Multiple platform build/check report for BioC 3.19 - CHECK results for HTSeqGenie on kunpeng2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"	4708
palomino3	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences"	4446
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"	4471
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences"	4426
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*

Package: HTSeqGenie

Version: 4.33.0

Command: /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:HTSeqGenie.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings HTSeqGenie_4.33.0.tar.gz

StartedAt: 2024-03-28 06:15:03 -0000 (Thu, 28 Mar 2024)

EndedAt: 2024-03-28 06:30:04 -0000 (Thu, 28 Mar 2024)

EllapsedTime: 901.7 seconds

RetCode: 0

Status: OK

CheckDir: HTSeqGenie.Rcheck

Warnings: 0

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### Running command:
###
###   /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:HTSeqGenie.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings HTSeqGenie_4.33.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/HTSeqGenie.Rcheck’
* using R Under development (unstable) (2024-03-19 r86153)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HTSeqGenie/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HTSeqGenie’ version ‘4.33.0’
* 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’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 7 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/HTSeqGenie.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL HTSeqGenie
###
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* installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/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)


R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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, 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/tmp/RtmppOEwKW/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/config/default-config.txt 
2024-03-28 06:22:21.331545 INFO::preprocessReads.R/preprocessReads: starting...
2024-03-28 06:22:21.340337 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-03-28 06:22:21.34574 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2024-03-28 06:22:21.348644 DEBUG::tools.R/processChunks: starting...
2024-03-28 06:22:24.727126 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-03-28 06:22:24.729184 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmppOEwKW/test.alignReads.158fd07407a43d/chunks/chunk_000001/logs/progress.log
2024-03-28 06:22:27.696418 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.049 minutes
2024-03-28 06:22:27.698449 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmppOEwKW/test.alignReads.158fd07407a43d/chunks/chunk_000002/logs/progress.log
2024-03-28 06:22:30.59006 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.048 minutes
2024-03-28 06:22:30.592232 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmppOEwKW/test.alignReads.158fd07407a43d/chunks/chunk_000003/logs/progress.log
2024-03-28 06:22:33.46203 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.048 minutes
2024-03-28 06:22:33.500892 DEBUG::tools.R/processChunks: done
2024-03-28 06:22:33.505729 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2024-03-28 06:22:33.508757 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.alignReads.158fd07407a43d/results/test_pe.adapter_contaminated_1.RData
2024-03-28 06:22:33.51252 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2024-03-28 06:22:33.514912 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.alignReads.158fd07407a43d/results/test_pe.adapter_contaminated_2.RData
2024-03-28 06:22:33.526829 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
2024-03-28 06:22:33.52988 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.alignReads.158fd07407a43d/results/test_pe.summary_preprocess.tab
2024-03-28 06:22:33.534148 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmppOEwKW/test.alignReads.158fd07407a43d/bams/processed.aligner_input_1.fastq ...
2024-03-28 06:22:33.540677 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmppOEwKW/test.alignReads.158fd07407a43d/bams/processed.aligner_input_2.fastq ...
2024-03-28 06:22:33.54644 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmppOEwKW/test.alignReads.158fd07407a43d/reports/shortReadReport_1 ...
2024-03-28 06:22:35.400311 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmppOEwKW/test.alignReads.158fd07407a43d/reports/shortReadReport_2 ...
2024-03-28 06:22:38.322418 INFO::preprocessReads.R/preprocessReads: done
2024-03-28 06:22:38.376878 INFO::alignReads.R/alignReads: starting alignment...
2024-03-28 06:22:38.383651 DEBUG::tools.R/processChunks: starting...
2024-03-28 06:22:42.823877 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-03-28 06:22:42.82616 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmppOEwKW/test.alignReads.158fd07407a43d/chunks/chunk_000001/logs/progress.log
2024-03-28 06:22:45.918485 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.052 minutes
2024-03-28 06:22:45.920868 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmppOEwKW/test.alignReads.158fd07407a43d/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.
2024-03-28 06:22:48.610952 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.045 minutes
2024-03-28 06:22:48.613311 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmppOEwKW/test.alignReads.158fd07407a43d/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.
2024-03-28 06:22:51.349051 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.046 minutes
2024-03-28 06:22:51.352606 DEBUG::tools.R/processChunks: done
2024-03-28 06:22:51.354665 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.
2024-03-28 06:22:51.683393 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2024-03-28 06:22:51.694892 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.alignReads.158fd07407a43d/results/test_pe.summary_alignment.tab
2024-03-28 06:22:51.705704 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.alignReads.158fd07407a43d/results/test_pe.summary_analyzed_bamstats.tab
2024-03-28 06:22:51.708297 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2024-03-28 06:22:51.982552 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.alignReads.158fd07407a43d/results/test_pe.summary_target_lengths.tab
2024-03-28 06:22:52.042979 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2024-03-28 06:22:52.044348 INFO::alignReads.R/alignReads: done
 done successfully.



Executing test function test.alignReads.sparsechunks  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmppOEwKW/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/config/default-config.txt 
2024-03-28 06:22:52.326513 INFO::preprocessReads.R/preprocessReads: starting...
2024-03-28 06:22:52.330152 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-03-28 06:22:52.41332 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 2 , totnbreads= 26 )
2024-03-28 06:22:52.420101 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-03-28 06:22:52.424492 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2024-03-28 06:22:52.427182 DEBUG::tools.R/processChunks: starting...
2024-03-28 06:22:57.139953 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-03-28 06:22:57.142083 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmppOEwKW/test.alignReads.sparsechunks.158fd03d34b986/chunks/chunk_000001/logs/progress.log
2024-03-28 06:22:59.995348 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.048 minutes
2024-03-28 06:22:59.997245 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmppOEwKW/test.alignReads.sparsechunks.158fd03d34b986/chunks/chunk_000002/logs/progress.log
2024-03-28 06:23:02.874797 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.048 minutes
2024-03-28 06:23:02.876922 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmppOEwKW/test.alignReads.sparsechunks.158fd03d34b986/chunks/chunk_000003/logs/progress.log
2024-03-28 06:23:05.816305 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.049 minutes
2024-03-28 06:23:05.818235 DEBUG::tools.R/processChunks: starting chunkid= 4 ; see logfile= /home/biocbuild/tmp/RtmppOEwKW/test.alignReads.sparsechunks.158fd03d34b986/chunks/chunk_000004/logs/progress.log
2024-03-28 06:23:08.639482 DEBUG::tools.R/processChunks: done with chunkid= 4 ; elapsed.time= 0.047 minutes
2024-03-28 06:23:08.683401 DEBUG::tools.R/processChunks: done
2024-03-28 06:23:08.688542 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2024-03-28 06:23:08.691922 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.alignReads.sparsechunks.158fd03d34b986/results/test_pe.adapter_contaminated_1.RData
2024-03-28 06:23:08.696377 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2024-03-28 06:23:08.699143 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.alignReads.sparsechunks.158fd03d34b986/results/test_pe.adapter_contaminated_2.RData
2024-03-28 06:23:08.713751 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
2024-03-28 06:23:08.716902 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.alignReads.sparsechunks.158fd03d34b986/results/test_pe.summary_preprocess.tab
2024-03-28 06:23:08.72188 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmppOEwKW/test.alignReads.sparsechunks.158fd03d34b986/bams/processed.aligner_input_1.fastq ...
2024-03-28 06:23:08.729226 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmppOEwKW/test.alignReads.sparsechunks.158fd03d34b986/bams/processed.aligner_input_2.fastq ...
2024-03-28 06:23:08.735059 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmppOEwKW/test.alignReads.sparsechunks.158fd03d34b986/reports/shortReadReport_1 ...
2024-03-28 06:23:10.679945 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmppOEwKW/test.alignReads.sparsechunks.158fd03d34b986/reports/shortReadReport_2 ...
2024-03-28 06:23:13.658652 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



