35.080253 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.alignReads.sparsechunks.25a8314118edc6/chunks/chunk_000003/logs/progress.log
2025-02-03 23:21:37.866498 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.046 minutes
2025-02-03 23:21:37.868025 DEBUG::tools.R/processChunks: starting chunkid= 4 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.alignReads.sparsechunks.25a8314118edc6/chunks/chunk_000004/logs/progress.log
2025-02-03 23:21:40.550937 DEBUG::tools.R/processChunks: done with chunkid= 4 ; elapsed.time= 0.045 minutes
2025-02-03 23:21:40.581051 DEBUG::tools.R/processChunks: done
2025-02-03 23:21:40.585468 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-02-03 23:21:40.587862 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.alignReads.sparsechunks.25a8314118edc6/results/test_pe.adapter_contaminated_1.RData
2025-02-03 23:21:40.590973 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-02-03 23:21:40.592604 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.alignReads.sparsechunks.25a8314118edc6/results/test_pe.adapter_contaminated_2.RData
2025-02-03 23:21:40.602803 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
2025-02-03 23:21:40.605016 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.alignReads.sparsechunks.25a8314118edc6/results/test_pe.summary_preprocess.tab
2025-02-03 23:21:40.608611 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.alignReads.sparsechunks.25a8314118edc6/bams/processed.aligner_input_1.fastq ...
2025-02-03 23:21:40.614015 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.alignReads.sparsechunks.25a8314118edc6/bams/processed.aligner_input_2.fastq ...
2025-02-03 23:21:40.618308 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.alignReads.sparsechunks.25a8314118edc6/reports/shortReadReport_1 ...
2025-02-03 23:21:41.973817 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.alignReads.sparsechunks.25a8314118edc6/reports/shortReadReport_2 ...
2025-02-03 23:21:43.062967 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/RtmpauYpVT/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-02-03 23:21:43.242407 INFO::alignReads.R/alignReadsChunk: running gsnap...
2025-02-03 23:21:43.246893 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/RtmpauYpVT/test.alignReadsOneSingleEnd.25a8315d834a5e/bams/test.alignReads /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq 2>&1
2025-02-03 23:21:43.487306 INFO::alignReads.R/createSummaryAlignment: counting unique bam reads...
2025-02-03 23:21:43.582221 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.alignReadsOneSingleEnd.25a8315d834a5e/results/test.alignReads.summary_alignment.tab
2025-02-03 23:21:43.627726 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.alignReadsOneSingleEnd.25a8315d834a5e/results/test.alignReads.summary_analyzed_bamstats.tab
2025-02-03 23:21:43.629349 INFO::alignReads.R/alignReadsChunk: done
 done successfully.



