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

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4764
palomino8	Windows Server 2022 Datacenter	x64	4.4.3 (2025-02-28 ucrt) -- "Trophy Case"	4495
merida1	macOS 12.7.5 Monterey	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4522
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.3 (2025-02-28) -- "Trophy Case"	4449
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.3 (2025-02-28) -- "Trophy Case"	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*

CHECK results for HTSeqGenie on taishan

To the developers/maintainers of the HTSeqGenie package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HTSeqGenie.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results

Summary

Package: HTSeqGenie

Version: 4.36.0

Command: /home/biocbuild/R/R/bin/R CMD check --install=check:HTSeqGenie.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings HTSeqGenie_4.36.0.tar.gz

StartedAt: 2025-04-01 07:25:13 -0000 (Tue, 01 Apr 2025)

EndedAt: 2025-04-01 08:05:14 -0000 (Tue, 01 Apr 2025)

EllapsedTime: 2400.9 seconds

RetCode: None

Status: TIMEOUT

CheckDir: HTSeqGenie.Rcheck

Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:HTSeqGenie.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings HTSeqGenie_4.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/HTSeqGenie.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HTSeqGenie/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HTSeqGenie’ version ‘4.36.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘HTSeqGenie’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘ShortRead:::.set_omp_threads’ ‘gmapR:::..gsnap’ ‘gmapR:::GeneGenome’
  ‘gmapR:::checkPackageInstalled’ ‘gmapR:::getDefaultGmapGenomePath’
  ‘gmapR:::getGeneRoi’ ‘gmapR:::subsetRegion’ ‘parallel:::mckill’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .Call(ShortRead:::.set_omp_threads, ...)
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
.makePreprocessAlignPlots: no visible binding for global variable
  ‘data’
.plot.in.out.min.max.readlength: no visible global function definition
  for ‘median’
FastQStreamer.init: no visible binding for '<<-' assignment to
  ‘FastQStreamer.lfqs’
FastQStreamer.init: no visible binding for '<<-' assignment to
  ‘FastQStreamer.chunkid’
FastQStreamer.init: no visible binding for '<<-' assignment to
  ‘FastQStreamer.subsampling_filter’
FastQStreamer.init: no visible binding for '<<-' assignment to
  ‘FastQStreamer.max_nbchunks’
addHandler: no visible binding for '<<-' assignment to
  ‘logging.handlers’
addHandler: no visible binding for global variable ‘logging.handlers’
addHandler: no visible binding for '<<-' assignment to ‘logging.file’
buildAnyFastaGenome: no visible global function definition for ‘getSeq’
buildGenomicFeaturesFromTxDb: no visible global function definition for
  ‘gaps’
buildGenomicFeaturesFromTxDb: no visible global function definition for
  ‘ranges’
buildTP53FastaGenome: no visible global function definition for
  ‘getSeq’
buildTallyParam: no visible global function definition for ‘seqinfo’
computeCoverage: no visible global function definition for ‘resize’
computeCoverage: no visible global function definition for ‘coverage’
estimateCutoffs : <anonymous>: no visible binding for global variable
  ‘quantile’
getGenomeSegments: no visible global function definition for ‘seqinfo’
hashVariants: no visible global function definition for ‘ranges’
isAboveQualityThresh: no visible global function definition for ‘Views’
isAboveQualityThresh: no visible global function definition for
  ‘viewMeans’
listIterator.init: no visible binding for '<<-' assignment to
  ‘listIterator.n’
listIterator.init: no visible binding for '<<-' assignment to
  ‘listIterator.x’
logReset: no visible binding for '<<-' assignment to ‘logging.handlers’
logReset: no visible binding for '<<-' assignment to ‘logging.loglevel’
logReset: no visible binding for '<<-' assignment to ‘logging.file’
loglevel: no visible binding for global variable ‘logging.loglevel’
loglevel: no visible binding for global variable ‘logging.handlers’
processChunks : tracefun: no visible binding for global variable
  ‘sjobs’
processChunks : tracefun: no visible binding for global variable
  ‘chunkid’
setLevel: no visible binding for '<<-' assignment to ‘logging.loglevel’
statCountFeatures: no visible global function definition for ‘quantile’
truncateReads: no visible global function definition for ‘subseq’
vcfStat: no visible global function definition for ‘quantile’
writeToFile: no visible binding for global variable ‘logging.file’
Undefined global functions or variables:
  Views chunkid coverage data gaps getSeq logging.file logging.handlers
  logging.loglevel median quantile ranges resize seqinfo sjobs subseq
  viewMeans
Consider adding
  importFrom("stats", "median", "quantile")
  importFrom("utils", "data")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) calculateTargetLengths.Rd:17: Lost braces; missing escapes or markup?
    17 | Target length table and writes two files in {save_dir}/reports/images/TargetLenghts.[pdf|png]"
       |                                             ^
checkRd: (-1) initLog.Rd:18: Lost braces; missing escapes or markup?
    18 | Setup logging file in {save_dir}/progress.log
       |                       ^
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
Documented arguments not in \usage in Rd file 'findVariantFile.Rd':
  ‘dir_path’

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

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

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

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

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

Installation output

HTSeqGenie.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL HTSeqGenie
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.3/site-library’
* installing *source* package ‘HTSeqGenie’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (HTSeqGenie)