Executing test function test.alignReadsOneSingleEnd  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmppOEwKW/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/config/default-config.txt 
2024-03-28 06:23:13.851729 INFO::alignReads.R/alignReadsChunk: running gsnap...
2024-03-28 06:23:13.857285 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/tmp/RtmppOEwKW/test.alignReadsOneSingleEnd.158fd036849489/bams/test.alignReads /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/test-data/unit_tests_1.fastq 2>&1
2024-03-28 06:23:14.01219 INFO::alignReads.R/createSummaryAlignment: counting unique bam reads...
2024-03-28 06:23:14.144532 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.alignReadsOneSingleEnd.158fd036849489/results/test.alignReads.summary_alignment.tab
2024-03-28 06:23:14.195561 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.alignReadsOneSingleEnd.158fd036849489/results/test.alignReads.summary_analyzed_bamstats.tab
2024-03-28 06:23:14.197839 INFO::alignReads.R/alignReadsChunk: done
 done successfully.



Executing test function test.annotateVariants  ... Timing stopped at: 0.002 0.002 0.004
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/tmp/RtmppOEwKW/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/config/default-config.txt 
2024-03-28 06:23:14.603412 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.genotype.158fd011e21f77/results/test_pe.coverage.RData
2024-03-28 06:23:14.605707 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.genotype.158fd011e21f77/results/test_pe.coverage.bw
2024-03-28 06:23:14.793293 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.genotype.158fd011e21f77/results/test_pe.summary_coverage.tab
2024-03-28 06:23:14.796074 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2024-03-28 06:23:27.895316 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2024-03-28 06:23:28.026857 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2024-03-28 06:23:28.059207 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2024-03-28 06:23:28.061307 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.genotype.158fd011e21f77/results/test_pe.raw_variants.RData
2024-03-28 06:23:28.064425 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.genotype.158fd011e21f77/results/test_pe.filtered_variants.RData
2024-03-28 06:23:28.066407 INFO::analyzeVariants.R/wrap.callVariants: ...done
2024-03-28 06:23:28.068209 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2024-03-28 06:23:28.679154 INFO::analyzeVariants.R/writeVCF: ...done
2024-03-28 06:23:28.680936 INFO::analyzeVariants.R/.callGenotypes: calling genotypes...
2024-03-28 06:24:58.167427 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2024-03-28 06:24:58.831261 INFO::analyzeVariants.R/writeVCF: ...done
2024-03-28 06:24:58.832617 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/tmp/RtmppOEwKW/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/config/default-config.txt 
2024-03-28 06:24:59.437761 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2024-03-28 06:25:12.672223 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2024-03-28 06:25:12.789738 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2024-03-28 06:25:12.814901 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2024-03-28 06:25:12.81684 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.wrap.callVariants.158fd068964d5a/results/test_pe.raw_variants.RData
2024-03-28 06:25:12.819946 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.wrap.callVariants.158fd068964d5a/results/test_pe.filtered_variants.RData
2024-03-28 06:25:12.821825 INFO::analyzeVariants.R/wrap.callVariants: ...done
 done successfully.



Executing test function test.wrap.callVariants.filters  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmppOEwKW/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/config/default-config.txt 
2024-03-28 06:25:13.017311 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2024-03-28 06:25:26.056997 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2024-03-28 06:25:26.144842 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2024-03-28 06:25:26.169715 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2024-03-28 06:25:26.171673 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.wrap.callVariants.filters.158fd053e08d9c/results/test_pe.raw_variants.RData
2024-03-28 06:25:26.17478 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.wrap.callVariants.filters.158fd053e08d9c/results/test_pe.filtered_variants.RData
2024-03-28 06:25:26.176556 INFO::analyzeVariants.R/wrap.callVariants: ...done
2024-03-28 06:25:26.178546 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2024-03-28 06:25:39.089259 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2024-03-28 06:25:39.149459 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2024-03-28 06:25:39.176416 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2024-03-28 06:25:39.178722 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.wrap.callVariants.filters.158fd053e08d9c/results/test_pe.raw_variants.RData
2024-03-28 06:25:39.182442 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.wrap.callVariants.filters.158fd053e08d9c/results/test_pe.filtered_variants.RData
2024-03-28 06:25:39.185298 INFO::analyzeVariants.R/wrap.callVariants: ...done
 done successfully.



Executing test function test.wrap.callVariants.which  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmppOEwKW/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/config/default-config.txt 
2024-03-28 06:25:39.498811 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2024-03-28 06:25:39.504193 INFO::analyzeVariants.R/buildTallyParam: restricting variant calls using 'which'
2024-03-28 06:25:43.319279 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2024-03-28 06:25:43.434035 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2024-03-28 06:25:43.459004 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2024-03-28 06:25:43.460989 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.wrap.callVariants.which.158fd05038e75b/results/test_pe.raw_variants.RData
2024-03-28 06:25:43.463403 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.wrap.callVariants.which.158fd05038e75b/results/test_pe.filtered_variants.RData
2024-03-28 06:25:43.465259 INFO::analyzeVariants.R/wrap.callVariants: ...done
 done successfully.