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



Executing test function test.callVariantsVariantTools.genotype  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-02-03 23:21:43.93124 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.genotype.25a8313789486e/results/test_pe.coverage.RData
2025-02-03 23:21:43.933111 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.genotype.25a8313789486e/results/test_pe.coverage.bw
2025-02-03 23:21:44.048988 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.genotype.25a8313789486e/results/test_pe.summary_coverage.tab
2025-02-03 23:21:44.050659 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-02-03 23:21:55.16163 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-02-03 23:21:55.276201 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-02-03 23:21:55.29924 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-02-03 23:21:55.301051 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.genotype.25a8313789486e/results/test_pe.raw_variants.RData
2025-02-03 23:21:55.303848 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.genotype.25a8313789486e/results/test_pe.filtered_variants.RData
2025-02-03 23:21:55.305454 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-02-03 23:21:55.306846 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-02-03 23:21:55.802429 INFO::analyzeVariants.R/writeVCF: ...done
2025-02-03 23:21:55.803767 INFO::analyzeVariants.R/.callGenotypes: calling genotypes...
2025-02-03 23:22:56.168029 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-02-03 23:22:56.636922 INFO::analyzeVariants.R/writeVCF: ...done
2025-02-03 23:22:56.637917 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/RtmpauYpVT/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-02-03 23:22:57.089169 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-02-03 23:23:07.635354 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-02-03 23:23:07.71488 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-02-03 23:23:07.731847 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-02-03 23:23:07.733138 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.wrap.callVariants.25a831652d6f03/results/test_pe.raw_variants.RData
2025-02-03 23:23:07.735515 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.wrap.callVariants.25a831652d6f03/results/test_pe.filtered_variants.RData
2025-02-03 23:23:07.736872 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/RtmpauYpVT/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-02-03 23:23:07.874184 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-02-03 23:23:18.103986 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-02-03 23:23:18.167125 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-02-03 23:23:18.184274 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-02-03 23:23:18.185668 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.wrap.callVariants.filters.25a831edef230/results/test_pe.raw_variants.RData
2025-02-03 23:23:18.18815 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.wrap.callVariants.filters.25a831edef230/results/test_pe.filtered_variants.RData
2025-02-03 23:23:18.189456 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-02-03 23:23:18.191092 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-02-03 23:23:28.162107 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-02-03 23:23:28.200816 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-02-03 23:23:28.218086 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-02-03 23:23:28.219482 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.wrap.callVariants.filters.25a831edef230/results/test_pe.raw_variants.RData
2025-02-03 23:23:28.222092 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.wrap.callVariants.filters.25a831edef230/results/test_pe.filtered_variants.RData
2025-02-03 23:23:28.224113 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/RtmpauYpVT/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-02-03 23:23:28.462957 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-02-03 23:23:28.464323 INFO::analyzeVariants.R/buildTallyParam: restricting variant calls using 'which'
2025-02-03 23:23:31.075375 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-02-03 23:23:31.142855 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-02-03 23:23:31.15784 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-02-03 23:23:31.159078 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.wrap.callVariants.which.25a831a5d6df4/results/test_pe.raw_variants.RData
2025-02-03 23:23:31.160592 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.wrap.callVariants.which.25a831a5d6df4/results/test_pe.filtered_variants.RData
2025-02-03 23:23:31.161762 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/RtmpauYpVT/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-02-03 23:23:31.288156 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-02-03 23:23:31.289354 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/RtmpauYpVT/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-02-03 23:23:32.671834 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-02-03 23:23:32.854917 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  ... 2025-02-03 23:24:23.932654 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/mrpylcze/merged/results/bla.coverage.RData
2025-02-03 23:24:23.935649 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/mrpylcze/merged/results/bla.coverage.bw
2025-02-03 23:24:24.017523 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/mrpylcze/merged/results/bla.summary_coverage.tab
 done successfully.



Executing test function test.mergeCoverage.sparse  ... 2025-02-03 23:24:25.113778 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/dhpxcnsb/merged/results/bla.coverage.RData
2025-02-03 23:24:25.115255 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/dhpxcnsb/merged/results/bla.coverage.bw
2025-02-03 23:24:25.126237 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/dhpxcnsb/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/RtmpauYpVT/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/RtmpauYpVT/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/RtmpauYpVT/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/RtmpauYpVT/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/RtmpauYpVT/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/RtmpauYpVT/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/RtmpauYpVT/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/RtmpauYpVT/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/RtmpauYpVT/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/RtmpauYpVT/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-02-03 23:24:26.277804 INFO::detectRRNA.R/detectRRNA: searching for rRNA contamination...
2025-02-03 23:24:26.278945 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.detectRRNA.25a83179fe2635/bams/rRNA_contam/input1.fastq
2025-02-03 23:24:26.2821 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/RtmpauYpVT/test.detectRRNA.25a83179fe2635/bams/rRNA_contam/test_se /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.detectRRNA.25a83179fe2635/bams/rRNA_contam/input1.fastq 2>&1
2025-02-03 23:24:26.419123 INFO::detectRRNA.R/detectRRNA: contaminated fraction= 1
2025-02-03 23:24:26.420081 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/RtmpauYpVT/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-02-03 23:24:26.534783 INFO::detectRRNA.R/detectRRNA: searching for rRNA contamination...
2025-02-03 23:24:26.535721 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.detectRRNA.paired_end.25a8317bd5bef5/bams/rRNA_contam/input1.fastq
2025-02-03 23:24:26.537134 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.detectRRNA.paired_end.25a8317bd5bef5/bams/rRNA_contam/input2.fastq
2025-02-03 23:24:26.539189 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/RtmpauYpVT/test.detectRRNA.paired_end.25a8317bd5bef5/bams/rRNA_contam/test_pe /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.detectRRNA.paired_end.25a8317bd5bef5/bams/rRNA_contam/input1.fastq -a paired /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.detectRRNA.paired_end.25a8317bd5bef5/bams/rRNA_contam/input2.fastq 2>&1
2025-02-03 23:24:26.762185 INFO::detectRRNA.R/detectRRNA: contaminated fraction= 1
2025-02-03 23:24:26.763156 INFO::detectRRNA.R/detectRRNA: done
 done successfully.