Tests output

HTSeqGenie.Rcheck/tests/doRUnit.Rout


R version 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: 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, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    findMatches

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

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

Attaching package: 'MatrixGenerics'

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

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

Loading required package: Biobase
Welcome to Bioconductor

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


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians

Loading required package: VariantAnnotation

Attaching package: 'VariantAnnotation'

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

    tabulate

> 
> source(getPackageFile("unitTests/runTests.R"))
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
did not source anything in dirname= ./R 


Executing test function test.alignReads  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpnbguOA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.3/site-library/HTSeqGenie/config/default-config.txt 
2025-04-01 07:31:48.098179 INFO::preprocessReads.R/preprocessReads: starting...
2025-04-01 07:31:48.107288 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4.3/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-04-01 07:31:48.112682 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4.3/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-04-01 07:31:48.115401 DEBUG::tools.R/processChunks: starting...
2025-04-01 07:31:50.87368 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-04-01 07:31:50.875632 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpnbguOA/test.alignReads.3203da715d2019/chunks/chunk_000001/logs/progress.log
2025-04-01 07:31:53.722038 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.047 minutes
2025-04-01 07:31:53.72387 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmpnbguOA/test.alignReads.3203da715d2019/chunks/chunk_000002/logs/progress.log
2025-04-01 07:31:56.544387 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.047 minutes
2025-04-01 07:31:56.546404 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmpnbguOA/test.alignReads.3203da715d2019/chunks/chunk_000003/logs/progress.log
2025-04-01 07:31:59.380013 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.047 minutes
2025-04-01 07:31:59.419124 DEBUG::tools.R/processChunks: done
2025-04-01 07:31:59.424242 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-04-01 07:31:59.427579 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.alignReads.3203da715d2019/results/test_pe.adapter_contaminated_1.RData
2025-04-01 07:31:59.431652 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-04-01 07:31:59.434227 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.alignReads.3203da715d2019/results/test_pe.adapter_contaminated_2.RData
2025-04-01 07:31:59.446877 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=26 highqual_reads=25 adapter_contam=1 read_length=75 rRNA_contam_reads=0 processed_reads=25 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-04-01 07:31:59.449917 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.alignReads.3203da715d2019/results/test_pe.summary_preprocess.tab
2025-04-01 07:31:59.45429 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpnbguOA/test.alignReads.3203da715d2019/bams/processed.aligner_input_1.fastq ...
2025-04-01 07:31:59.460837 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpnbguOA/test.alignReads.3203da715d2019/bams/processed.aligner_input_2.fastq ...
2025-04-01 07:31:59.466619 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpnbguOA/test.alignReads.3203da715d2019/reports/shortReadReport_1 ...
2025-04-01 07:32:01.340918 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpnbguOA/test.alignReads.3203da715d2019/reports/shortReadReport_2 ...
2025-04-01 07:32:02.87068 INFO::preprocessReads.R/preprocessReads: done
2025-04-01 07:32:02.928077 INFO::alignReads.R/alignReads: starting alignment...
2025-04-01 07:32:02.93388 DEBUG::tools.R/processChunks: starting...
2025-04-01 07:32:05.389872 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-04-01 07:32:05.391959 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpnbguOA/test.alignReads.3203da715d2019/chunks/chunk_000001/logs/progress.log
2025-04-01 07:32:08.489103 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.052 minutes
2025-04-01 07:32:08.49121 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmpnbguOA/test.alignReads.3203da715d2019/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.
2025-04-01 07:32:11.135676 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.044 minutes
2025-04-01 07:32:11.137872 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmpnbguOA/test.alignReads.3203da715d2019/chunks/chunk_000003/logs/progress.log
[bam_translate] PG tag "A" on read "highqualPE1GeneFusionMidExonDiffChrPE2MultimappingIntergenic:1:1:1:25#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-04-01 07:32:13.830961 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.045 minutes
2025-04-01 07:32:13.834404 DEBUG::tools.R/processChunks: done
2025-04-01 07:32:13.83638 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 "T" 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 "highqualPE1UniqueUtrPE2MultimappingIntergenic:1:1:1:18#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInOneTxOfMultiTxGene:1:1:1:15#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-04-01 07:32:14.204556 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-04-01 07:32:14.22217 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.alignReads.3203da715d2019/results/test_pe.summary_alignment.tab
2025-04-01 07:32:14.233497 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.alignReads.3203da715d2019/results/test_pe.summary_analyzed_bamstats.tab
2025-04-01 07:32:14.236111 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-04-01 07:32:14.538225 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.alignReads.3203da715d2019/results/test_pe.summary_target_lengths.tab
2025-04-01 07:32:14.600032 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-04-01 07:32:14.601364 INFO::alignReads.R/alignReads: done
 done successfully.



