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This page was generated on 2024-11-28 12:15 -0500 (Thu, 28 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4748
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4459
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4398
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 973/2272HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HTSeqGenie 4.37.0  (landing page)
Jens Reeder
Snapshot Date: 2024-11-27 13:40 -0500 (Wed, 27 Nov 2024)
git_url: https://git.bioconductor.org/packages/HTSeqGenie
git_branch: devel
git_last_commit: 721d51c
git_last_commit_date: 2024-10-29 09:43:08 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    TIMEOUT  
palomino7Windows Server 2022 Datacenter / x64... NOT SUPPORTED ...
lconwaymacOS 12.7.1 Monterey / x86_64... NOT SUPPORTED ...

CHECK results for HTSeqGenie on nebbiolo1

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

raw results


Summary

Package: HTSeqGenie
Version: 4.37.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:HTSeqGenie.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings HTSeqGenie_4.37.0.tar.gz
StartedAt: 2024-11-28 00:56:15 -0500 (Thu, 28 Nov 2024)
EndedAt: 2024-11-28 01:36:15 -0500 (Thu, 28 Nov 2024)
EllapsedTime: 2400.3 seconds
RetCode: None
Status:   TIMEOUT  
CheckDir: HTSeqGenie.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:HTSeqGenie.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings HTSeqGenie_4.37.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/HTSeqGenie.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘HTSeqGenie/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HTSeqGenie’ version ‘4.37.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘HTSeqGenie’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘ShortRead:::.set_omp_threads’ ‘gmapR:::..gsnap’ ‘gmapR:::GeneGenome’
  ‘gmapR:::checkPackageInstalled’ ‘gmapR:::getDefaultGmapGenomePath’
  ‘gmapR:::getGeneRoi’ ‘gmapR:::subsetRegion’ ‘parallel:::mckill’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .Call(ShortRead:::.set_omp_threads, ...)
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
.makePreprocessAlignPlots: no visible binding for global variable
  ‘data’
.plot.in.out.min.max.readlength: no visible global function definition
  for ‘median’
FastQStreamer.init: no visible binding for '<<-' assignment to
  ‘FastQStreamer.lfqs’
FastQStreamer.init: no visible binding for '<<-' assignment to
  ‘FastQStreamer.chunkid’
FastQStreamer.init: no visible binding for '<<-' assignment to
  ‘FastQStreamer.subsampling_filter’
FastQStreamer.init: no visible binding for '<<-' assignment to
  ‘FastQStreamer.max_nbchunks’
addHandler: no visible binding for '<<-' assignment to
  ‘logging.handlers’
addHandler: no visible binding for global variable ‘logging.handlers’
addHandler: no visible binding for '<<-' assignment to ‘logging.file’
buildAnyFastaGenome: no visible global function definition for ‘getSeq’
buildGenomicFeaturesFromTxDb: no visible global function definition for
  ‘gaps’
buildGenomicFeaturesFromTxDb: no visible global function definition for
  ‘ranges’
buildTP53FastaGenome: no visible global function definition for
  ‘getSeq’
buildTallyParam: no visible global function definition for ‘seqinfo’
computeCoverage: no visible global function definition for ‘resize’
computeCoverage: no visible global function definition for ‘coverage’
estimateCutoffs : <anonymous>: no visible binding for global variable
  ‘quantile’
getGenomeSegments: no visible global function definition for ‘seqinfo’
hashVariants: no visible global function definition for ‘ranges’
isAboveQualityThresh: no visible global function definition for ‘Views’
isAboveQualityThresh: no visible global function definition for
  ‘viewMeans’
listIterator.init: no visible binding for '<<-' assignment to
  ‘listIterator.n’
listIterator.init: no visible binding for '<<-' assignment to
  ‘listIterator.x’
logReset: no visible binding for '<<-' assignment to ‘logging.handlers’
logReset: no visible binding for '<<-' assignment to ‘logging.loglevel’
logReset: no visible binding for '<<-' assignment to ‘logging.file’
loglevel: no visible binding for global variable ‘logging.loglevel’
loglevel: no visible binding for global variable ‘logging.handlers’
processChunks : tracefun: no visible binding for global variable
  ‘sjobs’
processChunks : tracefun: no visible binding for global variable
  ‘chunkid’
setLevel: no visible binding for '<<-' assignment to ‘logging.loglevel’
statCountFeatures: no visible global function definition for ‘quantile’
truncateReads: no visible global function definition for ‘subseq’
vcfStat: no visible global function definition for ‘quantile’
writeToFile: no visible binding for global variable ‘logging.file’
Undefined global functions or variables:
  Views chunkid coverage data gaps getSeq logging.file logging.handlers
  logging.loglevel median quantile ranges resize seqinfo sjobs subseq
  viewMeans
Consider adding
  importFrom("stats", "median", "quantile")
  importFrom("utils", "data")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) calculateTargetLengths.Rd:17: Lost braces; missing escapes or markup?
    17 | Target length table and writes two files in {save_dir}/reports/images/TargetLenghts.[pdf|png]"
       |                                             ^
checkRd: (-1) initLog.Rd:18: Lost braces; missing escapes or markup?
    18 | Setup logging file in {save_dir}/progress.log
       |                       ^
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
Documented arguments not in \usage in Rd file 'findVariantFile.Rd':
  ‘dir_path’