Executing test function test.getRRNAIds  ... 2025-02-03 23:24:26.781363 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/RtmpauYpVT/test_get_rRNA_idscvhmfkiq/test_pe /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test_get_rRNA_idscvhmfkiq/1.fastq -a paired /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test_get_rRNA_idscvhmfkiq/2.fastq 2>&1
 done successfully.



Executing test function test.getRRNAIds_random  ... 2025-02-03 23:24:27.05516 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/RtmpauYpVT/test_get_rRNAIds_randomhydpiwje/test_pe /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test_get_rRNAIds_randomhydpiwje/1.fastq 2>&1
 done successfully.



Executing test function test.filterByLength  ... 2025-02-03 23:24:27.268662 INFO::filterQuality.R/filterQuality: filterByLength...
2025-02-03 23:24:27.270128 INFO::filterQuality.R/filterByLength: fraction of filtered short reads= 0.5
2025-02-03 23:24:27.271006 INFO::filterQuality.R/filterByLength: done
2025-02-03 23:24:27.317262 INFO::filterQuality.R/filterQuality: filterByLength...
2025-02-03 23:24:27.318179 INFO::filterQuality.R/filterByLength: fraction of filtered short reads= 1
2025-02-03 23:24:27.318964 INFO::filterQuality.R/filterByLength: done
 done successfully.



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



Executing test function test.trimTailsByQuality  ... 2025-02-03 23:24:27.366384 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-02-03 23:24:27.375618 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-02-03 23:24:27.376861 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-02-03 23:24:27.381433 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-02-03 23:24:27.382428 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-02-03 23:24:27.386774 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-02-03 23:24:27.387708 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-02-03 23:24:27.392018 INFO::preprocessReads.R/preprocessReadsChunk: done
 done successfully.