Executing test function test.alignReads.sparsechunks  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpnbguOA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.3/site-library/HTSeqGenie/config/default-config.txt 
2025-04-01 07:32:14.898288 INFO::preprocessReads.R/preprocessReads: starting...
2025-04-01 07:32:14.901729 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/R/R-4.4.3/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-04-01 07:32:14.992004 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 2 , totnbreads= 26 )
2025-04-01 07:32:14.999147 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4.3/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-04-01 07:32:15.003703 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4.3/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-04-01 07:32:15.00663 DEBUG::tools.R/processChunks: starting...
2025-04-01 07:32:17.778085 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-04-01 07:32:17.780161 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpnbguOA/test.alignReads.sparsechunks.3203da6551e83e/chunks/chunk_000001/logs/progress.log
2025-04-01 07:32:20.602844 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.047 minutes
2025-04-01 07:32:20.604673 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmpnbguOA/test.alignReads.sparsechunks.3203da6551e83e/chunks/chunk_000002/logs/progress.log
2025-04-01 07:32:23.376688 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.046 minutes
2025-04-01 07:32:23.378602 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmpnbguOA/test.alignReads.sparsechunks.3203da6551e83e/chunks/chunk_000003/logs/progress.log
2025-04-01 07:32:26.27304 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.048 minutes
2025-04-01 07:32:26.274883 DEBUG::tools.R/processChunks: starting chunkid= 4 ; see logfile= /home/biocbuild/tmp/RtmpnbguOA/test.alignReads.sparsechunks.3203da6551e83e/chunks/chunk_000004/logs/progress.log
2025-04-01 07:32:29.044557 DEBUG::tools.R/processChunks: done with chunkid= 4 ; elapsed.time= 0.046 minutes
2025-04-01 07:32:29.083815 DEBUG::tools.R/processChunks: done
2025-04-01 07:32:29.088631 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-04-01 07:32:29.092227 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.alignReads.sparsechunks.3203da6551e83e/results/test_pe.adapter_contaminated_1.RData
2025-04-01 07:32:29.096911 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-04-01 07:32:29.099753 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.alignReads.sparsechunks.3203da6551e83e/results/test_pe.adapter_contaminated_2.RData
2025-04-01 07:32:29.114436 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=2 highqual_reads=1 adapter_contam=0 read_length=75 rRNA_contam_reads=0 processed_reads=1 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-04-01 07:32:29.117597 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.alignReads.sparsechunks.3203da6551e83e/results/test_pe.summary_preprocess.tab
2025-04-01 07:32:29.122678 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpnbguOA/test.alignReads.sparsechunks.3203da6551e83e/bams/processed.aligner_input_1.fastq ...
2025-04-01 07:32:29.129906 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpnbguOA/test.alignReads.sparsechunks.3203da6551e83e/bams/processed.aligner_input_2.fastq ...
2025-04-01 07:32:29.135647 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpnbguOA/test.alignReads.sparsechunks.3203da6551e83e/reports/shortReadReport_1 ...
2025-04-01 07:32:31.022893 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpnbguOA/test.alignReads.sparsechunks.3203da6551e83e/reports/shortReadReport_2 ...
2025-04-01 07:32:32.500164 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



Executing test function test.alignReadsOneSingleEnd  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpnbguOA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.3/site-library/HTSeqGenie/config/default-config.txt 
2025-04-01 07:32:32.705891 INFO::alignReads.R/alignReadsChunk: running gsnap...
2025-04-01 07:32:32.712449 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/RtmpnbguOA/test.alignReadsOneSingleEnd.3203da2462c78d/bams/test.alignReads /home/biocbuild/R/R-4.4.3/site-library/HTSeqGenie/test-data/unit_tests_1.fastq 2>&1
2025-04-01 07:32:32.840272 INFO::alignReads.R/createSummaryAlignment: counting unique bam reads...
2025-04-01 07:32:32.980925 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.alignReadsOneSingleEnd.3203da2462c78d/results/test.alignReads.summary_alignment.tab
2025-04-01 07:32:33.029515 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.alignReadsOneSingleEnd.3203da2462c78d/results/test.alignReads.summary_analyzed_bamstats.tab
2025-04-01 07:32:33.031557 INFO::alignReads.R/alignReadsChunk: done
 done successfully.



