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	4.4.3 (2025-02-28) -- "Trophy Case"	4763
palomino8	Windows Server 2022 Datacenter	x64	4.4.3 (2025-02-28 ucrt) -- "Trophy Case"	4494
merida1	macOS 12.7.5 Monterey	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4521
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.3 (2025-02-28) -- "Trophy Case"	4448
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.3 (2025-02-28) -- "Trophy Case"	4414
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

CHECK results for HTSeqGenie on nebbiolo2

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

raw results

Summary

Package: HTSeqGenie

Version: 4.36.0

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

StartedAt: 2025-03-20 23:00:14 -0400 (Thu, 20 Mar 2025)

EndedAt: 2025-03-20 23:40:15 -0400 (Thu, 20 Mar 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 4.4.3 (2025-02-28)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘HTSeqGenie/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HTSeqGenie’ version ‘4.36.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘HTSeqGenie’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘ShortRead:::.set_omp_threads’ ‘gmapR:::..gsnap’ ‘gmapR:::GeneGenome’
  ‘gmapR:::checkPackageInstalled’ ‘gmapR:::getDefaultGmapGenomePath’
  ‘gmapR:::getGeneRoi’ ‘gmapR:::subsetRegion’ ‘parallel:::mckill’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .Call(ShortRead:::.set_omp_threads, ...)
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
.makePreprocessAlignPlots: no visible binding for global variable
  ‘data’
.plot.in.out.min.max.readlength: no visible global function definition
  for ‘median’
FastQStreamer.init: no visible binding for '<<-' assignment to
  ‘FastQStreamer.lfqs’
FastQStreamer.init: no visible binding for '<<-' assignment to
  ‘FastQStreamer.chunkid’
FastQStreamer.init: no visible binding for '<<-' assignment to
  ‘FastQStreamer.subsampling_filter’
FastQStreamer.init: no visible binding for '<<-' assignment to
  ‘FastQStreamer.max_nbchunks’
addHandler: no visible binding for '<<-' assignment to
  ‘logging.handlers’
addHandler: no visible binding for global variable ‘logging.handlers’
addHandler: no visible binding for '<<-' assignment to ‘logging.file’
buildAnyFastaGenome: no visible global function definition for ‘getSeq’
buildGenomicFeaturesFromTxDb: no visible global function definition for
  ‘gaps’
buildGenomicFeaturesFromTxDb: no visible global function definition for
  ‘ranges’
buildTP53FastaGenome: no visible global function definition for
  ‘getSeq’
buildTallyParam: no visible global function definition for ‘seqinfo’
computeCoverage: no visible global function definition for ‘resize’
computeCoverage: no visible global function definition for ‘coverage’
estimateCutoffs : <anonymous>: no visible binding for global variable
  ‘quantile’
getGenomeSegments: no visible global function definition for ‘seqinfo’
hashVariants: no visible global function definition for ‘ranges’
isAboveQualityThresh: no visible global function definition for ‘Views’
isAboveQualityThresh: no visible global function definition for
  ‘viewMeans’
listIterator.init: no visible binding for '<<-' assignment to
  ‘listIterator.n’
listIterator.init: no visible binding for '<<-' assignment to
  ‘listIterator.x’
logReset: no visible binding for '<<-' assignment to ‘logging.handlers’
logReset: no visible binding for '<<-' assignment to ‘logging.loglevel’
logReset: no visible binding for '<<-' assignment to ‘logging.file’
loglevel: no visible binding for global variable ‘logging.loglevel’
loglevel: no visible binding for global variable ‘logging.handlers’
processChunks : tracefun: no visible binding for global variable
  ‘sjobs’
processChunks : tracefun: no visible binding for global variable
  ‘chunkid’
setLevel: no visible binding for '<<-' assignment to ‘logging.loglevel’
statCountFeatures: no visible global function definition for ‘quantile’
truncateReads: no visible global function definition for ‘subseq’
vcfStat: no visible global function definition for ‘quantile’
writeToFile: no visible binding for global variable ‘logging.file’
Undefined global functions or variables:
  Views chunkid coverage data gaps getSeq logging.file logging.handlers
  logging.loglevel median quantile ranges resize seqinfo sjobs subseq
  viewMeans
Consider adding
  importFrom("stats", "median", "quantile")
  importFrom("utils", "data")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) calculateTargetLengths.Rd:17: Lost braces; missing escapes or markup?
    17 | Target length table and writes two files in {save_dir}/reports/images/TargetLenghts.[pdf|png]"
       |                                             ^
checkRd: (-1) initLog.Rd:18: Lost braces; missing escapes or markup?
    18 | Setup logging file in {save_dir}/progress.log
       |                       ^
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
Documented arguments not in \usage in Rd file 'findVariantFile.Rd':
  ‘dir_path’

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

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

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

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

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

Installation output

HTSeqGenie.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL HTSeqGenie
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘HTSeqGenie’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (HTSeqGenie)

Tests output

HTSeqGenie.Rcheck/tests/doRUnit.Rout


R version 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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

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

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

> library("HTSeqGenie")
Loading required package: gmapR
Loading required package: GenomeInfoDb
Loading required package: BiocGenerics