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

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

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

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

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

Installation output

HTSeqGenie.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL HTSeqGenie
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘HTSeqGenie’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (HTSeqGenie)

Tests output

HTSeqGenie.Rcheck/tests/doRUnit.Rout


R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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

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

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

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

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, 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= //tmp/Rtmp246ESM/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2024-11-28 01:04:51.563961 INFO::preprocessReads.R/preprocessReads: starting...
2024-11-28 01:04:51.571378 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-11-28 01:04:51.574705 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2024-11-28 01:04:51.576684 DEBUG::tools.R/processChunks: starting...
2024-11-28 01:04:53.891603 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-11-28 01:04:53.892855 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /tmp/Rtmp246ESM/test.alignReads.4c13d7a30512d/chunks/chunk_000001/logs/progress.log
2024-11-28 01:04:56.572795 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.045 minutes
2024-11-28 01:04:56.574168 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /tmp/Rtmp246ESM/test.alignReads.4c13d7a30512d/chunks/chunk_000002/logs/progress.log
2024-11-28 01:04:59.261564 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.045 minutes
2024-11-28 01:04:59.262874 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /tmp/Rtmp246ESM/test.alignReads.4c13d7a30512d/chunks/chunk_000003/logs/progress.log
2024-11-28 01:05:01.941408 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.045 minutes
2024-11-28 01:05:01.966525 DEBUG::tools.R/processChunks: done
2024-11-28 01:05:01.969805 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2024-11-28 01:05:01.97181 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.alignReads.4c13d7a30512d/results/test_pe.adapter_contaminated_1.RData
2024-11-28 01:05:01.974243 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2024-11-28 01:05:01.975767 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.alignReads.4c13d7a30512d/results/test_pe.adapter_contaminated_2.RData
2024-11-28 01:05:01.984024 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
2024-11-28 01:05:01.98604 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.alignReads.4c13d7a30512d/results/test_pe.summary_preprocess.tab
2024-11-28 01:05:01.988885 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/Rtmp246ESM/test.alignReads.4c13d7a30512d/bams/processed.aligner_input_1.fastq ...
2024-11-28 01:05:01.992656 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/Rtmp246ESM/test.alignReads.4c13d7a30512d/bams/processed.aligner_input_2.fastq ...
2024-11-28 01:05:01.995615 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/Rtmp246ESM/test.alignReads.4c13d7a30512d/reports/shortReadReport_1 ...
2024-11-28 01:05:03.260039 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/Rtmp246ESM/test.alignReads.4c13d7a30512d/reports/shortReadReport_2 ...
2024-11-28 01:05:06.296585 INFO::preprocessReads.R/preprocessReads: done
2024-11-28 01:05:06.366307 INFO::alignReads.R/alignReads: starting alignment...
2024-11-28 01:05:06.371881 DEBUG::tools.R/processChunks: starting...
2024-11-28 01:05:08.703256 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-11-28 01:05:08.704673 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /tmp/Rtmp246ESM/test.alignReads.4c13d7a30512d/chunks/chunk_000001/logs/progress.log
2024-11-28 01:05:11.445367 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.046 minutes
2024-11-28 01:05:11.4469 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /tmp/Rtmp246ESM/test.alignReads.4c13d7a30512d/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.
2024-11-28 01:05:14.048312 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.043 minutes
2024-11-28 01:05:14.049921 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /tmp/Rtmp246ESM/test.alignReads.4c13d7a30512d/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.
2024-11-28 01:05:16.635662 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.043 minutes
2024-11-28 01:05:16.639445 DEBUG::tools.R/processChunks: done
2024-11-28 01:05:16.641592 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.
2024-11-28 01:05:16.854336 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2024-11-28 01:05:16.861635 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.alignReads.4c13d7a30512d/results/test_pe.summary_alignment.tab
2024-11-28 01:05:16.867975 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.alignReads.4c13d7a30512d/results/test_pe.summary_analyzed_bamstats.tab
2024-11-28 01:05:16.869387 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2024-11-28 01:05:17.092342 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.alignReads.4c13d7a30512d/results/test_pe.summary_target_lengths.tab
2024-11-28 01:05:17.136254 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2024-11-28 01:05:17.137183 INFO::alignReads.R/alignReads: done
 done successfully.