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



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



Executing test function test.checkGATKJar  ... Timing stopped at: 0 0 0.001
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/RtmpauYpVT/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-02-03 23:24:27.646203 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
2025-02-03 23:24:27.648281 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/RtmpauYpVT/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-02-03 23:24:27.82214 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
2025-02-03 23:24:27.892653 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-02-03 23:24:27.895384 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
2025-02-03 23:24:27.897466 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/RtmpauYpVT/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-02-03 23:24:28.094484 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/RtmpauYpVT/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-02-03 23:24:28.234622 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/RtmpauYpVT/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-02-03 23:24:28.368839 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
2025-02-03 23:24:28.41826 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-02-03 23:24:28.420771 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
2025-02-03 23:24:28.423041 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/RtmpauYpVT/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-02-03 23:24:28.605731 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
2025-02-03 23:24:28.650744 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-02-03 23:24:28.653123 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
2025-02-03 23:24:28.655233 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/RtmpauYpVT/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/RtmpauYpVT/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-02-03 23:24:29.290224 INFO::preprocessReads.R/preprocessReads: starting...
2025-02-03 23:24:29.295948 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
2025-02-03 23:24:29.299105 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
2025-02-03 23:24:29.301238 DEBUG::tools.R/processChunks: starting...
2025-02-03 23:24:32.189218 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-02-03 23:24:32.190632 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/chunks/chunk_000001/logs/progress.log
2025-02-03 23:24:34.788599 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.043 minutes
2025-02-03 23:24:34.790136 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/chunks/chunk_000002/logs/progress.log
2025-02-03 23:24:37.37516 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.043 minutes
2025-02-03 23:24:37.376622 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/chunks/chunk_000003/logs/progress.log
2025-02-03 23:24:40.014363 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.044 minutes
2025-02-03 23:24:40.063823 DEBUG::tools.R/processChunks: done
2025-02-03 23:24:40.066677 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-02-03 23:24:40.068312 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/results/test_pe.adapter_contaminated_1.RData
2025-02-03 23:24:40.070358 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-02-03 23:24:40.071769 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/results/test_pe.adapter_contaminated_2.RData
2025-02-03 23:24:40.080425 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
2025-02-03 23:24:40.082299 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/results/test_pe.summary_preprocess.tab
2025-02-03 23:24:40.084887 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/bams/processed.aligner_input_1.fastq ...
2025-02-03 23:24:40.089417 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/bams/processed.aligner_input_2.fastq ...
2025-02-03 23:24:40.093861 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/reports/shortReadReport_1 ...
2025-02-03 23:24:41.418732 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/reports/shortReadReport_2 ...
2025-02-03 23:24:42.462473 INFO::preprocessReads.R/preprocessReads: done
2025-02-03 23:24:42.54312 INFO::alignReads.R/alignReads: starting alignment...
2025-02-03 23:24:42.546991 DEBUG::tools.R/processChunks: starting...
2025-02-03 23:24:45.332676 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-02-03 23:24:45.334371 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/chunks/chunk_000001/logs/progress.log
2025-02-03 23:24:47.918748 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.043 minutes
2025-02-03 23:24:47.920383 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/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.
2025-02-03 23:24:50.513593 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.043 minutes