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/RtmpDihunG/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-20 23:05:52.614797 INFO::preprocessReads.R/preprocessReads: starting...
2025-03-20 23:05:52.623744 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-03-20 23:05:52.62735 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-03-20 23:05:52.62961 DEBUG::tools.R/processChunks: starting...
2025-03-20 23:05:55.521198 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-20 23:05:55.522713 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.alignReads.39681052469826/chunks/chunk_000001/logs/progress.log
2025-03-20 23:05:58.311745 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.046 minutes
2025-03-20 23:05:58.313195 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.alignReads.39681052469826/chunks/chunk_000002/logs/progress.log
2025-03-20 23:06:01.030693 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.045 minutes
2025-03-20 23:06:01.031975 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.alignReads.39681052469826/chunks/chunk_000003/logs/progress.log
2025-03-20 23:06:03.79687 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.046 minutes
2025-03-20 23:06:03.827997 DEBUG::tools.R/processChunks: done
2025-03-20 23:06:03.832117 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-03-20 23:06:03.8344 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.alignReads.39681052469826/results/test_pe.adapter_contaminated_1.RData
2025-03-20 23:06:03.837155 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-03-20 23:06:03.838763 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.alignReads.39681052469826/results/test_pe.adapter_contaminated_2.RData
2025-03-20 23:06:03.847884 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=26 highqual_reads=25 adapter_contam=1 read_length=75 rRNA_contam_reads=0 processed_reads=25 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-03-20 23:06:03.850077 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.alignReads.39681052469826/results/test_pe.summary_preprocess.tab
2025-03-20 23:06:03.853471 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.alignReads.39681052469826/bams/processed.aligner_input_1.fastq ...
2025-03-20 23:06:03.857578 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.alignReads.39681052469826/bams/processed.aligner_input_2.fastq ...
2025-03-20 23:06:03.860741 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.alignReads.39681052469826/reports/shortReadReport_1 ...
2025-03-20 23:06:05.287095 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.alignReads.39681052469826/reports/shortReadReport_2 ...
2025-03-20 23:06:06.487411 INFO::preprocessReads.R/preprocessReads: done
2025-03-20 23:06:06.574172 INFO::alignReads.R/alignReads: starting alignment...
2025-03-20 23:06:06.580312 DEBUG::tools.R/processChunks: starting...
2025-03-20 23:06:09.48985 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-20 23:06:09.49137 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.alignReads.39681052469826/chunks/chunk_000001/logs/progress.log
2025-03-20 23:06:12.347644 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.048 minutes
2025-03-20 23:06:12.350099 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.alignReads.39681052469826/chunks/chunk_000002/logs/progress.log
[bam_translate] PG tag "A" on read "highqualPEsInManyTxsOfMultiTxGene:1:1:1:16#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1MicrobialPE2MultimappingIntergenic:1:1:1:19#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInOneTxOfMultiTxGene:1:1:1:15#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1UniqueUtrPE2MultimappingIntergenic:1:1:1:18#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-03-20 23:06:15.044621 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.045 minutes
2025-03-20 23:06:15.046413 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.alignReads.39681052469826/chunks/chunk_000003/logs/progress.log
[bam_translate] PG tag "A" on read "highqualPE1GeneFusionMidExonDiffChrPE2MultimappingIntergenic:1:1:1:25#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-03-20 23:06:17.731008 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.045 minutes
2025-03-20 23:06:17.733706 DEBUG::tools.R/processChunks: done
2025-03-20 23:06:17.735344 INFO::alignReads.R/mergeBAMsAcrossDirs: starting...
[bam_translate] PG tag "A" on read "highqualAdapterContamIn3PrimeEnd:1:1:1:7#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInManyTxsOfMultiTxGene:1:1:1:16#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1MicrobialPE2MultimappingIntergenic:1:1:1:19#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1GeneFusionMidExonDiffChrPE2MultimappingIntergenic:1:1:1:25#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1UniqueUtrPE2MultimappingIntergenic:1:1:1:18#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInOneTxOfMultiTxGene:1:1:1:15#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-03-20 23:06:17.956601 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-03-20 23:06:17.965191 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.alignReads.39681052469826/results/test_pe.summary_alignment.tab
2025-03-20 23:06:17.972267 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.alignReads.39681052469826/results/test_pe.summary_analyzed_bamstats.tab
2025-03-20 23:06:17.973923 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-03-20 23:06:18.218838 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.alignReads.39681052469826/results/test_pe.summary_target_lengths.tab
2025-03-20 23:06:18.266325 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-03-20 23:06:18.267385 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/RtmpDihunG/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-20 23:06:18.568022 INFO::preprocessReads.R/preprocessReads: starting...
2025-03-20 23:06:18.572071 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-03-20 23:06:18.669597 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 2 , totnbreads= 26 )
2025-03-20 23:06:18.677094 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-03-20 23:06:18.681688 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-03-20 23:06:18.684374 DEBUG::tools.R/processChunks: starting...
2025-03-20 23:06:21.725514 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-20 23:06:21.726961 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.alignReads.sparsechunks.3968105ce6cee0/chunks/chunk_000001/logs/progress.log
2025-03-20 23:06:24.396278 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.044 minutes
2025-03-20 23:06:24.398198 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.alignReads.sparsechunks.3968105ce6cee0/chunks/chunk_000002/logs/progress.log
2025-03-20 23:06:27.049185 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.044 minutes
2025-03-20 23:06:27.050501 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.alignReads.sparsechunks.3968105ce6cee0/chunks/chunk_000003/logs/progress.log
2025-03-20 23:06:29.779392 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.045 minutes
2025-03-20 23:06:29.781004 DEBUG::tools.R/processChunks: starting chunkid= 4 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.alignReads.sparsechunks.3968105ce6cee0/chunks/chunk_000004/logs/progress.log
2025-03-20 23:06:32.426376 DEBUG::tools.R/processChunks: done with chunkid= 4 ; elapsed.time= 0.044 minutes
2025-03-20 23:06:32.452249 DEBUG::tools.R/processChunks: done
2025-03-20 23:06:32.455379 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-03-20 23:06:32.457492 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.alignReads.sparsechunks.3968105ce6cee0/results/test_pe.adapter_contaminated_1.RData
2025-03-20 23:06:32.460283 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-03-20 23:06:32.461871 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.alignReads.sparsechunks.3968105ce6cee0/results/test_pe.adapter_contaminated_2.RData
2025-03-20 23:06:32.471266 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=2 highqual_reads=1 adapter_contam=0 read_length=75 rRNA_contam_reads=0 processed_reads=1 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-03-20 23:06:32.473243 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.alignReads.sparsechunks.3968105ce6cee0/results/test_pe.summary_preprocess.tab
2025-03-20 23:06:32.47638 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.alignReads.sparsechunks.3968105ce6cee0/bams/processed.aligner_input_1.fastq ...
2025-03-20 23:06:32.481071 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.alignReads.sparsechunks.3968105ce6cee0/bams/processed.aligner_input_2.fastq ...
2025-03-20 23:06:32.483988 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.alignReads.sparsechunks.3968105ce6cee0/reports/shortReadReport_1 ...
2025-03-20 23:06:33.89426 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.alignReads.sparsechunks.3968105ce6cee0/reports/shortReadReport_2 ...
2025-03-20 23:06:34.898578 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/RtmpDihunG/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-20 23:06:35.058612 INFO::alignReads.R/alignReadsChunk: running gsnap...
2025-03-20 23:06:35.063417 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/RtmpDihunG/test.alignReadsOneSingleEnd.3968101c4b4ded/bams/test.alignReads /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq 2>&1
2025-03-20 23:06:35.246381 INFO::alignReads.R/createSummaryAlignment: counting unique bam reads...
2025-03-20 23:06:35.339935 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.alignReadsOneSingleEnd.3968101c4b4ded/results/test.alignReads.summary_alignment.tab
2025-03-20 23:06:35.387766 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.alignReadsOneSingleEnd.3968101c4b4ded/results/test.alignReads.summary_analyzed_bamstats.tab
2025-03-20 23:06:35.389276 INFO::alignReads.R/alignReadsChunk: done
 done successfully.