Executing test function test.annotateVariants  ... Timing stopped at: 0.003 0 0.003
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/RtmpnbguOA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.3/site-library/HTSeqGenie/config/default-config.txt 
2025-04-01 07:32:33.432933 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.genotype.3203da685ce22c/results/test_pe.coverage.RData
2025-04-01 07:32:33.435291 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.genotype.3203da685ce22c/results/test_pe.coverage.bw
2025-04-01 07:32:33.590986 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.genotype.3203da685ce22c/results/test_pe.summary_coverage.tab
2025-04-01 07:32:33.593579 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-04-01 07:32:45.042797 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-04-01 07:32:45.188374 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-04-01 07:32:45.217989 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-04-01 07:32:45.220321 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.genotype.3203da685ce22c/results/test_pe.raw_variants.RData
2025-04-01 07:32:45.223771 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.genotype.3203da685ce22c/results/test_pe.filtered_variants.RData
2025-04-01 07:32:45.226058 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-04-01 07:32:45.228019 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-04-01 07:32:45.907241 INFO::analyzeVariants.R/writeVCF: ...done
2025-04-01 07:32:45.908995 INFO::analyzeVariants.R/.callGenotypes: calling genotypes...
2025-04-01 07:34:11.232456 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-04-01 07:34:11.846282 INFO::analyzeVariants.R/writeVCF: ...done
2025-04-01 07:34:11.847697 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/RtmpnbguOA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.3/site-library/HTSeqGenie/config/default-config.txt 
2025-04-01 07:34:12.509626 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-04-01 07:34:24.124061 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-04-01 07:34:24.239978 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-04-01 07:34:24.264602 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-04-01 07:34:24.266584 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.wrap.callVariants.3203da11c52cf4/results/test_pe.raw_variants.RData
2025-04-01 07:34:24.2698 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.wrap.callVariants.3203da11c52cf4/results/test_pe.filtered_variants.RData
2025-04-01 07:34:24.271718 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/RtmpnbguOA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.3/site-library/HTSeqGenie/config/default-config.txt 
2025-04-01 07:34:24.453702 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-04-01 07:34:35.910063 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-04-01 07:34:36.002074 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-04-01 07:34:36.029121 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-04-01 07:34:36.031101 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.wrap.callVariants.filters.3203da6ed9bcb0/results/test_pe.raw_variants.RData
2025-04-01 07:34:36.034231 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.wrap.callVariants.filters.3203da6ed9bcb0/results/test_pe.filtered_variants.RData
2025-04-01 07:34:36.036032 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-04-01 07:34:36.03841 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-04-01 07:34:47.308897 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-04-01 07:34:47.367654 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-04-01 07:34:47.392702 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-04-01 07:34:47.39476 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.wrap.callVariants.filters.3203da6ed9bcb0/results/test_pe.raw_variants.RData
2025-04-01 07:34:47.401362 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.wrap.callVariants.filters.3203da6ed9bcb0/results/test_pe.filtered_variants.RData
2025-04-01 07:34:47.403952 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/RtmpnbguOA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.3/site-library/HTSeqGenie/config/default-config.txt 
2025-04-01 07:34:47.781883 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-04-01 07:34:47.783999 INFO::analyzeVariants.R/buildTallyParam: restricting variant calls using 'which'
2025-04-01 07:34:51.979629 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-04-01 07:34:52.089204 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-04-01 07:34:52.11285 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-04-01 07:34:52.114809 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.wrap.callVariants.which.3203da60d3f215/results/test_pe.raw_variants.RData
2025-04-01 07:34:52.117305 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.wrap.callVariants.which.3203da60d3f215/results/test_pe.filtered_variants.RData
2025-04-01 07:34:52.119141 INFO::analyzeVariants.R/wrap.callVariants: ...done
 done successfully.



Executing test function test.writeVCF.NULL  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpnbguOA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.3/site-library/HTSeqGenie/config/default-config.txt 
2025-04-01 07:34:52.367402 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-04-01 07:34:52.369197 INFO::analyzeVariants.R/writeVCF: ...done
 done successfully.



Executing test function test.writeVCF.vcfStat  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpnbguOA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.3/site-library/HTSeqGenie/config/default-config.txt 
2025-04-01 07:34:54.231041 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-04-01 07:34:54.508589 INFO::analyzeVariants.R/writeVCF: ...done
 done successfully.



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



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



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



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



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



Executing test function test.mergeCoverage  ... 2025-04-01 07:36:00.092149 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/yzjqrwnu/merged/results/bla.coverage.RData
2025-04-01 07:36:00.095603 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/RtmpnbguOA/yzjqrwnu/merged/results/bla.coverage.bw
2025-04-01 07:36:00.177978 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/yzjqrwnu/merged/results/bla.summary_coverage.tab
 done successfully.



Executing test function test.mergeCoverage.sparse  ... 2025-04-01 07:36:01.202575 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/hxmcafks/merged/results/bla.coverage.RData
2025-04-01 07:36:01.204578 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/RtmpnbguOA/hxmcafks/merged/results/bla.coverage.bw
2025-04-01 07:36:01.218914 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/hxmcafks/merged/results/bla.summary_coverage.tab
 done successfully.



Executing test function test.checkConfig.analyzeVariants  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpnbguOA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.3/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/RtmpnbguOA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.3/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpnbguOA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.3/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpnbguOA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.3/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpnbguOA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.3/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/RtmpnbguOA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.3/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpnbguOA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.3/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpnbguOA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.3/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpnbguOA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.3/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/RtmpnbguOA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.3/site-library/HTSeqGenie/config/default-config.txt 
2025-04-01 07:36:02.710928 INFO::detectRRNA.R/detectRRNA: searching for rRNA contamination...
2025-04-01 07:36:02.712424 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/tmp/RtmpnbguOA/test.detectRRNA.3203da12a7a848/bams/rRNA_contam/input1.fastq
2025-04-01 07:36:02.716801 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/RtmpnbguOA/test.detectRRNA.3203da12a7a848/bams/rRNA_contam/test_se /home/biocbuild/tmp/RtmpnbguOA/test.detectRRNA.3203da12a7a848/bams/rRNA_contam/input1.fastq 2>&1
2025-04-01 07:36:02.844276 INFO::detectRRNA.R/detectRRNA: contaminated fraction= 1
2025-04-01 07:36:02.845724 INFO::detectRRNA.R/detectRRNA: done
 done successfully.