2025-02-03 23:24:50.515244 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/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.
2025-02-03 23:24:53.103208 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.043 minutes
2025-02-03 23:24:53.105812 DEBUG::tools.R/processChunks: done
2025-02-03 23:24:53.107386 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.
2025-02-03 23:24:53.300959 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-02-03 23:24:53.308352 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/results/test_pe.summary_alignment.tab
2025-02-03 23:24:53.314926 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/results/test_pe.summary_analyzed_bamstats.tab
2025-02-03 23:24:53.316691 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-02-03 23:24:53.53531 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/results/test_pe.summary_target_lengths.tab
2025-02-03 23:24:53.581149 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-02-03 23:24:53.582247 INFO::alignReads.R/alignReads: done
2025-02-03 23:24:53.684973 INFO::countGenomicFeatures.R/countGenomicFeatures: starting...
2025-02-03 23:24:53.706608 DEBUG::tools.R/processChunks: starting...
2025-02-03 23:24:56.903642 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-02-03 23:24:56.905671 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/chunks/chunk_000001/logs/progress.log
2025-02-03 23:24:59.39678 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.041 minutes
2025-02-03 23:24:59.398395 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/chunks/chunk_000002/logs/progress.log
2025-02-03 23:25:01.866205 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.041 minutes
2025-02-03 23:25:01.868033 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/chunks/chunk_000003/logs/progress.log
2025-02-03 23:25:04.332785 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.041 minutes
2025-02-03 23:25:04.335312 DEBUG::tools.R/processChunks: done
2025-02-03 23:25:04.336992 INFO::countGenomicFeatures.R/mergeCounts: starting...
2025-02-03 23:25:04.35082 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/results/test_pe.counts_exon.tab
2025-02-03 23:25:04.361616 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/results/test_pe.counts_exon_disjoint.tab
2025-02-03 23:25:04.368372 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/results/test_pe.counts_gene.tab
2025-02-03 23:25:04.373597 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/results/test_pe.counts_gene_coding.tab
2025-02-03 23:25:04.378978 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/results/test_pe.counts_gene_exonic.tab
2025-02-03 23:25:04.384455 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/results/test_pe.counts_intergenic.tab
2025-02-03 23:25:04.394191 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/results/test_pe.counts_intron.tab
2025-02-03 23:25:04.396944 INFO::countGenomicFeatures.R/mergeCounts: done
2025-02-03 23:25:04.402673 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/results/test_pe.summary_counts.tab
2025-02-03 23:25:04.404397 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2025-02-03 23:25:04.709734 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2025-02-03 23:25:04.71078 INFO::countGenomicFeatures.R/countGenomicFeatures: done...
2025-02-03 23:25:04.830339 INFO::coverage.R/calculateCoverage: starting...
2025-02-03 23:25:04.835013 DEBUG::tools.R/processChunks: starting...
2025-02-03 23:25:08.180143 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-02-03 23:25:08.182007 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/chunks/chunk_000001/logs/progress.log
2025-02-03 23:25:10.536706 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.039 minutes
2025-02-03 23:25:10.539551 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/chunks/chunk_000002/logs/progress.log
2025-02-03 23:25:13.089922 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.042 minutes
2025-02-03 23:25:13.097623 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/chunks/chunk_000003/logs/progress.log
2025-02-03 23:25:15.871572 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.046 minutes
2025-02-03 23:25:15.879493 DEBUG::tools.R/processChunks: done
2025-02-03 23:25:20.245743 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/results/test_pe.coverage.RData
2025-02-03 23:25:20.252038 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/results/test_pe.coverage.bw
2025-02-03 23:25:20.278643 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/results/test_pe.summary_coverage.tab
2025-02-03 23:25:20.281393 INFO::coverage.R/calculateCoverage: done
2025-02-03 23:25:20.284613 INFO::analyzeVariants/analyzeVariants: starting ...
2025-02-03 23:25:20.678022 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-02-03 23:25:29.252045 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-02-03 23:25:29.621278 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-02-03 23:25:29.6565 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-02-03 23:25:29.659187 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/results/test_pe.raw_variants.RData