Executing test function test.annotateVariants  ... Timing stopped at: 0.001 0.001 0.001
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/RtmpDihunG/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-20 23:06:35.681635 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.genotype.39681036331890/results/test_pe.coverage.RData
2025-03-20 23:06:35.683556 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.genotype.39681036331890/results/test_pe.coverage.bw
2025-03-20 23:06:35.808269 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.genotype.39681036331890/results/test_pe.summary_coverage.tab
2025-03-20 23:06:35.810119 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-03-20 23:06:46.3167 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-03-20 23:06:46.393929 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-03-20 23:06:46.409045 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-03-20 23:06:46.410372 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.genotype.39681036331890/results/test_pe.raw_variants.RData
2025-03-20 23:06:46.412636 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.genotype.39681036331890/results/test_pe.filtered_variants.RData
2025-03-20 23:06:46.413911 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-03-20 23:06:46.414961 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-03-20 23:06:46.817804 INFO::analyzeVariants.R/writeVCF: ...done
2025-03-20 23:06:46.818983 INFO::analyzeVariants.R/.callGenotypes: calling genotypes...
2025-03-20 23:07:46.052126 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-03-20 23:07:46.53314 INFO::analyzeVariants.R/writeVCF: ...done
2025-03-20 23:07:46.534056 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/RtmpDihunG/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-20 23:07:47.000494 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-03-20 23:07:57.511506 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-03-20 23:07:57.592507 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-03-20 23:07:57.610483 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-03-20 23:07:57.612017 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.wrap.callVariants.3968105a6ec6a9/results/test_pe.raw_variants.RData
2025-03-20 23:07:57.61475 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.wrap.callVariants.3968105a6ec6a9/results/test_pe.filtered_variants.RData
2025-03-20 23:07:57.616264 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/RtmpDihunG/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-20 23:07:57.772011 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-03-20 23:08:08.03274 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-03-20 23:08:08.096188 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-03-20 23:08:08.113921 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-03-20 23:08:08.115473 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.wrap.callVariants.filters.396810269f3b45/results/test_pe.raw_variants.RData
2025-03-20 23:08:08.118129 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.wrap.callVariants.filters.396810269f3b45/results/test_pe.filtered_variants.RData
2025-03-20 23:08:08.119455 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-03-20 23:08:08.121222 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-03-20 23:08:18.787441 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-03-20 23:08:18.826645 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-03-20 23:08:18.843853 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-03-20 23:08:18.845355 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.wrap.callVariants.filters.396810269f3b45/results/test_pe.raw_variants.RData
2025-03-20 23:08:18.848071 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.wrap.callVariants.filters.396810269f3b45/results/test_pe.filtered_variants.RData
2025-03-20 23:08:18.850138 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/RtmpDihunG/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-20 23:08:19.13466 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-03-20 23:08:19.136098 INFO::analyzeVariants.R/buildTallyParam: restricting variant calls using 'which'
2025-03-20 23:08:22.021886 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-03-20 23:08:22.108483 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-03-20 23:08:22.126082 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-03-20 23:08:22.127434 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.wrap.callVariants.which.39681074c83f13/results/test_pe.raw_variants.RData
2025-03-20 23:08:22.129127 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.wrap.callVariants.which.39681074c83f13/results/test_pe.filtered_variants.RData
2025-03-20 23:08:22.1304 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/RtmpDihunG/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-20 23:08:22.277793 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-03-20 23:08:22.279101 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/RtmpDihunG/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-20 23:08:23.85406 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-03-20 23:08:24.043751 INFO::analyzeVariants.R/writeVCF: ...done
 done successfully.