Executing test function test.writeVCF.NULL  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmppOEwKW/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/config/default-config.txt 
2024-03-28 06:25:43.665041 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2024-03-28 06:25:43.666889 INFO::analyzeVariants.R/writeVCF: ...done
 done successfully.



Executing test function test.writeVCF.vcfStat  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmppOEwKW/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/config/default-config.txt 
2024-03-28 06:25:43.90365 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2024-03-28 06:25:44.231205 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  ... 2024-03-28 06:27:01.784821 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/ogitwnld/merged/results/bla.coverage.RData
2024-03-28 06:27:01.787917 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/RtmppOEwKW/ogitwnld/merged/results/bla.coverage.bw
2024-03-28 06:27:01.903945 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/ogitwnld/merged/results/bla.summary_coverage.tab
 done successfully.



Executing test function test.mergeCoverage.sparse  ... 2024-03-28 06:27:03.266849 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/myzcnxab/merged/results/bla.coverage.RData
2024-03-28 06:27:03.269163 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/RtmppOEwKW/myzcnxab/merged/results/bla.coverage.bw
2024-03-28 06:27:03.286488 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/myzcnxab/merged/results/bla.summary_coverage.tab
 done successfully.



Executing test function test.checkConfig.analyzeVariants  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmppOEwKW/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4-devel-2024.03.20/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/tmp/RtmppOEwKW/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmppOEwKW/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmppOEwKW/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmppOEwKW/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/config/default-config.txt 
 done successfully.



Executing test function test.checkConfig.alignReads  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmppOEwKW/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmppOEwKW/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmppOEwKW/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmppOEwKW/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4-devel-2024.03.20/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/tmp/RtmppOEwKW/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/config/default-config.txt 
2024-03-28 06:27:04.945645 INFO::detectRRNA.R/detectRRNA: searching for rRNA contamination...
2024-03-28 06:27:04.947345 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/tmp/RtmppOEwKW/test.detectRRNA.158fd03c20769e/bams/rRNA_contam/input1.fastq
2024-03-28 06:27:04.952668 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/tmp/RtmppOEwKW/test.detectRRNA.158fd03c20769e/bams/rRNA_contam/test_se /home/biocbuild/tmp/RtmppOEwKW/test.detectRRNA.158fd03c20769e/bams/rRNA_contam/input1.fastq 2>&1
2024-03-28 06:27:05.065971 INFO::detectRRNA.R/detectRRNA: contaminated fraction= 1
2024-03-28 06:27:05.06745 INFO::detectRRNA.R/detectRRNA: done
 done successfully.



Executing test function test.detectRRNA.paired_end  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmppOEwKW/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/config/default-config.txt 
2024-03-28 06:27:05.236422 INFO::detectRRNA.R/detectRRNA: searching for rRNA contamination...
2024-03-28 06:27:05.237973 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/tmp/RtmppOEwKW/test.detectRRNA.paired_end.158fd048e01042/bams/rRNA_contam/input1.fastq
2024-03-28 06:27:05.240558 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/tmp/RtmppOEwKW/test.detectRRNA.paired_end.158fd048e01042/bams/rRNA_contam/input2.fastq
2024-03-28 06:27:05.244352 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/tmp/RtmppOEwKW/test.detectRRNA.paired_end.158fd048e01042/bams/rRNA_contam/test_pe /home/biocbuild/tmp/RtmppOEwKW/test.detectRRNA.paired_end.158fd048e01042/bams/rRNA_contam/input1.fastq -a paired /home/biocbuild/tmp/RtmppOEwKW/test.detectRRNA.paired_end.158fd048e01042/bams/rRNA_contam/input2.fastq 2>&1
2024-03-28 06:27:05.529225 INFO::detectRRNA.R/detectRRNA: contaminated fraction= 1
2024-03-28 06:27:05.530822 INFO::detectRRNA.R/detectRRNA: done
 done successfully.



Executing test function test.getRRNAIds  ... 2024-03-28 06:27:05.56227 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/tmp/RtmppOEwKW/test_get_rRNA_idswrqtpzdc/test_pe /home/biocbuild/tmp/RtmppOEwKW/test_get_rRNA_idswrqtpzdc/1.fastq -a paired /home/biocbuild/tmp/RtmppOEwKW/test_get_rRNA_idswrqtpzdc/2.fastq 2>&1
 done successfully.



Executing test function test.getRRNAIds_random  ... 2024-03-28 06:27:05.878096 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/tmp/RtmppOEwKW/test_get_rRNAIds_randomfvpbecos/test_pe /home/biocbuild/tmp/RtmppOEwKW/test_get_rRNAIds_randomfvpbecos/1.fastq 2>&1
 done successfully.



Executing test function test.filterByLength  ... 2024-03-28 06:27:06.062609 INFO::filterQuality.R/filterQuality: filterByLength...
2024-03-28 06:27:06.064705 INFO::filterQuality.R/filterByLength: fraction of filtered short reads= 0.5
2024-03-28 06:27:06.066069 INFO::filterQuality.R/filterByLength: done
2024-03-28 06:27:06.173083 INFO::filterQuality.R/filterQuality: filterByLength...
2024-03-28 06:27:06.174372 INFO::filterQuality.R/filterByLength: fraction of filtered short reads= 1
2024-03-28 06:27:06.175689 INFO::filterQuality.R/filterByLength: done
 done successfully.



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



Executing test function test.trimTailsByQuality  ... 2024-03-28 06:27:06.253605 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2024-03-28 06:27:06.267098 INFO::preprocessReads.R/preprocessReadsChunk: done
2024-03-28 06:27:06.268685 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2024-03-28 06:27:06.275622 INFO::preprocessReads.R/preprocessReadsChunk: done
2024-03-28 06:27:06.277226 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2024-03-28 06:27:06.284357 INFO::preprocessReads.R/preprocessReadsChunk: done
2024-03-28 06:27:06.285974 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2024-03-28 06:27:06.293045 INFO::preprocessReads.R/preprocessReadsChunk: done
 done successfully.