Executing test function test.alignReads.sparsechunks  ... checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmp246ESM/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2024-11-28 01:05:17.368031 INFO::preprocessReads.R/preprocessReads: starting...
2024-11-28 01:05:17.371637 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-11-28 01:05:17.458431 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 2 , totnbreads= 26 )
2024-11-28 01:05:17.463196 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-11-28 01:05:17.466137 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2024-11-28 01:05:17.46803 DEBUG::tools.R/processChunks: starting...
2024-11-28 01:05:20.097365 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-11-28 01:05:20.098791 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /tmp/Rtmp246ESM/test.alignReads.sparsechunks.4c13d7ba72b83/chunks/chunk_000001/logs/progress.log
2024-11-28 01:05:22.733614 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.044 minutes
2024-11-28 01:05:22.734952 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /tmp/Rtmp246ESM/test.alignReads.sparsechunks.4c13d7ba72b83/chunks/chunk_000002/logs/progress.log
2024-11-28 01:05:25.353874 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.044 minutes
2024-11-28 01:05:25.355221 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /tmp/Rtmp246ESM/test.alignReads.sparsechunks.4c13d7ba72b83/chunks/chunk_000003/logs/progress.log
2024-11-28 01:05:28.06185 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.045 minutes
2024-11-28 01:05:28.063135 DEBUG::tools.R/processChunks: starting chunkid= 4 ; see logfile= /tmp/Rtmp246ESM/test.alignReads.sparsechunks.4c13d7ba72b83/chunks/chunk_000004/logs/progress.log
2024-11-28 01:05:30.645476 DEBUG::tools.R/processChunks: done with chunkid= 4 ; elapsed.time= 0.043 minutes
2024-11-28 01:05:30.668954 DEBUG::tools.R/processChunks: done
2024-11-28 01:05:30.672125 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2024-11-28 01:05:30.674422 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.alignReads.sparsechunks.4c13d7ba72b83/results/test_pe.adapter_contaminated_1.RData
2024-11-28 01:05:30.677397 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2024-11-28 01:05:30.679218 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.alignReads.sparsechunks.4c13d7ba72b83/results/test_pe.adapter_contaminated_2.RData
2024-11-28 01:05:30.689296 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
2024-11-28 01:05:30.691462 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.alignReads.sparsechunks.4c13d7ba72b83/results/test_pe.summary_preprocess.tab
2024-11-28 01:05:30.694917 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/Rtmp246ESM/test.alignReads.sparsechunks.4c13d7ba72b83/bams/processed.aligner_input_1.fastq ...
2024-11-28 01:05:30.699919 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/Rtmp246ESM/test.alignReads.sparsechunks.4c13d7ba72b83/bams/processed.aligner_input_2.fastq ...
2024-11-28 01:05:30.704141 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/Rtmp246ESM/test.alignReads.sparsechunks.4c13d7ba72b83/reports/shortReadReport_1 ...
2024-11-28 01:05:31.899514 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/Rtmp246ESM/test.alignReads.sparsechunks.4c13d7ba72b83/reports/shortReadReport_2 ...
2024-11-28 01:05:33.931268 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