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



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



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



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



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



Executing test function test.mergeCoverage  ... 2025-03-20 23:09:18.715086 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/gtsdiczk/merged/results/bla.coverage.RData
2025-03-20 23:09:18.718612 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/gtsdiczk/merged/results/bla.coverage.bw
2025-03-20 23:09:18.806223 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/gtsdiczk/merged/results/bla.summary_coverage.tab
 done successfully.



Executing test function test.mergeCoverage.sparse  ... 2025-03-20 23:09:19.99882 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/zxcmnyoq/merged/results/bla.coverage.RData
2025-03-20 23:09:20.000213 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/zxcmnyoq/merged/results/bla.coverage.bw
2025-03-20 23:09:20.010973 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/zxcmnyoq/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/RtmpDihunG/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/RtmpDihunG/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/RtmpDihunG/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/RtmpDihunG/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/RtmpDihunG/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/RtmpDihunG/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/RtmpDihunG/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/RtmpDihunG/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/RtmpDihunG/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/RtmpDihunG/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-20 23:09:21.156163 INFO::detectRRNA.R/detectRRNA: searching for rRNA contamination...
2025-03-20 23:09:21.157244 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.detectRRNA.396810cd32963/bams/rRNA_contam/input1.fastq
2025-03-20 23:09:21.160387 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/RtmpDihunG/test.detectRRNA.396810cd32963/bams/rRNA_contam/test_se /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.detectRRNA.396810cd32963/bams/rRNA_contam/input1.fastq 2>&1
2025-03-20 23:09:21.293149 INFO::detectRRNA.R/detectRRNA: contaminated fraction= 1
2025-03-20 23:09:21.294205 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/RtmpDihunG/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-20 23:09:21.407958 INFO::detectRRNA.R/detectRRNA: searching for rRNA contamination...
2025-03-20 23:09:21.408887 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.detectRRNA.paired_end.3968106424bba/bams/rRNA_contam/input1.fastq
2025-03-20 23:09:21.410301 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.detectRRNA.paired_end.3968106424bba/bams/rRNA_contam/input2.fastq
2025-03-20 23:09:21.412331 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/RtmpDihunG/test.detectRRNA.paired_end.3968106424bba/bams/rRNA_contam/test_pe /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.detectRRNA.paired_end.3968106424bba/bams/rRNA_contam/input1.fastq -a paired /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.detectRRNA.paired_end.3968106424bba/bams/rRNA_contam/input2.fastq 2>&1
2025-03-20 23:09:21.636501 INFO::detectRRNA.R/detectRRNA: contaminated fraction= 1
2025-03-20 23:09:21.637452 INFO::detectRRNA.R/detectRRNA: done
 done successfully.



Executing test function test.getRRNAIds  ... 2025-03-20 23:09:21.655645 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/RtmpDihunG/test_get_rRNA_idsmodzvgci/test_pe /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test_get_rRNA_idsmodzvgci/1.fastq -a paired /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test_get_rRNA_idsmodzvgci/2.fastq 2>&1
 done successfully.



Executing test function test.getRRNAIds_random  ... 2025-03-20 23:09:21.928277 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/RtmpDihunG/test_get_rRNAIds_randomzneybuiw/test_pe /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test_get_rRNAIds_randomzneybuiw/1.fastq 2>&1
 done successfully.



Executing test function test.filterByLength  ... 2025-03-20 23:09:22.143751 INFO::filterQuality.R/filterQuality: filterByLength...
2025-03-20 23:09:22.145388 INFO::filterQuality.R/filterByLength: fraction of filtered short reads= 0.5
2025-03-20 23:09:22.14635 INFO::filterQuality.R/filterByLength: done
2025-03-20 23:09:22.194444 INFO::filterQuality.R/filterQuality: filterByLength...
2025-03-20 23:09:22.195359 INFO::filterQuality.R/filterByLength: fraction of filtered short reads= 1
2025-03-20 23:09:22.196172 INFO::filterQuality.R/filterByLength: done
 done successfully.



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



Executing test function test.trimTailsByQuality  ... 2025-03-20 23:09:22.243995 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-03-20 23:09:22.253174 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-03-20 23:09:22.254218 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-03-20 23:09:22.258437 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-03-20 23:09:22.259337 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-03-20 23:09:22.263494 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-03-20 23:09:22.264369 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-03-20 23:09:22.268449 INFO::preprocessReads.R/preprocessReadsChunk: done
 done successfully.



Executing test function test.callVariantsGATK  ... Timing stopped at: 0.001 0 0
Error in DEACTIVATED("callVariantsGATK() tests need gatk.path option set") : 
  callVariantsGATK() tests need gatk.path option set
In addition: There were 50 or more warnings (use warnings() to see the first 50)
 done successfully.



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



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



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



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



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



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



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



Executing test function test_zipUp  ...  done successfully.