Executing test function test.detectRRNA.paired_end  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpnbguOA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.3/site-library/HTSeqGenie/config/default-config.txt 
2025-04-01 07:36:02.998164 INFO::detectRRNA.R/detectRRNA: searching for rRNA contamination...
2025-04-01 07:36:02.999463 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/tmp/RtmpnbguOA/test.detectRRNA.paired_end.3203da4ebe84cc/bams/rRNA_contam/input1.fastq
2025-04-01 07:36:03.001583 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/tmp/RtmpnbguOA/test.detectRRNA.paired_end.3203da4ebe84cc/bams/rRNA_contam/input2.fastq
2025-04-01 07:36:03.004686 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/RtmpnbguOA/test.detectRRNA.paired_end.3203da4ebe84cc/bams/rRNA_contam/test_pe /home/biocbuild/tmp/RtmpnbguOA/test.detectRRNA.paired_end.3203da4ebe84cc/bams/rRNA_contam/input1.fastq -a paired /home/biocbuild/tmp/RtmpnbguOA/test.detectRRNA.paired_end.3203da4ebe84cc/bams/rRNA_contam/input2.fastq 2>&1
2025-04-01 07:36:03.276577 INFO::detectRRNA.R/detectRRNA: contaminated fraction= 1
2025-04-01 07:36:03.278048 INFO::detectRRNA.R/detectRRNA: done
 done successfully.



Executing test function test.getRRNAIds  ... 2025-04-01 07:36:03.305904 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/RtmpnbguOA/test_get_rRNA_idsyrnqzmas/test_pe /home/biocbuild/tmp/RtmpnbguOA/test_get_rRNA_idsyrnqzmas/1.fastq -a paired /home/biocbuild/tmp/RtmpnbguOA/test_get_rRNA_idsyrnqzmas/2.fastq 2>&1
 done successfully.



Executing test function test.getRRNAIds_random  ... 2025-04-01 07:36:03.644875 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/RtmpnbguOA/test_get_rRNAIds_randomcsvfupog/test_pe /home/biocbuild/tmp/RtmpnbguOA/test_get_rRNAIds_randomcsvfupog/1.fastq 2>&1
 done successfully.



Executing test function test.filterByLength  ... 2025-04-01 07:36:03.801413 INFO::filterQuality.R/filterQuality: filterByLength...
2025-04-01 07:36:03.803329 INFO::filterQuality.R/filterByLength: fraction of filtered short reads= 0.5
2025-04-01 07:36:03.804528 INFO::filterQuality.R/filterByLength: done
2025-04-01 07:36:03.869673 INFO::filterQuality.R/filterQuality: filterByLength...
2025-04-01 07:36:03.870897 INFO::filterQuality.R/filterByLength: fraction of filtered short reads= 1
2025-04-01 07:36:03.872053 INFO::filterQuality.R/filterByLength: done
 done successfully.



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



Executing test function test.trimTailsByQuality  ... 2025-04-01 07:36:03.943068 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-04-01 07:36:03.955692 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-04-01 07:36:03.957303 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-04-01 07:36:03.96377 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-04-01 07:36:03.965254 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-04-01 07:36:03.9716 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-04-01 07:36:03.973067 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-04-01 07:36:03.979445 INFO::preprocessReads.R/preprocessReadsChunk: done
 done successfully.



Executing test function test.callVariantsGATK  ... Timing stopped at: 0 0 0.001
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: 0.001 0 0
Error in DEACTIVATED("gatk() tests need gatk.path option set") : 
  gatk() tests need gatk.path option set
 done successfully.



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



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



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



Executing test function test_zipUp  ...  done successfully.



Executing test function test.FastQStreamer.getReads.pefq  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpnbguOA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.3/site-library/HTSeqGenie/config/default-config.txt 
2025-04-01 07:36:04.331963 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4.3/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-04-01 07:36:04.335213 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4.3/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/RtmpnbguOA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.3/site-library/HTSeqGenie/config/default-config.txt 
2025-04-01 07:36:04.553438 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/R/R-4.4.3/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-04-01 07:36:04.643337 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-04-01 07:36:04.647191 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4.3/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-04-01 07:36:04.650326 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4.3/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/RtmpnbguOA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.3/site-library/HTSeqGenie/config/default-config.txt 
2025-04-01 07:36:04.897979 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4.3/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/RtmpnbguOA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.3/site-library/HTSeqGenie/config/default-config.txt 
2025-04-01 07:36:05.075401 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4.3/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/RtmpnbguOA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.3/site-library/HTSeqGenie/config/default-config.txt 
2025-04-01 07:36:05.242181 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/R/R-4.4.3/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-04-01 07:36:05.294939 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-04-01 07:36:05.298444 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4.3/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-04-01 07:36:05.3016 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4.3/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpnbguOA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.3/site-library/HTSeqGenie/config/default-config.txt 
2025-04-01 07:36:05.531142 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/R/R-4.4.3/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-04-01 07:36:05.585678 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-04-01 07:36:05.589145 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4.3/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-04-01 07:36:05.592225 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4.3/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/RtmpnbguOA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.3/site-library/HTSeqGenie/config/default-config.txt 
 done successfully.