2025-02-03 23:25:29.662374 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/results/test_pe.filtered_variants.RData
2025-02-03 23:25:29.66485 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-02-03 23:25:29.666602 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-02-03 23:25:30.446 INFO::analyzeVariants.R/writeVCF: ...done
2025-02-03 23:25:30.683611 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/results/test_pe.summary_variants.tab
2025-02-03 23:25:30.688186 INFO::analyzeVariants/analyzeVariants: done
2025-02-03 23:25:30.703301 INFO::Pipeline run successful.
2025-02-03 23:25:31.2757 INFO::mergeLanes.R/doMergeLanes: starting...
2025-02-03 23:25:31.287665 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-02-03 23:25:31.293247 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/merged/results/merged.adapter_contaminated_1.RData
2025-02-03 23:25:31.300042 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-02-03 23:25:31.30502 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/merged/results/merged.adapter_contaminated_2.RData
2025-02-03 23:25:31.332399 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
2025-02-03 23:25:31.338363 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/merged/results/merged.summary_preprocess.tab
2025-02-03 23:25:31.343842 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.
2025-02-03 23:25:31.896131 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-02-03 23:25:31.909847 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/merged/results/merged.summary_alignment.tab
2025-02-03 23:25:31.925205 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/merged/results/merged.summary_analyzed_bamstats.tab
2025-02-03 23:25:31.929299 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-02-03 23:25:32.33115 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/merged/results/merged.summary_target_lengths.tab
2025-02-03 23:25:32.424347 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-02-03 23:25:32.547089 INFO::countGenomicFeatures.R/mergeCounts: starting...
2025-02-03 23:25:32.580099 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/merged/results/merged.counts_exon.tab
2025-02-03 23:25:32.595695 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/merged/results/merged.counts_exon_disjoint.tab
2025-02-03 23:25:32.608084 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/merged/results/merged.counts_gene.tab
2025-02-03 23:25:32.615926 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/merged/results/merged.counts_gene_coding.tab
2025-02-03 23:25:32.623072 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/merged/results/merged.counts_gene_exonic.tab
2025-02-03 23:25:32.632714 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/merged/results/merged.counts_intergenic.tab
2025-02-03 23:25:32.649348 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/merged/results/merged.counts_intron.tab
2025-02-03 23:25:32.654191 INFO::countGenomicFeatures.R/mergeCounts: done
2025-02-03 23:25:32.665183 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/merged/results/merged.summary_counts.tab
2025-02-03 23:25:32.667599 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2025-02-03 23:25:32.977932 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2025-02-03 23:25:35.7063 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/merged/results/merged.coverage.RData
2025-02-03 23:25:35.710039 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/merged/results/merged.coverage.bw
2025-02-03 23:25:35.726386 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/merged/results/merged.summary_coverage.tab
2025-02-03 23:25:35.87642 INFO::analyzeVariants/analyzeVariants: starting ...
2025-02-03 23:25:36.1662 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-02-03 23:25:42.405733 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-02-03 23:25:42.57164 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-02-03 23:25:42.608883 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-02-03 23:25:42.611397 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/merged/results/merged.raw_variants.RData
2025-02-03 23:25:42.614436 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/merged/results/merged.filtered_variants.RData
2025-02-03 23:25:42.617027 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-02-03 23:25:42.618977 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-02-03 23:25:43.077682 INFO::analyzeVariants.R/writeVCF: ...done
2025-02-03 23:25:43.35553 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.mergeLanes.25a8318c4c48c/merged/results/merged.summary_variants.tab
2025-02-03 23:25:43.359709 INFO::analyzeVariants/analyzeVariants: done
2025-02-03 23:25:43.365417 INFO::mergeLanes.R/doMergeLanes: merge lanes successful.
 done successfully.