Executing test function test.FastQStreamer.getReads.pefq  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-20 23:09:22.516088 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-03-20 23:09:22.518263 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/RtmpDihunG/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-20 23:09:22.692147 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-03-20 23:09:22.761382 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-03-20 23:09:22.764079 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-03-20 23:09:22.766194 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/RtmpDihunG/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-20 23:09:22.956506 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/RtmpDihunG/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-20 23:09:23.092568 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/RtmpDihunG/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-20 23:09:23.219783 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-03-20 23:09:23.264386 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-03-20 23:09:23.266715 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-03-20 23:09:23.268841 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/RtmpDihunG/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-20 23:09:23.44828 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-03-20 23:09:23.51574 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-03-20 23:09:23.519329 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-03-20 23:09:23.522624 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/RtmpDihunG/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/RtmpDihunG/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-20 23:09:24.198266 INFO::preprocessReads.R/preprocessReads: starting...
2025-03-20 23:09:24.204901 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-03-20 23:09:24.208325 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-03-20 23:09:24.210639 DEBUG::tools.R/processChunks: starting...
2025-03-20 23:09:28.31486 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-20 23:09:28.316293 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/chunks/chunk_000001/logs/progress.log
2025-03-20 23:09:30.935281 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.044 minutes
2025-03-20 23:09:30.937004 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/chunks/chunk_000002/logs/progress.log
2025-03-20 23:09:33.562766 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.044 minutes
2025-03-20 23:09:33.564281 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/chunks/chunk_000003/logs/progress.log
2025-03-20 23:09:36.204277 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.044 minutes
2025-03-20 23:09:36.248479 DEBUG::tools.R/processChunks: done
2025-03-20 23:09:36.251173 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-03-20 23:09:36.2528 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/results/test_pe.adapter_contaminated_1.RData
2025-03-20 23:09:36.254841 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-03-20 23:09:36.256264 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/results/test_pe.adapter_contaminated_2.RData
2025-03-20 23:09:36.264033 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=26 highqual_reads=25 adapter_contam=1 read_length=75 rRNA_contam_reads=0 processed_reads=25 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-03-20 23:09:36.265699 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/results/test_pe.summary_preprocess.tab
2025-03-20 23:09:36.267963 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/bams/processed.aligner_input_1.fastq ...
2025-03-20 23:09:36.271764 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/bams/processed.aligner_input_2.fastq ...
2025-03-20 23:09:36.274783 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/reports/shortReadReport_1 ...
2025-03-20 23:09:37.570598 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/reports/shortReadReport_2 ...
2025-03-20 23:09:38.64534 INFO::preprocessReads.R/preprocessReads: done
2025-03-20 23:09:38.77786 INFO::alignReads.R/alignReads: starting alignment...
2025-03-20 23:09:38.782517 DEBUG::tools.R/processChunks: starting...
2025-03-20 23:09:41.879854 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-20 23:09:41.881514 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/chunks/chunk_000001/logs/progress.log
2025-03-20 23:09:44.487014 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.043 minutes
2025-03-20 23:09:44.488554 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/chunks/chunk_000002/logs/progress.log
[bam_translate] PG tag "A" on read "highqualPEsInManyTxsOfMultiTxGene:1:1:1:16#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1MicrobialPE2MultimappingIntergenic:1:1:1:19#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInOneTxOfMultiTxGene:1:1:1:15#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1UniqueUtrPE2MultimappingIntergenic:1:1:1:18#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-03-20 23:09:47.076437 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.043 minutes
2025-03-20 23:09:47.078019 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/chunks/chunk_000003/logs/progress.log
[bam_translate] PG tag "A" on read "highqualPE1GeneFusionMidExonDiffChrPE2MultimappingIntergenic:1:1:1:25#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-03-20 23:09:50.231709 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.053 minutes
2025-03-20 23:09:50.239118 DEBUG::tools.R/processChunks: done
2025-03-20 23:09:50.24297 INFO::alignReads.R/mergeBAMsAcrossDirs: starting...
[bam_translate] PG tag "A" on read "highqualAdapterContamIn3PrimeEnd:1:1:1:7#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInManyTxsOfMultiTxGene:1:1:1:16#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1MicrobialPE2MultimappingIntergenic:1:1:1:19#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1GeneFusionMidExonDiffChrPE2MultimappingIntergenic:1:1:1:25#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1UniqueUtrPE2MultimappingIntergenic:1:1:1:18#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInOneTxOfMultiTxGene:1:1:1:15#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-03-20 23:09:50.823038 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-03-20 23:09:50.838194 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/results/test_pe.summary_alignment.tab
2025-03-20 23:09:50.851951 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/results/test_pe.summary_analyzed_bamstats.tab
2025-03-20 23:09:50.855534 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-03-20 23:09:51.389072 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/results/test_pe.summary_target_lengths.tab
2025-03-20 23:09:51.467622 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-03-20 23:09:51.470089 INFO::alignReads.R/alignReads: done
2025-03-20 23:09:51.85588 INFO::countGenomicFeatures.R/countGenomicFeatures: starting...
2025-03-20 23:09:51.910069 DEBUG::tools.R/processChunks: starting...
2025-03-20 23:09:59.011466 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-20 23:09:59.015168 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/chunks/chunk_000001/logs/progress.log
2025-03-20 23:10:02.141209 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.052 minutes
2025-03-20 23:10:02.14407 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/chunks/chunk_000002/logs/progress.log
2025-03-20 23:10:05.744639 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.06 minutes
2025-03-20 23:10:05.751701 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/chunks/chunk_000003/logs/progress.log
2025-03-20 23:10:09.248556 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.058 minutes
2025-03-20 23:10:09.262349 DEBUG::tools.R/processChunks: done
2025-03-20 23:10:09.274691 INFO::countGenomicFeatures.R/mergeCounts: starting...
2025-03-20 23:10:09.341567 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/results/test_pe.counts_exon.tab
2025-03-20 23:10:09.401158 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/results/test_pe.counts_exon_disjoint.tab
2025-03-20 23:10:09.431597 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/results/test_pe.counts_gene.tab