Executing test function test.mergeLanes  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpnbguOA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.3/site-library/HTSeqGenie/config/default-config.txt 
2025-04-01 07:36:06.388801 INFO::preprocessReads.R/preprocessReads: starting...
2025-04-01 07:36:06.395932 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4.3/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-04-01 07:36:06.400545 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4.3/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-04-01 07:36:06.403759 DEBUG::tools.R/processChunks: starting...
2025-04-01 07:36:09.081087 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-04-01 07:36:09.083116 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/chunks/chunk_000001/logs/progress.log
2025-04-01 07:36:11.737894 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.044 minutes
2025-04-01 07:36:11.739913 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/chunks/chunk_000002/logs/progress.log
2025-04-01 07:36:14.395009 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.044 minutes
2025-04-01 07:36:14.396931 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/chunks/chunk_000003/logs/progress.log
2025-04-01 07:36:17.065482 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.044 minutes
2025-04-01 07:36:17.112232 DEBUG::tools.R/processChunks: done
2025-04-01 07:36:17.115804 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-04-01 07:36:17.118119 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/results/test_pe.adapter_contaminated_1.RData
2025-04-01 07:36:17.120951 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-04-01 07:36:17.12315 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/results/test_pe.adapter_contaminated_2.RData
2025-04-01 07:36:17.133893 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=26 highqual_reads=25 adapter_contam=1 read_length=75 rRNA_contam_reads=0 processed_reads=25 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-04-01 07:36:17.136451 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/results/test_pe.summary_preprocess.tab
2025-04-01 07:36:17.139953 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/bams/processed.aligner_input_1.fastq ...
2025-04-01 07:36:17.146206 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/bams/processed.aligner_input_2.fastq ...
2025-04-01 07:36:17.151663 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/reports/shortReadReport_1 ...
2025-04-01 07:36:18.992483 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/reports/shortReadReport_2 ...
2025-04-01 07:36:20.440321 INFO::preprocessReads.R/preprocessReads: done
2025-04-01 07:36:20.513757 INFO::alignReads.R/alignReads: starting alignment...
2025-04-01 07:36:20.518867 DEBUG::tools.R/processChunks: starting...
2025-04-01 07:36:23.343798 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-04-01 07:36:23.346254 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/chunks/chunk_000001/logs/progress.log
2025-04-01 07:36:25.945599 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.043 minutes
2025-04-01 07:36:25.947687 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/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.
2025-04-01 07:36:28.562312 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.044 minutes
2025-04-01 07:36:28.564449 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/chunks/chunk_000003/logs/progress.log
[bam_translate] PG tag "A" on read "highqualPE1GeneFusionMidExonDiffChrPE2MultimappingIntergenic:1:1:1:25#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-04-01 07:36:31.201901 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.044 minutes
2025-04-01 07:36:31.205322 DEBUG::tools.R/processChunks: done
2025-04-01 07:36:31.207416 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 "T" 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 "highqualPE1UniqueUtrPE2MultimappingIntergenic:1:1:1:18#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInOneTxOfMultiTxGene:1:1:1:15#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-04-01 07:36:31.509644 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-04-01 07:36:31.52057 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/results/test_pe.summary_alignment.tab
2025-04-01 07:36:31.531008 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/results/test_pe.summary_analyzed_bamstats.tab
2025-04-01 07:36:31.533715 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-04-01 07:36:31.791728 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/results/test_pe.summary_target_lengths.tab
2025-04-01 07:36:31.853688 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-04-01 07:36:31.85513 INFO::alignReads.R/alignReads: done
2025-04-01 07:36:31.927614 INFO::countGenomicFeatures.R/countGenomicFeatures: starting...
2025-04-01 07:36:31.948538 DEBUG::tools.R/processChunks: starting...
2025-04-01 07:36:34.615869 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-04-01 07:36:34.618127 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/chunks/chunk_000001/logs/progress.log
2025-04-01 07:36:37.160522 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.042 minutes
2025-04-01 07:36:37.16271 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/chunks/chunk_000002/logs/progress.log
2025-04-01 07:36:39.707731 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.042 minutes
2025-04-01 07:36:39.710017 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/chunks/chunk_000003/logs/progress.log
2025-04-01 07:36:42.283773 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.043 minutes
2025-04-01 07:36:42.287246 DEBUG::tools.R/processChunks: done
2025-04-01 07:36:42.289533 INFO::countGenomicFeatures.R/mergeCounts: starting...
2025-04-01 07:36:42.307459 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/results/test_pe.counts_exon.tab
2025-04-01 07:36:42.3223 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/results/test_pe.counts_exon_disjoint.tab
2025-04-01 07:36:42.331861 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/results/test_pe.counts_gene.tab
2025-04-01 07:36:42.339629 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/results/test_pe.counts_gene_coding.tab
2025-04-01 07:36:42.347346 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/results/test_pe.counts_gene_exonic.tab
2025-04-01 07:36:42.355021 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/results/test_pe.counts_intergenic.tab
2025-04-01 07:36:42.366737 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/results/test_pe.counts_intron.tab
2025-04-01 07:36:42.370337 INFO::countGenomicFeatures.R/mergeCounts: done
2025-04-01 07:36:42.37779 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/results/test_pe.summary_counts.tab
2025-04-01 07:36:42.380061 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2025-04-01 07:36:42.733044 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2025-04-01 07:36:42.734245 INFO::countGenomicFeatures.R/countGenomicFeatures: done...