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



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



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



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



Executing test function test.gatk  ... Timing stopped at: 0 0 0.001
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: 0.001 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/tmp/RtmppOEwKW/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/config/default-config.txt 
2024-03-28 06:27:06.666066 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-03-28 06:27:06.669926 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4-devel-2024.03.20/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/tmp/RtmppOEwKW/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/config/default-config.txt 
2024-03-28 06:27:06.866116 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-03-28 06:27:06.961461 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2024-03-28 06:27:06.965447 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-03-28 06:27:06.968963 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4-devel-2024.03.20/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/tmp/RtmppOEwKW/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/config/default-config.txt 
2024-03-28 06:27:07.228886 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4-devel-2024.03.20/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/tmp/RtmppOEwKW/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/config/default-config.txt 
2024-03-28 06:27:07.419783 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4-devel-2024.03.20/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/tmp/RtmppOEwKW/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/config/default-config.txt 
2024-03-28 06:27:07.641244 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-03-28 06:27:07.702305 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2024-03-28 06:27:07.706057 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-03-28 06:27:07.709696 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmppOEwKW/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/config/default-config.txt 
2024-03-28 06:27:07.974485 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-03-28 06:27:08.034348 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2024-03-28 06:27:08.038165 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-03-28 06:27:08.041745 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4-devel-2024.03.20/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/tmp/RtmppOEwKW/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/config/default-config.txt 
 done successfully.