2025-03-20 23:10:09.464439 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/results/test_pe.counts_gene_coding.tab
2025-03-20 23:10:09.494677 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/results/test_pe.counts_gene_exonic.tab
2025-03-20 23:10:09.520371 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/results/test_pe.counts_intergenic.tab
2025-03-20 23:10:09.548882 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/results/test_pe.counts_intron.tab
2025-03-20 23:10:09.554576 INFO::countGenomicFeatures.R/mergeCounts: done
2025-03-20 23:10:09.566247 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/results/test_pe.summary_counts.tab
2025-03-20 23:10:09.569704 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2025-03-20 23:10:10.392968 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2025-03-20 23:10:10.399642 INFO::countGenomicFeatures.R/countGenomicFeatures: done...
2025-03-20 23:10:10.887279 INFO::coverage.R/calculateCoverage: starting...
2025-03-20 23:10:10.911695 DEBUG::tools.R/processChunks: starting...
2025-03-20 23:10:15.911155 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-20 23:10:15.913672 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/chunks/chunk_000001/logs/progress.log
2025-03-20 23:10:18.328187 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.04 minutes
2025-03-20 23:10:18.331575 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/chunks/chunk_000002/logs/progress.log
2025-03-20 23:10:20.762909 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.04 minutes
2025-03-20 23:10:20.766224 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/chunks/chunk_000003/logs/progress.log
2025-03-20 23:10:23.220063 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.041 minutes
2025-03-20 23:10:23.234695 DEBUG::tools.R/processChunks: done
2025-03-20 23:10:26.974062 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/results/test_pe.coverage.RData
2025-03-20 23:10:26.978104 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/results/test_pe.coverage.bw
2025-03-20 23:10:27.0143 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/results/test_pe.summary_coverage.tab
2025-03-20 23:10:27.017897 INFO::coverage.R/calculateCoverage: done
2025-03-20 23:10:27.042767 INFO::analyzeVariants/analyzeVariants: starting ...
2025-03-20 23:10:27.435229 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-03-20 23:10:33.506176 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-03-20 23:10:33.604865 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-03-20 23:10:33.629714 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-03-20 23:10:33.632029 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/results/test_pe.raw_variants.RData
2025-03-20 23:10:33.634592 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/results/test_pe.filtered_variants.RData
2025-03-20 23:10:33.636558 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-03-20 23:10:33.637908 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-03-20 23:10:33.914001 INFO::analyzeVariants.R/writeVCF: ...done
2025-03-20 23:10:34.035498 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/results/test_pe.summary_variants.tab
2025-03-20 23:10:34.038271 INFO::analyzeVariants/analyzeVariants: done
2025-03-20 23:10:34.042718 INFO::Pipeline run successful.
2025-03-20 23:10:34.401761 INFO::mergeLanes.R/doMergeLanes: starting...
2025-03-20 23:10:34.410117 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-03-20 23:10:34.414053 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/merged/results/merged.adapter_contaminated_1.RData
2025-03-20 23:10:34.418006 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-03-20 23:10:34.420901 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/merged/results/merged.adapter_contaminated_2.RData
2025-03-20 23:10:34.438669 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=26 highqual_reads=25 adapter_contam=1 read_length=75 rRNA_contam_reads=0 processed_reads=25 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-03-20 23:10:34.442259 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/merged/results/merged.summary_preprocess.tab
2025-03-20 23:10:34.446124 INFO::alignReads.R/mergeBAMsAcrossDirs: starting...
[bam_translate] PG tag "A" on read "highqualAdapterContamIn3PrimeEnd:1:1:1:7#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInManyTxsOfMultiTxGene:1:1:1:16#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1MicrobialPE2MultimappingIntergenic:1:1:1:19#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1GeneFusionMidExonDiffChrPE2MultimappingIntergenic:1:1:1:25#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1UniqueUtrPE2MultimappingIntergenic:1:1:1:18#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInOneTxOfMultiTxGene:1:1:1:15#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-03-20 23:10:34.788962 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-03-20 23:10:34.797501 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/merged/results/merged.summary_alignment.tab
2025-03-20 23:10:34.807748 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/merged/results/merged.summary_analyzed_bamstats.tab
2025-03-20 23:10:34.810464 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-03-20 23:10:35.095205 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/merged/results/merged.summary_target_lengths.tab
2025-03-20 23:10:35.152959 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-03-20 23:10:35.226731 INFO::countGenomicFeatures.R/mergeCounts: starting...
2025-03-20 23:10:35.254405 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/merged/results/merged.counts_exon.tab
2025-03-20 23:10:35.270592 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/merged/results/merged.counts_exon_disjoint.tab
2025-03-20 23:10:35.280428 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/merged/results/merged.counts_gene.tab
2025-03-20 23:10:35.28863 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/merged/results/merged.counts_gene_coding.tab
2025-03-20 23:10:35.2962 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/merged/results/merged.counts_gene_exonic.tab
2025-03-20 23:10:35.3062 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/merged/results/merged.counts_intergenic.tab
2025-03-20 23:10:35.328461 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/merged/results/merged.counts_intron.tab
2025-03-20 23:10:35.333549 INFO::countGenomicFeatures.R/mergeCounts: done
2025-03-20 23:10:35.344827 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/merged/results/merged.summary_counts.tab
2025-03-20 23:10:35.348071 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2025-03-20 23:10:35.74194 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2025-03-20 23:10:39.381198 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/merged/results/merged.coverage.RData
2025-03-20 23:10:39.384957 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/merged/results/merged.coverage.bw
2025-03-20 23:10:39.401563 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/merged/results/merged.summary_coverage.tab
2025-03-20 23:10:39.468843 INFO::analyzeVariants/analyzeVariants: starting ...
2025-03-20 23:10:39.568047 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-03-20 23:10:43.343749 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-03-20 23:10:43.418658 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-03-20 23:10:43.435679 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-03-20 23:10:43.437043 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/merged/results/merged.raw_variants.RData
2025-03-20 23:10:43.438606 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/merged/results/merged.filtered_variants.RData
2025-03-20 23:10:43.439852 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-03-20 23:10:43.440758 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-03-20 23:10:43.666828 INFO::analyzeVariants.R/writeVCF: ...done
2025-03-20 23:10:43.768216 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.mergeLanes.39681061b7fbeb/merged/results/merged.summary_variants.tab
2025-03-20 23:10:43.770528 INFO::analyzeVariants/analyzeVariants: done
2025-03-20 23:10:43.774545 INFO::mergeLanes.R/doMergeLanes: merge lanes successful.
 done successfully.