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



Executing test function test.markDuplicates_w_outfile  ... Timing stopped at: 0 0 0
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/RtmpauYpVT/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-02-03 23:25:43.990313 INFO::preprocessReads.R/preprocessReads: starting...
2025-02-03 23:25:44.003953 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
2025-02-03 23:25:44.012137 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
2025-02-03 23:25:44.017359 DEBUG::tools.R/processChunks: starting...
2025-02-03 23:25:50.329158 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-02-03 23:25:50.332141 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.preprocessReads.25a8314c1113be/chunks/chunk_000001/logs/progress.log
2025-02-03 23:25:53.73597 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.057 minutes
2025-02-03 23:25:53.852721 DEBUG::tools.R/processChunks: done
2025-02-03 23:25:53.858412 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-02-03 23:25:53.861971 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.preprocessReads.25a8314c1113be/results/test_pe.adapter_contaminated_1.RData
2025-02-03 23:25:53.866113 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-02-03 23:25:53.869543 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.preprocessReads.25a8314c1113be/results/test_pe.adapter_contaminated_2.RData
2025-02-03 23:25:53.884514 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
2025-02-03 23:25:53.888952 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.preprocessReads.25a8314c1113be/results/test_pe.summary_preprocess.tab
2025-02-03 23:25:53.894486 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.preprocessReads.25a8314c1113be/bams/processed.aligner_input_1.fastq ...
2025-02-03 23:25:53.904606 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.preprocessReads.25a8314c1113be/bams/processed.aligner_input_2.fastq ...
2025-02-03 23:25:53.914666 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.preprocessReads.25a8314c1113be/reports/shortReadReport_1 ...
2025-02-03 23:25:56.563507 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.preprocessReads.25a8314c1113be/reports/shortReadReport_2 ...
2025-02-03 23:25:58.459716 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/RtmpauYpVT/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-02-03 23:25:58.911387 INFO::preprocessReads.R/preprocessReads: starting...
2025-02-03 23:25:58.918708 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
2025-02-03 23:25:58.922924 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
2025-02-03 23:25:58.92547 DEBUG::tools.R/processChunks: starting...
2025-02-03 23:26:02.464182 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-02-03 23:26:02.465723 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.preprocessReads.minichunks.25a831735128b9/chunks/chunk_000001/logs/progress.log
2025-02-03 23:26:05.110782 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.044 minutes
2025-02-03 23:26:05.113168 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.preprocessReads.minichunks.25a831735128b9/chunks/chunk_000002/logs/progress.log
2025-02-03 23:26:07.751984 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.044 minutes
2025-02-03 23:26:07.753401 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.preprocessReads.minichunks.25a831735128b9/chunks/chunk_000003/logs/progress.log
2025-02-03 23:26:10.365082 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.044 minutes
2025-02-03 23:26:10.416314 DEBUG::tools.R/processChunks: done
2025-02-03 23:26:10.419201 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-02-03 23:26:10.420829 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.preprocessReads.minichunks.25a831735128b9/results/test_pe.adapter_contaminated_1.RData
2025-02-03 23:26:10.422884 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-02-03 23:26:10.424325 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.preprocessReads.minichunks.25a831735128b9/results/test_pe.adapter_contaminated_2.RData
2025-02-03 23:26:10.432589 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
2025-02-03 23:26:10.434572 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.preprocessReads.minichunks.25a831735128b9/results/test_pe.summary_preprocess.tab
2025-02-03 23:26:10.437333 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.preprocessReads.minichunks.25a831735128b9/bams/processed.aligner_input_1.fastq ...
2025-02-03 23:26:10.441636 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.preprocessReads.minichunks.25a831735128b9/bams/processed.aligner_input_2.fastq ...
2025-02-03 23:26:10.445835 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.preprocessReads.minichunks.25a831735128b9/reports/shortReadReport_1 ...
2025-02-03 23:26:11.840842 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.preprocessReads.minichunks.25a831735128b9/reports/shortReadReport_2 ...
2025-02-03 23:26:13.0876 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/RtmpauYpVT/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-02-03 23:26:13.340275 INFO::preprocessReads.R/preprocessReads: starting...
2025-02-03 23:26:13.346583 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