Executing test function test.mergeLanes  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmppOEwKW/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/config/default-config.txt 
2024-03-28 06:27:08.886842 INFO::preprocessReads.R/preprocessReads: starting...
2024-03-28 06:27:08.893348 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-03-28 06:27:08.897892 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2024-03-28 06:27:08.900671 DEBUG::tools.R/processChunks: starting...
2024-03-28 06:27:12.24924 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-03-28 06:27:12.251334 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/chunks/chunk_000001/logs/progress.log
2024-03-28 06:27:14.991183 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.046 minutes
2024-03-28 06:27:14.993105 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/chunks/chunk_000002/logs/progress.log
2024-03-28 06:27:17.774976 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.046 minutes
2024-03-28 06:27:17.776892 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/chunks/chunk_000003/logs/progress.log
2024-03-28 06:27:20.543435 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.046 minutes
2024-03-28 06:27:20.596989 DEBUG::tools.R/processChunks: done
2024-03-28 06:27:20.600659 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2024-03-28 06:27:20.603054 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/results/test_pe.adapter_contaminated_1.RData
2024-03-28 06:27:20.606015 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2024-03-28 06:27:20.608277 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/results/test_pe.adapter_contaminated_2.RData
2024-03-28 06:27:20.61897 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
2024-03-28 06:27:20.621687 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/results/test_pe.summary_preprocess.tab
2024-03-28 06:27:20.625424 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/bams/processed.aligner_input_1.fastq ...
2024-03-28 06:27:20.632457 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/bams/processed.aligner_input_2.fastq ...
2024-03-28 06:27:20.63855 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/reports/shortReadReport_1 ...
2024-03-28 06:27:22.528196 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/reports/shortReadReport_2 ...
2024-03-28 06:27:24.098583 INFO::preprocessReads.R/preprocessReads: done
2024-03-28 06:27:24.172258 INFO::alignReads.R/alignReads: starting alignment...
2024-03-28 06:27:24.177407 DEBUG::tools.R/processChunks: starting...
2024-03-28 06:27:29.036802 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-03-28 06:27:29.039445 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/chunks/chunk_000001/logs/progress.log
2024-03-28 06:27:31.644616 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.043 minutes
2024-03-28 06:27:31.646792 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/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.
2024-03-28 06:27:34.304886 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.044 minutes
2024-03-28 06:27:34.307125 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/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.
2024-03-28 06:27:36.921644 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.044 minutes
2024-03-28 06:27:36.924926 DEBUG::tools.R/processChunks: done
2024-03-28 06:27:36.926793 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.
2024-03-28 06:27:37.223547 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2024-03-28 06:27:37.233794 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/results/test_pe.summary_alignment.tab
2024-03-28 06:27:37.243703 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/results/test_pe.summary_analyzed_bamstats.tab
2024-03-28 06:27:37.246218 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2024-03-28 06:27:37.491371 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/results/test_pe.summary_target_lengths.tab
2024-03-28 06:27:37.551866 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2024-03-28 06:27:37.553302 INFO::alignReads.R/alignReads: done
2024-03-28 06:27:37.627172 INFO::countGenomicFeatures.R/countGenomicFeatures: starting...
2024-03-28 06:27:37.64608 DEBUG::tools.R/processChunks: starting...
2024-03-28 06:27:41.053008 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-03-28 06:27:41.055283 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/chunks/chunk_000001/logs/progress.log
2024-03-28 06:27:43.654032 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.043 minutes
2024-03-28 06:27:43.656379 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/chunks/chunk_000002/logs/progress.log
2024-03-28 06:27:46.22493 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.043 minutes
2024-03-28 06:27:46.227316 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/chunks/chunk_000003/logs/progress.log
2024-03-28 06:27:48.798339 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.043 minutes
2024-03-28 06:27:48.801829 DEBUG::tools.R/processChunks: done
2024-03-28 06:27:48.804184 INFO::countGenomicFeatures.R/mergeCounts: starting...
2024-03-28 06:27:48.822481 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/results/test_pe.counts_exon.tab
2024-03-28 06:27:48.837138 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/results/test_pe.counts_exon_disjoint.tab
2024-03-28 06:27:48.846746 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/results/test_pe.counts_gene.tab
2024-03-28 06:27:48.854433 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/results/test_pe.counts_gene_coding.tab
2024-03-28 06:27:48.862478 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/results/test_pe.counts_gene_exonic.tab
2024-03-28 06:27:48.870436 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/results/test_pe.counts_intergenic.tab
2024-03-28 06:27:48.883317 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/results/test_pe.counts_intron.tab
2024-03-28 06:27:48.887235 INFO::countGenomicFeatures.R/mergeCounts: done
2024-03-28 06:27:48.895289 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/results/test_pe.summary_counts.tab
2024-03-28 06:27:48.897754 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2024-03-28 06:27:49.250898 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2024-03-28 06:27:49.252432 INFO::countGenomicFeatures.R/countGenomicFeatures: done...
2024-03-28 06:27:49.328954 INFO::coverage.R/calculateCoverage: starting...
2024-03-28 06:27:49.333434 DEBUG::tools.R/processChunks: starting...
2024-03-28 06:27:52.847903 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-03-28 06:27:52.850397 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/chunks/chunk_000001/logs/progress.log
2024-03-28 06:27:55.047595 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.037 minutes
2024-03-28 06:27:55.049779 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/chunks/chunk_000002/logs/progress.log
2024-03-28 06:27:57.249317 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.037 minutes
2024-03-28 06:27:57.251599 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/chunks/chunk_000003/logs/progress.log
2024-03-28 06:27:59.442513 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.036 minutes
2024-03-28 06:27:59.445819 DEBUG::tools.R/processChunks: done
2024-03-28 06:28:01.179682 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/results/test_pe.coverage.RData
2024-03-28 06:28:01.181486 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/results/test_pe.coverage.bw
2024-03-28 06:28:01.19686 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/results/test_pe.summary_coverage.tab
2024-03-28 06:28:01.198672 INFO::coverage.R/calculateCoverage: done
2024-03-28 06:28:01.200875 INFO::analyzeVariants/analyzeVariants: starting ...
2024-03-28 06:28:01.277753 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2024-03-28 06:28:05.04472 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2024-03-28 06:28:05.166549 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2024-03-28 06:28:05.193628 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2024-03-28 06:28:05.195623 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/results/test_pe.raw_variants.RData
2024-03-28 06:28:05.198119 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/results/test_pe.filtered_variants.RData
2024-03-28 06:28:05.200191 INFO::analyzeVariants.R/wrap.callVariants: ...done
2024-03-28 06:28:05.201915 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2024-03-28 06:28:05.530204 INFO::analyzeVariants.R/writeVCF: ...done
2024-03-28 06:28:05.678229 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/results/test_pe.summary_variants.tab
2024-03-28 06:28:05.681104 INFO::analyzeVariants/analyzeVariants: done
2024-03-28 06:28:05.685081 INFO::Pipeline run successful.
2024-03-28 06:28:05.860195 INFO::mergeLanes.R/doMergeLanes: starting...
2024-03-28 06:28:05.865657 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2024-03-28 06:28:05.868888 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/merged/results/merged.adapter_contaminated_1.RData
2024-03-28 06:28:05.873314 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2024-03-28 06:28:05.876373 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/merged/results/merged.adapter_contaminated_2.RData
2024-03-28 06:28:05.891337 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
2024-03-28 06:28:05.894708 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/merged/results/merged.summary_preprocess.tab
2024-03-28 06:28:05.897777 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.
2024-03-28 06:28:06.236063 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2024-03-28 06:28:06.245566 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/merged/results/merged.summary_alignment.tab
2024-03-28 06:28:06.256572 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/merged/results/merged.summary_analyzed_bamstats.tab
2024-03-28 06:28:06.259498 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2024-03-28 06:28:06.521153 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/merged/results/merged.summary_target_lengths.tab
2024-03-28 06:28:06.584971 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2024-03-28 06:28:06.626047 INFO::countGenomicFeatures.R/mergeCounts: starting...
2024-03-28 06:28:06.649941 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/merged/results/merged.counts_exon.tab
2024-03-28 06:28:06.665562 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/merged/results/merged.counts_exon_disjoint.tab
2024-03-28 06:28:06.675319 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/merged/results/merged.counts_gene.tab
2024-03-28 06:28:06.6833 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/merged/results/merged.counts_gene_coding.tab
2024-03-28 06:28:06.691338 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/merged/results/merged.counts_gene_exonic.tab
2024-03-28 06:28:06.699699 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/merged/results/merged.counts_intergenic.tab
2024-03-28 06:28:06.7145 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/merged/results/merged.counts_intron.tab
2024-03-28 06:28:06.718547 INFO::countGenomicFeatures.R/mergeCounts: done
2024-03-28 06:28:06.727439 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/merged/results/merged.summary_counts.tab
2024-03-28 06:28:06.730052 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2024-03-28 06:28:07.010108 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2024-03-28 06:28:09.266975 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/merged/results/merged.coverage.RData
2024-03-28 06:28:09.270136 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/merged/results/merged.coverage.bw
2024-03-28 06:28:09.287422 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/merged/results/merged.summary_coverage.tab
2024-03-28 06:28:09.327288 INFO::analyzeVariants/analyzeVariants: starting ...
2024-03-28 06:28:09.41467 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2024-03-28 06:28:13.113709 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2024-03-28 06:28:13.222683 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2024-03-28 06:28:13.247422 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2024-03-28 06:28:13.249332 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/merged/results/merged.raw_variants.RData
2024-03-28 06:28:13.251975 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/merged/results/merged.filtered_variants.RData
2024-03-28 06:28:13.25401 INFO::analyzeVariants.R/wrap.callVariants: ...done
2024-03-28 06:28:13.25562 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2024-03-28 06:28:13.58207 INFO::analyzeVariants.R/writeVCF: ...done
2024-03-28 06:28:13.726858 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.mergeLanes.158fd05dfc2e0e/merged/results/merged.summary_variants.tab
2024-03-28 06:28:13.729588 INFO::analyzeVariants/analyzeVariants: done
2024-03-28 06:28:13.732877 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/tmp/RtmppOEwKW/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/config/default-config.txt 
2024-03-28 06:28:14.074273 INFO::preprocessReads.R/preprocessReads: starting...
2024-03-28 06:28:14.09638 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-03-28 06:28:14.116751 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2024-03-28 06:28:14.120001 DEBUG::tools.R/processChunks: starting...
2024-03-28 06:28:17.532293 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-03-28 06:28:17.534288 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmppOEwKW/test.preprocessReads.158fd07908d1d6/chunks/chunk_000001/logs/progress.log
2024-03-28 06:28:20.348352 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.047 minutes
2024-03-28 06:28:20.401832 DEBUG::tools.R/processChunks: done
2024-03-28 06:28:20.404779 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2024-03-28 06:28:20.406881 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.preprocessReads.158fd07908d1d6/results/test_pe.adapter_contaminated_1.RData
2024-03-28 06:28:20.409224 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2024-03-28 06:28:20.411243 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.preprocessReads.158fd07908d1d6/results/test_pe.adapter_contaminated_2.RData
2024-03-28 06:28:20.419408 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
2024-03-28 06:28:20.421922 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.preprocessReads.158fd07908d1d6/results/test_pe.summary_preprocess.tab
2024-03-28 06:28:20.4249 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmppOEwKW/test.preprocessReads.158fd07908d1d6/bams/processed.aligner_input_1.fastq ...
2024-03-28 06:28:20.431027 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmppOEwKW/test.preprocessReads.158fd07908d1d6/bams/processed.aligner_input_2.fastq ...
2024-03-28 06:28:20.436614 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmppOEwKW/test.preprocessReads.158fd07908d1d6/reports/shortReadReport_1 ...
2024-03-28 06:28:22.333306 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmppOEwKW/test.preprocessReads.158fd07908d1d6/reports/shortReadReport_2 ...
2024-03-28 06:28:23.905509 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