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



Executing test function test.markDuplicates_w_outfile  ... Timing stopped at: 0 0 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/RtmpDihunG/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-20 23:10:44.264072 INFO::preprocessReads.R/preprocessReads: starting...
2025-03-20 23:10:44.331435 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-03-20 23:10:44.336938 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-03-20 23:10:44.340705 DEBUG::tools.R/processChunks: starting...
2025-03-20 23:10:49.256127 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-20 23:10:49.258044 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.preprocessReads.3968107fc01d6f/chunks/chunk_000001/logs/progress.log
2025-03-20 23:10:51.919412 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.044 minutes
2025-03-20 23:10:51.972289 DEBUG::tools.R/processChunks: done
2025-03-20 23:10:51.974772 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-03-20 23:10:51.97632 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.preprocessReads.3968107fc01d6f/results/test_pe.adapter_contaminated_1.RData
2025-03-20 23:10:51.978033 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-03-20 23:10:51.979345 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.preprocessReads.3968107fc01d6f/results/test_pe.adapter_contaminated_2.RData
2025-03-20 23:10:51.985594 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=26 highqual_reads=25 adapter_contam=1 read_length=75 rRNA_contam_reads=0 processed_reads=25 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-03-20 23:10:51.987323 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.preprocessReads.3968107fc01d6f/results/test_pe.summary_preprocess.tab
2025-03-20 23:10:51.989353 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.preprocessReads.3968107fc01d6f/bams/processed.aligner_input_1.fastq ...
2025-03-20 23:10:51.993369 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.preprocessReads.3968107fc01d6f/bams/processed.aligner_input_2.fastq ...
2025-03-20 23:10:51.996477 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.preprocessReads.3968107fc01d6f/reports/shortReadReport_1 ...
2025-03-20 23:10:53.380433 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.preprocessReads.3968107fc01d6f/reports/shortReadReport_2 ...
2025-03-20 23:10:54.533443 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/RtmpDihunG/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-20 23:10:54.86817 INFO::preprocessReads.R/preprocessReads: starting...
2025-03-20 23:10:54.874798 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-03-20 23:10:54.87849 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-03-20 23:10:54.880826 DEBUG::tools.R/processChunks: starting...
2025-03-20 23:10:58.035118 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-20 23:10:58.036519 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.preprocessReads.minichunks.396810b1166a5/chunks/chunk_000001/logs/progress.log
2025-03-20 23:11:00.655806 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.044 minutes
2025-03-20 23:11:00.657254 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.preprocessReads.minichunks.396810b1166a5/chunks/chunk_000002/logs/progress.log
2025-03-20 23:11:03.284357 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.044 minutes
2025-03-20 23:11:03.285821 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.preprocessReads.minichunks.396810b1166a5/chunks/chunk_000003/logs/progress.log
2025-03-20 23:11:05.918334 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.044 minutes
2025-03-20 23:11:05.965815 DEBUG::tools.R/processChunks: done
2025-03-20 23:11:05.968484 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-03-20 23:11:05.970049 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.preprocessReads.minichunks.396810b1166a5/results/test_pe.adapter_contaminated_1.RData
2025-03-20 23:11:05.972024 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-03-20 23:11:05.97345 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.preprocessReads.minichunks.396810b1166a5/results/test_pe.adapter_contaminated_2.RData
2025-03-20 23:11:05.981053 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=26 highqual_reads=25 adapter_contam=1 read_length=75 rRNA_contam_reads=0 processed_reads=25 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-03-20 23:11:05.98278 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.preprocessReads.minichunks.396810b1166a5/results/test_pe.summary_preprocess.tab
2025-03-20 23:11:05.985089 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.preprocessReads.minichunks.396810b1166a5/bams/processed.aligner_input_1.fastq ...
2025-03-20 23:11:05.988919 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.preprocessReads.minichunks.396810b1166a5/bams/processed.aligner_input_2.fastq ...
2025-03-20 23:11:05.991942 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.preprocessReads.minichunks.396810b1166a5/reports/shortReadReport_1 ...
2025-03-20 23:11:07.293623 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.preprocessReads.minichunks.396810b1166a5/reports/shortReadReport_2 ...
2025-03-20 23:11:08.347358 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/RtmpDihunG/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-20 23:11:08.561922 INFO::preprocessReads.R/preprocessReads: starting...
2025-03-20 23:11:08.579719 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-03-20 23:11:08.582264 DEBUG::tools.R/processChunks: starting...
2025-03-20 23:11:11.765337 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-20 23:11:11.766677 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.preprocessReads_single_end.396810630ef868/chunks/chunk_000001/logs/progress.log
2025-03-20 23:11:14.13779 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.04 minutes
2025-03-20 23:11:14.173461 DEBUG::tools.R/processChunks: done
2025-03-20 23:11:14.175932 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-03-20 23:11:14.177434 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.preprocessReads_single_end.396810630ef868/results/test_se.adapter_contaminated_1.RData
2025-03-20 23:11:14.183483 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=26 highqual_reads=25 adapter_contam=1 read_length=75 rRNA_contam_reads=0 processed_reads=25 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-03-20 23:11:14.185043 INFO::io.R/saveWithID: saving file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.preprocessReads_single_end.396810630ef868/results/test_se.summary_preprocess.tab
2025-03-20 23:11:14.186743 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.preprocessReads_single_end.396810630ef868/bams/processed.aligner_input_1.fastq ...
2025-03-20 23:11:14.190718 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpDihunG/test.preprocessReads_single_end.396810630ef868/reports/shortReadReport_1 ...
2025-03-20 23:11:15.455845 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