2025-02-03 23:26:13.349124 DEBUG::tools.R/processChunks: starting...
2025-02-03 23:26:16.374178 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-02-03 23:26:16.375616 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.preprocessReads_single_end.25a8311fbf195/chunks/chunk_000001/logs/progress.log
2025-02-03 23:26:18.744823 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.039 minutes
2025-02-03 23:26:18.786889 DEBUG::tools.R/processChunks: done
2025-02-03 23:26:18.789372 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-02-03 23:26:18.79117 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.preprocessReads_single_end.25a8311fbf195/results/test_se.adapter_contaminated_1.RData
2025-02-03 23:26:18.797426 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
2025-02-03 23:26:18.799115 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.preprocessReads_single_end.25a8311fbf195/results/test_se.summary_preprocess.tab
2025-02-03 23:26:18.800934 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.preprocessReads_single_end.25a8311fbf195/bams/processed.aligner_input_1.fastq ...
2025-02-03 23:26:18.804465 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpauYpVT/test.preprocessReads_single_end.25a8311fbf195/reports/shortReadReport_1 ...
2025-02-03 23:26:20.159352 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 
2025-02-03 23:26:20.774072 INFO::preprocessReads.R/preprocessReads: starting...
2025-02-03 23:26:20.780046 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
2025-02-03 23:26:20.783703 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
2025-02-03 23:26:20.786002 DEBUG::tools.R/processChunks: starting...
2025-02-03 23:26:23.805567 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-02-03 23:26:23.806966 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= test/chunks/chunk_000001/logs/progress.log
2025-02-03 23:26:26.585808 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.046 minutes
2025-02-03 23:26:26.625902 DEBUG::tools.R/processChunks: done
2025-02-03 23:26:26.627995 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-02-03 23:26:26.629313 INFO::io.R/saveWithID: saving file= test/results/test.adapter_contaminated_1.RData
2025-02-03 23:26:26.630753 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-02-03 23:26:26.631932 INFO::io.R/saveWithID: saving file= test/results/test.adapter_contaminated_2.RData
2025-02-03 23:26:26.637348 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
2025-02-03 23:26:26.63889 INFO::io.R/saveWithID: saving file= test/results/test.summary_preprocess.tab
2025-02-03 23:26:26.640672 INFO::preprocessReads.R/mergePreprocessedReads: merging file= test/bams/processed.aligner_input_1.fastq ...
2025-02-03 23:26:26.645161 INFO::preprocessReads.R/mergePreprocessedReads: merging file= test/bams/processed.aligner_input_2.fastq ...
2025-02-03 23:26:26.649981 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= test/reports/shortReadReport_1 ...
2025-02-03 23:27:20.80192 DEBUG::tools.R/traceMem: wired.mem=-80.751444 GiB
2025-02-03 23:28:20.868705 DEBUG::tools.R/traceMem: wired.mem=-73.317114 GiB
2025-02-03 23:29:20.934465 DEBUG::tools.R/traceMem: wired.mem=-74.048913 GiB
2025-02-03 23:30:21.002955 DEBUG::tools.R/traceMem: wired.mem=-66.336981 GiB
2025-02-03 23:31:21.069622 DEBUG::tools.R/traceMem: wired.mem=-69.884232 GiB
2025-02-03 23:32:21.133939 DEBUG::tools.R/traceMem: wired.mem=-68.198572 GiB
2025-02-03 23:33:21.200954 DEBUG::tools.R/traceMem: wired.mem=-61.529211 GiB
2025-02-03 23:34:21.265868 DEBUG::tools.R/traceMem: wired.mem=-69.079220 GiB
2025-02-03 23:35:21.331231 DEBUG::tools.R/traceMem: wired.mem=-65.461051 GiB
2025-02-03 23:36:21.398871 DEBUG::tools.R/traceMem: wired.mem=-71.663141 GiB
2025-02-03 23:37:21.463289 DEBUG::tools.R/traceMem: wired.mem=-72.596996 GiB
2025-02-03 23:38:21.530487 DEBUG::tools.R/traceMem: wired.mem=-70.809362 GiB
2025-02-03 23:39:21.570726 DEBUG::tools.R/traceMem: wired.mem=-71.681090 GiB
2025-02-03 23:40:21.635728 DEBUG::tools.R/traceMem: wired.mem=-73.222193 GiB
2025-02-03 23:41:21.701682 DEBUG::tools.R/traceMem: wired.mem=-69.855863 GiB
2025-02-03 23:42:21.766135 DEBUG::tools.R/traceMem: wired.mem=-78.747419 GiB
2025-02-03 23:43:21.831436 DEBUG::tools.R/traceMem: wired.mem=-72.096309 GiB
2025-02-03 23:44:21.897864 DEBUG::tools.R/traceMem: wired.mem=-74.529980 GiB
2025-02-03 23:45:21.90989 DEBUG::tools.R/traceMem: wired.mem=-82.859377 GiB
2025-02-03 23:46:21.974227 DEBUG::tools.R/traceMem: wired.mem=-70.642696 GiB
2025-02-03 23:47:22.038686 DEBUG::tools.R/traceMem: wired.mem=-72.001356 GiB
2025-02-03 23:48:22.102954 DEBUG::tools.R/traceMem: wired.mem=-76.850684 GiB
2025-02-03 23:49:22.167297 DEBUG::tools.R/traceMem: wired.mem=-78.416609 GiB
2025-02-03 23:50:22.234509 DEBUG::tools.R/traceMem: wired.mem=-70.852764 GiB
2025-02-03 23:51:22.301996 DEBUG::tools.R/traceMem: wired.mem=-62.806721 GiB
2025-02-03 23:52:22.368174 DEBUG::tools.R/traceMem: wired.mem=-66.571731 GiB
2025-02-03 23:53:22.432923 DEBUG::tools.R/traceMem: wired.mem=-67.431637 GiB
2025-02-03 23:54:22.496949 DEBUG::tools.R/traceMem: wired.mem=-76.220711 GiB

Example timings

HTSeqGenie.Rcheck/HTSeqGenie-Ex.timings

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