Executing test function test.preprocessReads.minichunks  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmppOEwKW/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/config/default-config.txt 
2024-03-28 06:28:24.165955 INFO::preprocessReads.R/preprocessReads: starting...
2024-03-28 06:28:24.173117 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-03-28 06:28:24.177883 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2024-03-28 06:28:24.180974 DEBUG::tools.R/processChunks: starting...
2024-03-28 06:28:28.928843 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-03-28 06:28:28.930987 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmppOEwKW/test.preprocessReads.minichunks.158fd022efbf70/chunks/chunk_000001/logs/progress.log
2024-03-28 06:28:31.66048 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.045 minutes
2024-03-28 06:28:31.662481 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmppOEwKW/test.preprocessReads.minichunks.158fd022efbf70/chunks/chunk_000002/logs/progress.log
2024-03-28 06:28:34.435231 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.046 minutes
2024-03-28 06:28:34.437372 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmppOEwKW/test.preprocessReads.minichunks.158fd022efbf70/chunks/chunk_000003/logs/progress.log
2024-03-28 06:28:37.216061 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.046 minutes
2024-03-28 06:28:37.268728 DEBUG::tools.R/processChunks: done
2024-03-28 06:28:37.272393 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2024-03-28 06:28:37.274754 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.preprocessReads.minichunks.158fd022efbf70/results/test_pe.adapter_contaminated_1.RData
2024-03-28 06:28:37.277704 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2024-03-28 06:28:37.279971 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.preprocessReads.minichunks.158fd022efbf70/results/test_pe.adapter_contaminated_2.RData
2024-03-28 06:28:37.290754 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
2024-03-28 06:28:37.293477 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.preprocessReads.minichunks.158fd022efbf70/results/test_pe.summary_preprocess.tab
2024-03-28 06:28:37.297149 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmppOEwKW/test.preprocessReads.minichunks.158fd022efbf70/bams/processed.aligner_input_1.fastq ...
2024-03-28 06:28:37.304556 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmppOEwKW/test.preprocessReads.minichunks.158fd022efbf70/bams/processed.aligner_input_2.fastq ...
2024-03-28 06:28:37.31058 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmppOEwKW/test.preprocessReads.minichunks.158fd022efbf70/reports/shortReadReport_1 ...
2024-03-28 06:28:39.200488 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmppOEwKW/test.preprocessReads.minichunks.158fd022efbf70/reports/shortReadReport_2 ...
2024-03-28 06:28:40.758704 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