2025-04-01 07:36:42.813597 INFO::coverage.R/calculateCoverage: starting...
2025-04-01 07:36:42.818061 DEBUG::tools.R/processChunks: starting...
2025-04-01 07:36:45.46172 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-04-01 07:36:45.46381 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/chunks/chunk_000001/logs/progress.log
2025-04-01 07:36:47.649656 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.036 minutes
2025-04-01 07:36:47.65181 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/chunks/chunk_000002/logs/progress.log
2025-04-01 07:36:49.841553 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.036 minutes
2025-04-01 07:36:49.843757 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/chunks/chunk_000003/logs/progress.log
2025-04-01 07:36:52.036103 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.036 minutes
2025-04-01 07:36:52.039432 DEBUG::tools.R/processChunks: done
2025-04-01 07:36:53.825462 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/results/test_pe.coverage.RData
2025-04-01 07:36:53.827362 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/results/test_pe.coverage.bw
2025-04-01 07:36:53.842887 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/results/test_pe.summary_coverage.tab
2025-04-01 07:36:53.844706 INFO::coverage.R/calculateCoverage: done
2025-04-01 07:36:53.847055 INFO::analyzeVariants/analyzeVariants: starting ...
2025-04-01 07:36:53.922679 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-04-01 07:36:57.169218 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-04-01 07:36:57.280416 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-04-01 07:36:57.305693 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-04-01 07:36:57.307763 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/results/test_pe.raw_variants.RData
2025-04-01 07:36:57.310336 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/results/test_pe.filtered_variants.RData
2025-04-01 07:36:57.312309 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-04-01 07:36:57.314029 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-04-01 07:36:57.649859 INFO::analyzeVariants.R/writeVCF: ...done
2025-04-01 07:36:57.797358 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/results/test_pe.summary_variants.tab
2025-04-01 07:36:57.800411 INFO::analyzeVariants/analyzeVariants: done
2025-04-01 07:36:57.808488 INFO::Pipeline run successful.
2025-04-01 07:36:58.038544 INFO::mergeLanes.R/doMergeLanes: starting...
2025-04-01 07:36:58.043936 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-04-01 07:36:58.047137 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/merged/results/merged.adapter_contaminated_1.RData
2025-04-01 07:36:58.051048 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-04-01 07:36:58.054047 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/merged/results/merged.adapter_contaminated_2.RData
2025-04-01 07:36:58.068433 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=26 highqual_reads=25 adapter_contam=1 read_length=75 rRNA_contam_reads=0 processed_reads=25 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-04-01 07:36:58.071869 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/merged/results/merged.summary_preprocess.tab
2025-04-01 07:36:58.074961 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 "T" 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 "highqualPE1UniqueUtrPE2MultimappingIntergenic:1:1:1:18#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInOneTxOfMultiTxGene:1:1:1:15#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-04-01 07:36:58.410766 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-04-01 07:36:58.420105 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/merged/results/merged.summary_alignment.tab
2025-04-01 07:36:58.431108 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/merged/results/merged.summary_analyzed_bamstats.tab
2025-04-01 07:36:58.433964 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-04-01 07:36:58.710538 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/merged/results/merged.summary_target_lengths.tab
2025-04-01 07:36:58.776816 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-04-01 07:36:58.818362 INFO::countGenomicFeatures.R/mergeCounts: starting...
2025-04-01 07:36:58.842113 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/merged/results/merged.counts_exon.tab
2025-04-01 07:36:58.857445 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/merged/results/merged.counts_exon_disjoint.tab
2025-04-01 07:36:58.867108 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/merged/results/merged.counts_gene.tab
2025-04-01 07:36:58.875612 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/merged/results/merged.counts_gene_coding.tab
2025-04-01 07:36:58.884522 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/merged/results/merged.counts_gene_exonic.tab
2025-04-01 07:36:58.893128 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/merged/results/merged.counts_intergenic.tab
2025-04-01 07:36:58.908264 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/merged/results/merged.counts_intron.tab
2025-04-01 07:36:58.912112 INFO::countGenomicFeatures.R/mergeCounts: done
2025-04-01 07:36:58.92078 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/merged/results/merged.summary_counts.tab
2025-04-01 07:36:58.923436 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2025-04-01 07:36:59.216957 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2025-04-01 07:37:01.058628 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/merged/results/merged.coverage.RData
2025-04-01 07:37:01.061336 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/merged/results/merged.coverage.bw
2025-04-01 07:37:01.076293 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/merged/results/merged.summary_coverage.tab
2025-04-01 07:37:01.114206 INFO::analyzeVariants/analyzeVariants: starting ...
2025-04-01 07:37:01.185287 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-04-01 07:37:04.204401 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-04-01 07:37:04.31877 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-04-01 07:37:04.344123 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-04-01 07:37:04.346066 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/merged/results/merged.raw_variants.RData
2025-04-01 07:37:04.348304 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/merged/results/merged.filtered_variants.RData
2025-04-01 07:37:04.350177 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-04-01 07:37:04.351603 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-04-01 07:37:04.687313 INFO::analyzeVariants.R/writeVCF: ...done
2025-04-01 07:37:04.831813 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.mergeLanes.3203da58585d43/merged/results/merged.summary_variants.tab
2025-04-01 07:37:04.834539 INFO::analyzeVariants/analyzeVariants: done
2025-04-01 07:37:04.837511 INFO::mergeLanes.R/doMergeLanes: merge lanes successful.
 done successfully.