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



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



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



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



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



Executing test function test.runPipeline  ... checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2025-03-20 23:11:16.148554 INFO::preprocessReads.R/preprocessReads: starting...
2025-03-20 23:11:16.15443 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/extdata/H1993_TP53_subset2500_1.fastq.gz
2025-03-20 23:11:16.158092 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.20-bioc/R/site-library/HTSeqGenie/extdata/H1993_TP53_subset2500_2.fastq.gz
2025-03-20 23:11:16.160324 DEBUG::tools.R/processChunks: starting...
2025-03-20 23:11:19.086073 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-03-20 23:11:19.087664 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= test/chunks/chunk_000001/logs/progress.log
2025-03-20 23:11:21.879425 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.047 minutes
2025-03-20 23:11:21.913813 DEBUG::tools.R/processChunks: done
2025-03-20 23:11:21.915792 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-03-20 23:11:21.91702 INFO::io.R/saveWithID: saving file= test/results/test.adapter_contaminated_1.RData
2025-03-20 23:11:21.918363 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-03-20 23:11:21.919486 INFO::io.R/saveWithID: saving file= test/results/test.adapter_contaminated_2.RData
2025-03-20 23:11:21.92468 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=2500 highqual_reads=2500 adapter_contam=0 read_length=100 rRNA_contam_reads=0 processed_reads=2500 input_min_read_length=100 input_max_read_length=100 processed_min_read_length=71 processed_max_read_length=100
2025-03-20 23:11:21.926137 INFO::io.R/saveWithID: saving file= test/results/test.summary_preprocess.tab
2025-03-20 23:11:21.927827 INFO::preprocessReads.R/mergePreprocessedReads: merging file= test/bams/processed.aligner_input_1.fastq ...
2025-03-20 23:11:21.931534 INFO::preprocessReads.R/mergePreprocessedReads: merging file= test/bams/processed.aligner_input_2.fastq ...
2025-03-20 23:11:21.934869 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= test/reports/shortReadReport_1 ...
2025-03-20 23:12:16.164146 DEBUG::tools.R/traceMem: wired.mem=-77.010878 GiB
2025-03-20 23:13:16.230762 DEBUG::tools.R/traceMem: wired.mem=-70.074991 GiB
2025-03-20 23:14:16.297361 DEBUG::tools.R/traceMem: wired.mem=-75.277607 GiB
2025-03-20 23:15:16.365273 DEBUG::tools.R/traceMem: wired.mem=-71.632839 GiB
2025-03-20 23:16:16.431077 DEBUG::tools.R/traceMem: wired.mem=-66.120942 GiB
2025-03-20 23:17:16.497428 DEBUG::tools.R/traceMem: wired.mem=-68.754751 GiB
2025-03-20 23:18:16.562222 DEBUG::tools.R/traceMem: wired.mem=-62.663926 GiB
2025-03-20 23:19:16.627643 DEBUG::tools.R/traceMem: wired.mem=-67.676021 GiB
2025-03-20 23:20:16.693472 DEBUG::tools.R/traceMem: wired.mem=-56.781373 GiB
2025-03-20 23:21:16.759922 DEBUG::tools.R/traceMem: wired.mem=-68.638573 GiB
2025-03-20 23:22:16.826203 DEBUG::tools.R/traceMem: wired.mem=-69.694964 GiB
2025-03-20 23:23:16.893167 DEBUG::tools.R/traceMem: wired.mem=-69.620023 GiB
2025-03-20 23:24:16.959768 DEBUG::tools.R/traceMem: wired.mem=-71.935681 GiB
2025-03-20 23:25:16.993892 DEBUG::tools.R/traceMem: wired.mem=-67.519332 GiB
2025-03-20 23:26:17.060497 DEBUG::tools.R/traceMem: wired.mem=-60.709798 GiB
2025-03-20 23:27:17.128134 DEBUG::tools.R/traceMem: wired.mem=-70.060270 GiB
2025-03-20 23:28:17.196044 DEBUG::tools.R/traceMem: wired.mem=-73.827549 GiB
2025-03-20 23:29:17.261719 DEBUG::tools.R/traceMem: wired.mem=-75.482464 GiB
2025-03-20 23:30:17.326045 DEBUG::tools.R/traceMem: wired.mem=-79.015797 GiB
2025-03-20 23:31:17.389781 DEBUG::tools.R/traceMem: wired.mem=-71.674495 GiB
2025-03-20 23:32:17.454619 DEBUG::tools.R/traceMem: wired.mem=-74.892837 GiB
2025-03-20 23:33:17.463 DEBUG::tools.R/traceMem: wired.mem=-77.561356 GiB
2025-03-20 23:34:17.528676 DEBUG::tools.R/traceMem: wired.mem=-78.319100 GiB
2025-03-20 23:35:17.594089 DEBUG::tools.R/traceMem: wired.mem=-69.678998 GiB
2025-03-20 23:36:17.660426 DEBUG::tools.R/traceMem: wired.mem=-75.514421 GiB
2025-03-20 23:37:17.728381 DEBUG::tools.R/traceMem: wired.mem=-69.668905 GiB
2025-03-20 23:38:17.793999 DEBUG::tools.R/traceMem: wired.mem=-74.069541 GiB
2025-03-20 23:39:17.858658 DEBUG::tools.R/traceMem: wired.mem=-77.650092 GiB

Example timings

HTSeqGenie.Rcheck/HTSeqGenie-Ex.timings

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