Executing test function test.preprocessReads_single_end  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmppOEwKW/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/config/default-config.txt 
2024-03-28 06:28:41.053209 INFO::preprocessReads.R/preprocessReads: starting...
2024-03-28 06:28:41.07534 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-03-28 06:28:41.07855 DEBUG::tools.R/processChunks: starting...
2024-03-28 06:28:44.456377 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-03-28 06:28:44.458486 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmppOEwKW/test.preprocessReads_single_end.158fd06a750535/chunks/chunk_000001/logs/progress.log
2024-03-28 06:28:46.926894 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.041 minutes
2024-03-28 06:28:46.976063 DEBUG::tools.R/processChunks: done
2024-03-28 06:28:46.979599 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2024-03-28 06:28:46.982177 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.preprocessReads_single_end.158fd06a750535/results/test_se.adapter_contaminated_1.RData
2024-03-28 06:28:46.99158 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
2024-03-28 06:28:46.994208 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.preprocessReads_single_end.158fd06a750535/results/test_se.summary_preprocess.tab
2024-03-28 06:28:46.997059 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmppOEwKW/test.preprocessReads_single_end.158fd06a750535/bams/processed.aligner_input_1.fastq ...
2024-03-28 06:28:47.003025 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmppOEwKW/test.preprocessReads_single_end.158fd06a750535/reports/shortReadReport_1 ...
2024-03-28 06:28:48.849687 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/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/config/default-config.txt 
2024-03-28 06:28:49.582031 INFO::preprocessReads.R/preprocessReads: starting...
2024-03-28 06:28:49.604599 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/extdata/H1993_TP53_subset2500_1.fastq.gz
2024-03-28 06:28:49.626148 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/extdata/H1993_TP53_subset2500_2.fastq.gz
2024-03-28 06:28:49.629073 DEBUG::tools.R/processChunks: starting...
2024-03-28 06:28:53.13492 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-03-28 06:28:53.136977 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= test/chunks/chunk_000001/logs/progress.log
2024-03-28 06:28:56.104851 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.049 minutes
2024-03-28 06:28:56.160231 DEBUG::tools.R/processChunks: done
2024-03-28 06:28:56.163306 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2024-03-28 06:28:56.165415 INFO::io.R/saveWithID: saving file= test/results/test.adapter_contaminated_1.RData
2024-03-28 06:28:56.167776 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2024-03-28 06:28:56.169777 INFO::io.R/saveWithID: saving file= test/results/test.adapter_contaminated_2.RData
2024-03-28 06:28:56.178144 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
2024-03-28 06:28:56.180626 INFO::io.R/saveWithID: saving file= test/results/test.summary_preprocess.tab
2024-03-28 06:28:56.183696 INFO::preprocessReads.R/mergePreprocessedReads: merging file= test/bams/processed.aligner_input_1.fastq ...
2024-03-28 06:28:56.191186 INFO::preprocessReads.R/mergePreprocessedReads: merging file= test/bams/processed.aligner_input_2.fastq ...
2024-03-28 06:28:56.198075 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= test/reports/shortReadReport_1 ...
2024-03-28 06:28:58.306221 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= test/reports/shortReadReport_2 ...
2024-03-28 06:29:00.036053 INFO::preprocessReads.R/preprocessReads: done
2024-03-28 06:29:00.110942 INFO::alignReads.R/alignReads: starting alignment...
2024-03-28 06:29:00.115574 DEBUG::tools.R/processChunks: starting...
2024-03-28 06:29:03.606965 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-03-28 06:29:03.609148 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= test/chunks/chunk_000001/logs/progress.log
[bam_translate] PG tag "A" on read "HISEQ1:109:D093LACXX:4:2205:16499:6611" 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 "HISEQ1:109:D093LACXX:4:1206:17367:135118" 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 "HISEQ1:109:D093LACXX:4:1304:1838:53573" 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 "HISEQ1:109:D093LACXX:4:2303:2956:116587" 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 "M" on read "HISEQ1:109:D093LACXX:4:2205:16499:6611" 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 "T" on read "HISEQ1:109:D093LACXX:4:1206:20028:108227" 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 "T" on read "HISEQ1:109:D093LACXX:4:1207:19518:143960" 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 "T" on read "HISEQ1:109:D093LACXX:4:2207:4065:173048" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2024-03-28 06:29:09.656318 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.101 minutes
2024-03-28 06:29:09.659608 DEBUG::tools.R/processChunks: done
2024-03-28 06:29:09.661393 INFO::alignReads.R/mergeBAMsAcrossDirs: starting...
2024-03-28 06:29:09.695374 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2024-03-28 06:29:09.703334 INFO::io.R/saveWithID: saving file= test/results/test.summary_alignment.tab
2024-03-28 06:29:09.710646 INFO::io.R/saveWithID: saving file= test/results/test.summary_analyzed_bamstats.tab
2024-03-28 06:29:09.71331 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2024-03-28 06:29:09.896652 INFO::io.R/saveWithID: saving file= test/results/test.summary_target_lengths.tab
2024-03-28 06:29:09.955622 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2024-03-28 06:29:09.956989 INFO::alignReads.R/alignReads: done
2024-03-28 06:29:10.033482 INFO::countGenomicFeatures.R/countGenomicFeatures: starting...
2024-03-28 06:29:10.051847 DEBUG::tools.R/processChunks: starting...
2024-03-28 06:29:14.862509 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-03-28 06:29:14.864929 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= test/chunks/chunk_000001/logs/progress.log
2024-03-28 06:29:17.551003 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.045 minutes
2024-03-28 06:29:17.554283 DEBUG::tools.R/processChunks: done
2024-03-28 06:29:17.556301 INFO::countGenomicFeatures.R/mergeCounts: starting...
2024-03-28 06:29:17.567767 INFO::io.R/saveWithID: saving file= test/results/test.counts_exon.tab
2024-03-28 06:29:17.577456 INFO::io.R/saveWithID: saving file= test/results/test.counts_exon_disjoint.tab
2024-03-28 06:29:17.584684 INFO::io.R/saveWithID: saving file= test/results/test.counts_gene.tab
2024-03-28 06:29:17.589869 INFO::io.R/saveWithID: saving file= test/results/test.counts_gene_coding.tab
2024-03-28 06:29:17.594915 INFO::io.R/saveWithID: saving file= test/results/test.counts_gene_exonic.tab
2024-03-28 06:29:17.599923 INFO::io.R/saveWithID: saving file= test/results/test.counts_intergenic.tab
2024-03-28 06:29:17.6077 INFO::io.R/saveWithID: saving file= test/results/test.counts_intron.tab
2024-03-28 06:29:17.611711 INFO::countGenomicFeatures.R/mergeCounts: done
2024-03-28 06:29:17.616462 INFO::io.R/saveWithID: saving file= test/results/test.summary_counts.tab
2024-03-28 06:29:17.618848 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2024-03-28 06:29:17.885499 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2024-03-28 06:29:17.886948 INFO::countGenomicFeatures.R/countGenomicFeatures: done...
2024-03-28 06:29:17.97366 INFO::coverage.R/calculateCoverage: starting...
2024-03-28 06:29:17.978146 DEBUG::tools.R/processChunks: starting...
2024-03-28 06:29:22.448174 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-03-28 06:29:22.450588 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= test/chunks/chunk_000001/logs/progress.log
2024-03-28 06:29:24.848603 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.04 minutes
2024-03-28 06:29:24.851956 DEBUG::tools.R/processChunks: done
2024-03-28 06:29:28.615535 INFO::io.R/saveWithID: saving file= test/results/test.coverage.RData
2024-03-28 06:29:28.617643 INFO::coverage.R/saveCoverage: saving file= test/results/test.coverage.bw
2024-03-28 06:29:28.724964 INFO::io.R/saveWithID: saving file= test/results/test.summary_coverage.tab
2024-03-28 06:29:28.726883 INFO::coverage.R/calculateCoverage: done
2024-03-28 06:29:28.728693 INFO::analyzeVariants/analyzeVariants: starting ...
2024-03-28 06:29:28.810395 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2024-03-28 06:29:42.399673 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2024-03-28 06:29:42.522208 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2024-03-28 06:29:42.54661 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2024-03-28 06:29:42.548524 INFO::io.R/saveWithID: saving file= test/results/test.raw_variants.RData
2024-03-28 06:29:42.551558 INFO::io.R/saveWithID: saving file= test/results/test.filtered_variants.RData
2024-03-28 06:29:42.553357 INFO::analyzeVariants.R/wrap.callVariants: ...done
2024-03-28 06:29:42.554781 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2024-03-28 06:29:42.872407 INFO::analyzeVariants.R/writeVCF: ...done
2024-03-28 06:29:43.014884 INFO::io.R/saveWithID: saving file= test/results/test.summary_variants.tab
2024-03-28 06:29:43.01756 INFO::analyzeVariants/analyzeVariants: done
2024-03-28 06:29:43.022933 INFO::Pipeline run successful.
 done successfully.



Executing test function test.calculateTargetLength  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmppOEwKW/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/config/default-config.txt 
2024-03-28 06:29:43.302741 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmppOEwKW/test.calcTargetLengths.158fd07b14ddbf/results/test_pe.summary_target_lengths.tab
 done successfully.



Executing test function test.sclapply  ...  done successfully.



Executing test function test.tryKeepTraceback  ...  done successfully.



Executing test function test.truncateReads  ...  done successfully.



Executing test function test.truncateReads.trim5  ...  done successfully.