Executing test function test.alignReadsOneSingleEnd  ... checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmp246ESM/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2024-11-28 01:05:34.104912 INFO::alignReads.R/alignReadsChunk: running gsnap...
2024-11-28 01:05:34.108858 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 /tmp/Rtmp246ESM/test.alignReadsOneSingleEnd.4c13d16c319e8/bams/test.alignReads /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq 2>&1
2024-11-28 01:05:34.320428 INFO::alignReads.R/createSummaryAlignment: counting unique bam reads...
2024-11-28 01:05:34.403927 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.alignReadsOneSingleEnd.4c13d16c319e8/results/test.alignReads.summary_alignment.tab
2024-11-28 01:05:34.448535 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.alignReadsOneSingleEnd.4c13d16c319e8/results/test.alignReads.summary_analyzed_bamstats.tab
2024-11-28 01:05:34.449908 INFO::alignReads.R/alignReadsChunk: done
 done successfully.



Executing test function test.annotateVariants  ... Timing stopped at: 0.001 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= //tmp/Rtmp246ESM/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2024-11-28 01:05:34.724027 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.genotype.4c13d3c94954e/results/test_pe.coverage.RData
2024-11-28 01:05:34.725688 INFO::coverage.R/saveCoverage: saving file= /tmp/Rtmp246ESM/test.genotype.4c13d3c94954e/results/test_pe.coverage.bw
2024-11-28 01:05:34.830232 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.genotype.4c13d3c94954e/results/test_pe.summary_coverage.tab
2024-11-28 01:05:34.83176 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2024-11-28 01:05:44.903771 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2024-11-28 01:05:44.999315 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2024-11-28 01:05:45.018027 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2024-11-28 01:05:45.019619 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.genotype.4c13d3c94954e/results/test_pe.raw_variants.RData
2024-11-28 01:05:45.022126 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.genotype.4c13d3c94954e/results/test_pe.filtered_variants.RData
2024-11-28 01:05:45.023614 INFO::analyzeVariants.R/wrap.callVariants: ...done
2024-11-28 01:05:45.024939 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2024-11-28 01:05:45.457797 INFO::analyzeVariants.R/writeVCF: ...done
2024-11-28 01:05:45.459019 INFO::analyzeVariants.R/.callGenotypes: calling genotypes...
2024-11-28 01:06:37.321417 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2024-11-28 01:06:37.873475 INFO::analyzeVariants.R/writeVCF: ...done
2024-11-28 01:06:37.874737 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= //tmp/Rtmp246ESM/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2024-11-28 01:06:38.481671 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2024-11-28 01:06:48.442877 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2024-11-28 01:06:48.512414 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2024-11-28 01:06:48.527488 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2024-11-28 01:06:48.528754 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.wrap.callVariants.4c13d46b49852/results/test_pe.raw_variants.RData
2024-11-28 01:06:48.530977 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.wrap.callVariants.4c13d46b49852/results/test_pe.filtered_variants.RData
2024-11-28 01:06:48.532291 INFO::analyzeVariants.R/wrap.callVariants: ...done
 done successfully.



Executing test function test.wrap.callVariants.filters  ... checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmp246ESM/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2024-11-28 01:06:48.669163 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2024-11-28 01:06:58.063411 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2024-11-28 01:06:58.114206 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2024-11-28 01:06:58.128602 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2024-11-28 01:06:58.129807 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.wrap.callVariants.filters.4c13d3ada349b/results/test_pe.raw_variants.RData
2024-11-28 01:06:58.132045 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.wrap.callVariants.filters.4c13d3ada349b/results/test_pe.filtered_variants.RData
2024-11-28 01:06:58.133308 INFO::analyzeVariants.R/wrap.callVariants: ...done
2024-11-28 01:06:58.134598 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2024-11-28 01:07:07.432222 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2024-11-28 01:07:07.468635 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2024-11-28 01:07:07.484179 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2024-11-28 01:07:07.48545 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.wrap.callVariants.filters.4c13d3ada349b/results/test_pe.raw_variants.RData
2024-11-28 01:07:07.487769 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.wrap.callVariants.filters.4c13d3ada349b/results/test_pe.filtered_variants.RData
2024-11-28 01:07:07.489583 INFO::analyzeVariants.R/wrap.callVariants: ...done
 done successfully.