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



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



Executing test function test.preprocessReads  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpnbguOA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.3/site-library/HTSeqGenie/config/default-config.txt 
2025-04-01 07:37:05.125067 INFO::preprocessReads.R/preprocessReads: starting...
2025-04-01 07:37:05.13154 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4.3/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-04-01 07:37:05.135975 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4.3/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-04-01 07:37:05.138777 DEBUG::tools.R/processChunks: starting...
2025-04-01 07:37:07.766169 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-04-01 07:37:07.768095 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpnbguOA/test.preprocessReads.3203da1d13d1d6/chunks/chunk_000001/logs/progress.log
2025-04-01 07:37:10.468185 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.045 minutes
2025-04-01 07:37:10.525094 DEBUG::tools.R/processChunks: done
2025-04-01 07:37:10.528273 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-04-01 07:37:10.530549 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.preprocessReads.3203da1d13d1d6/results/test_pe.adapter_contaminated_1.RData
2025-04-01 07:37:10.533097 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-04-01 07:37:10.53524 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.preprocessReads.3203da1d13d1d6/results/test_pe.adapter_contaminated_2.RData
2025-04-01 07:37:10.5442 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=26 highqual_reads=25 adapter_contam=1 read_length=75 rRNA_contam_reads=0 processed_reads=25 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-04-01 07:37:10.546865 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpnbguOA/test.preprocessReads.3203da1d13d1d6/results/test_pe.summary_preprocess.tab
2025-04-01 07:37:10.550235 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpnbguOA/test.preprocessReads.3203da1d13d1d6/bams/processed.aligner_input_1.fastq ...
2025-04-01 07:37:10.556423 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpnbguOA/test.preprocessReads.3203da1d13d1d6/bams/processed.aligner_input_2.fastq ...
2025-04-01 07:37:10.562393 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpnbguOA/test.preprocessReads.3203da1d13d1d6/reports/shortReadReport_1 ...
2025-04-01 07:37:12.411379 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpnbguOA/test.preprocessReads.3203da1d13d1d6/reports/shortReadReport_2 ...
2025-04-01 07:37:13.949231 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



Executing test function test.preprocessReads.minichunks  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpnbguOA/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.4.3/site-library/HTSeqGenie/config/default-config.txt 
2025-04-01 07:37:14.246805 INFO::preprocessReads.R/preprocessReads: starting...
2025-04-01 07:37:14.253711 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4.3/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-04-01 07:37:14.258814 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.4.3/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-04-01 07:37:14.261998 DEBUG::tools.R/processChunks: starting...
2025-04-01 07:38:14.284475 DEBUG::tools.R/traceMem: wired.mem=-25.280954 GiB
2025-04-01 07:39:14.351773 DEBUG::tools.R/traceMem: wired.mem=-22.545646 GiB
2025-04-01 07:40:14.417847 DEBUG::tools.R/traceMem: wired.mem=-19.859620 GiB
2025-04-01 07:41:14.482038 DEBUG::tools.R/traceMem: wired.mem=-27.029291 GiB
2025-04-01 07:42:14.545711 DEBUG::tools.R/traceMem: wired.mem=-21.015781 GiB
2025-04-01 07:43:14.609524 DEBUG::tools.R/traceMem: wired.mem=-19.531874 GiB
2025-04-01 07:44:14.678005 DEBUG::tools.R/traceMem: wired.mem=-19.458646 GiB
2025-04-01 07:45:14.741987 DEBUG::tools.R/traceMem: wired.mem=-18.404311 GiB
2025-04-01 07:46:14.805564 DEBUG::tools.R/traceMem: wired.mem=-12.259181 GiB
2025-04-01 07:47:14.870097 DEBUG::tools.R/traceMem: wired.mem=-19.053535 GiB
2025-04-01 07:48:14.934005 DEBUG::tools.R/traceMem: wired.mem=-20.237713 GiB
2025-04-01 07:49:14.997902 DEBUG::tools.R/traceMem: wired.mem=-22.547677 GiB
2025-04-01 07:50:15.061488 DEBUG::tools.R/traceMem: wired.mem=-24.684454 GiB
2025-04-01 07:51:15.126438 DEBUG::tools.R/traceMem: wired.mem=-21.560001 GiB
2025-04-01 07:52:15.190048 DEBUG::tools.R/traceMem: wired.mem=-13.622968 GiB
2025-04-01 07:53:15.256959 DEBUG::tools.R/traceMem: wired.mem=-17.804173 GiB
2025-04-01 07:54:15.321478 DEBUG::tools.R/traceMem: wired.mem=-22.802711 GiB
2025-04-01 07:55:15.385801 DEBUG::tools.R/traceMem: wired.mem=-22.853984 GiB
2025-04-01 07:56:15.449777 DEBUG::tools.R/traceMem: wired.mem=-24.960729 GiB
2025-04-01 07:57:15.513433 DEBUG::tools.R/traceMem: wired.mem=-30.345552 GiB
2025-04-01 07:58:15.577765 DEBUG::tools.R/traceMem: wired.mem=-23.931019 GiB
2025-04-01 07:59:15.64917 DEBUG::tools.R/traceMem: wired.mem=-16.816652 GiB
2025-04-01 08:00:15.713942 DEBUG::tools.R/traceMem: wired.mem=-20.830061 GiB
2025-04-01 08:01:15.781857 DEBUG::tools.R/traceMem: wired.mem=-20.762853 GiB
2025-04-01 08:02:15.849644 DEBUG::tools.R/traceMem: wired.mem=-9.198461 GiB
2025-04-01 08:03:15.917766 DEBUG::tools.R/traceMem: wired.mem=-7.515808 GiB
2025-04-01 08:04:15.98527 DEBUG::tools.R/traceMem: wired.mem=-28.007465 GiB

Example timings

HTSeqGenie.Rcheck/HTSeqGenie-Ex.timings

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