RUNIT TEST PROTOCOL -- Thu Mar 28 06:29:58 2024 
*********************************************** 
Number of test functions: 61 
Number of deactivated test functions: 10 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
HTSeqGenie unit testing - 61 test functions, 0 errors, 0 failures



Details 
*************************** 
Test Suite: HTSeqGenie unit testing 
Test function regexp: ^test.+ 
Test file regexp: ^runit.+\.[rR]$ 
Involved directory: 
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/unitTests 
--------------------------- 
Test file: /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/unitTests/runit.alignReads.R 
test.alignReads: (2 checks) ... OK (32.47 seconds)
test.alignReads.sparsechunks: (2 checks) ... OK (21.61 seconds)
test.alignReadsOneSingleEnd: (2 checks) ... OK (0.54 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/unitTests/runit.analyzeVariants.R 
test.annotateVariants : DEACTIVATED, Skipped annotateVariants() test
test.callVariantsVariantTools.genotype: (2 checks) ... OK (105.06 seconds)
test.wrap.callVariants: (4 checks) ... OK (13.56 seconds)
test.wrap.callVariants.filters: (2 checks) ... OK (26.36 seconds)
test.wrap.callVariants.which: (1 checks) ... OK (4.28 seconds)
test.writeVCF.NULL: (1 checks) ... OK (0.2 seconds)
test.writeVCF.vcfStat: (4 checks) ... OK (0.72 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/unitTests/runit.bamUtils.R 
test.isFirstFragment: (5 checks) ... OK (0 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/unitTests/runit.buildGenomicFeatures.R 
test.buildCountsGRangesList: (3 checks) ... OK (40.53 seconds)
test.generateSingleGeneDERs: (4 checks) ... OK (34.18 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/unitTests/runit.calculateCoverage.R 
test.computeCoverage: (9 checks) ... OK (0.98 seconds)
test.isSparse: (5 checks) ... OK (0.14 seconds)
test.mergeCoverage: (1 checks) ... OK (1.68 seconds)
test.mergeCoverage.sparse: (2 checks) ... OK (1.41 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/unitTests/runit.checkConfig.R 
test.checkConfig.analyzeVariants: (5 checks) ... OK (0.21 seconds)
test.findTemplate: (5 checks) ... OK (0.01 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/unitTests/runit.config.R 
test.checkConfig: (5 checks) ... OK (0.39 seconds)
test.checkConfig.alignReads: (5 checks) ... OK (0.46 seconds)
test.getConfig: (14 checks) ... OK (0 seconds)
test.loadConfig: (2 checks) ... OK (0 seconds)
test.parseDCF: (7 checks) ... OK (0 seconds)
test.updateConfig: (1 checks) ... OK (0 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/unitTests/runit.detectAdapterContam.R 
test.getAdapterSeqs: (5 checks) ... OK (0.05 seconds)
test.isAdapter: (5 checks) ... OK (0.16 seconds)
test.isAdapter3.primeEnd: (1 checks) ... OK (0.13 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/unitTests/runit.detectRRNA.R 
test.detectRRNA: (1 checks) ... OK (0.32 seconds)
test.detectRRNA.paired_end: (1 checks) ... OK (0.46 seconds)
test.getRRNAIds: (1 checks) ... OK (0.31 seconds)
test.getRRNAIds_random: (1 checks) ... OK (0.21 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/unitTests/runit.filterQuality.R 
test.filterByLength: (2 checks) ... OK (0.12 seconds)
test.isAboveQualityThresh: (3 checks) ... OK (0.06 seconds)
test.trimTailsByQuality: (4 checks) ... OK (0.05 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/unitTests/runit.gatk.R 
test.callVariantsGATK : DEACTIVATED, callVariantsGATK() tests need gatk.path option set
test.callVariantsGATK.withFiltering : DEACTIVATED, callVariantsGATK() tests need gatk.path option set
test.checkGATKJar : DEACTIVATED, checkGATKJar() test needs gatk.path option set
test.excludeVariantsByRegion: (3 checks) ... OK (0.22 seconds)
test.gatk : DEACTIVATED, gatk() tests need gatk.path option set
test.realignIndels : DEACTIVATED, test.realignIndels() tests need gatk.path option set
test.realignIndelsGATK : DEACTIVATED, realignIndelsGATK() tests need gatk.path option set
test.realignIndelsGATK.parallel : DEACTIVATED, realignIndelsGATK() tests need gatk.path option set
test_zipUp: (3 checks) ... OK (0 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/unitTests/runit.io.R 
test.FastQStreamer.getReads.pefq: (1 checks) ... OK (0.2 seconds)
test.FastQStreamer.getReads.pefq.subsample: (1 checks) ... OK (0.35 seconds)
test.FastQStreamer.getReads.segz: (1 checks) ... OK (0.2 seconds)
test.FastQStreamer.getReads.truncated: (1 checks) ... OK (0.18 seconds)
test.FastQStreamer.subsampler.isdeterministic: (3 checks) ... OK (0.67 seconds)
test.createTmpDir: (4 checks) ... OK (0 seconds)
test.detectQualityInFASTQFile: (3 checks) ... OK (0.15 seconds)
test.getObjectFilename: (4 checks) ... OK (0.01 seconds)
test.safeUnlink: (2 checks) ... OK (0.01 seconds)
test.writeAudit: (0 checks) ... OK (0.21 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/unitTests/runit.mergeLanes.R 
test.mergeLanes: (6 checks) ... OK (65.26 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/unitTests/runit.picard.R 
test.markDuplicates : DEACTIVATED, Skipped markDuplicates() test
test.markDuplicates_w_outfile : DEACTIVATED, Skipped markDuplicates() test
--------------------------- 
Test file: /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/unitTests/runit.preprocessReads.R 
test.preprocessReads: (5 checks) ... OK (10.12 seconds)
test.preprocessReads.minichunks: (5 checks) ... OK (16.85 seconds)
test.preprocessReads_single_end: (5 checks) ... OK (8.09 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/unitTests/runit.readRNASeqEnds.R 
test.readRNASeqEnds: (6 checks) ... OK (0.11 seconds)
test.readRNASeqEnds.dupmark: (2 checks) ... OK (0.13 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/unitTests/runit.reportPipelineQA.R 
test.how_many: (3 checks) ... OK (0 seconds)
test.plotDF: (3 checks) ... OK (0.14 seconds)
test.relativeBarPlot: (2 checks) ... OK (0.05 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/unitTests/runit.runPipeline.R 
test.runPipeline: (1 checks) ... OK (53.73 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/unitTests/runit.targetLengths.R 
test.calculateTargetLength: (4 checks) ... OK (0.28 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/unitTests/runit.tools.R 
test.sclapply: (10 checks) ... OK (15.22 seconds)
test.tryKeepTraceback: (3 checks) ... OK (0.01 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/HTSeqGenie/unitTests/runit.trimReads.R 
test.truncateReads: (7 checks) ... OK (0.08 seconds)
test.truncateReads.trim5: (15 checks) ... OK (0.25 seconds) 

runTests.R: OK !
There were 50 or more warnings (use warnings() to see the first 50)
> 
> proc.time()
   user  system elapsed 
325.602 106.524 479.547

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

CHECK results for HTSeqGenie on kunpeng2

Summary

Command output

Installation output

Tests output

Example timings