Executing test function test.wrap.callVariants.which  ... checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmp246ESM/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2024-11-28 01:07:07.701089 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2024-11-28 01:07:07.702504 INFO::analyzeVariants.R/buildTallyParam: restricting variant calls using 'which'
2024-11-28 01:07:09.916615 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2024-11-28 01:07:09.981348 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2024-11-28 01:07:09.995755 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2024-11-28 01:07:09.997001 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.wrap.callVariants.which.4c13d6ba80459/results/test_pe.raw_variants.RData
2024-11-28 01:07:09.998527 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.wrap.callVariants.which.4c13d6ba80459/results/test_pe.filtered_variants.RData
2024-11-28 01:07:09.999679 INFO::analyzeVariants.R/wrap.callVariants: ...done
 done successfully.



Executing test function test.writeVCF.NULL  ... checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmp246ESM/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2024-11-28 01:07:10.125874 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2024-11-28 01:07:10.127009 INFO::analyzeVariants.R/writeVCF: ...done
 done successfully.



Executing test function test.writeVCF.vcfStat  ... checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmp246ESM/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2024-11-28 01:07:10.277895 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2024-11-28 01:07:10.459659 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  ... 2024-11-28 01:07:57.199516 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/pgquakdz/merged/results/bla.coverage.RData
2024-11-28 01:07:57.202155 INFO::coverage.R/saveCoverage: saving file= /tmp/Rtmp246ESM/pgquakdz/merged/results/bla.coverage.bw
2024-11-28 01:07:57.273927 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/pgquakdz/merged/results/bla.summary_coverage.tab
 done successfully.



Executing test function test.mergeCoverage.sparse  ... 2024-11-28 01:07:58.224322 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/apzvgokh/merged/results/bla.coverage.RData
2024-11-28 01:07:58.225716 INFO::coverage.R/saveCoverage: saving file= /tmp/Rtmp246ESM/apzvgokh/merged/results/bla.coverage.bw
2024-11-28 01:07:58.236252 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/apzvgokh/merged/results/bla.summary_coverage.tab
 done successfully.



Executing test function test.checkConfig.analyzeVariants  ... checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmp246ESM/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
 done successfully.



Executing test function test.findTemplate  ...  done successfully.



Executing test function test.checkConfig  ... checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmp246ESM/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmp246ESM/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmp246ESM/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmp246ESM/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
 done successfully.



Executing test function test.checkConfig.alignReads  ... checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmp246ESM/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmp246ESM/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmp246ESM/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmp246ESM/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
 done successfully.



Executing test function test.getConfig  ...  done successfully.



Executing test function test.loadConfig  ...  done successfully.



Executing test function test.parseDCF  ...  done successfully.



Executing test function test.updateConfig  ...  done successfully.



Executing test function test.getAdapterSeqs  ...  done successfully.



Executing test function test.isAdapter  ...  done successfully.



Executing test function test.isAdapter3.primeEnd  ...  done successfully.



Executing test function test.detectRRNA  ... checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmp246ESM/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2024-11-28 01:07:59.330882 INFO::detectRRNA.R/detectRRNA: searching for rRNA contamination...
2024-11-28 01:07:59.331944 INFO::io.R/writeFastQFiles: writing filename= /tmp/Rtmp246ESM/test.detectRRNA.4c13d1dca3643/bams/rRNA_contam/input1.fastq
2024-11-28 01:07:59.334979 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 /tmp/Rtmp246ESM/test.detectRRNA.4c13d1dca3643/bams/rRNA_contam/test_se /tmp/Rtmp246ESM/test.detectRRNA.4c13d1dca3643/bams/rRNA_contam/input1.fastq 2>&1
2024-11-28 01:07:59.461733 INFO::detectRRNA.R/detectRRNA: contaminated fraction= 1
2024-11-28 01:07:59.462687 INFO::detectRRNA.R/detectRRNA: done
 done successfully.



Executing test function test.detectRRNA.paired_end  ... checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmp246ESM/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2024-11-28 01:07:59.595898 INFO::detectRRNA.R/detectRRNA: searching for rRNA contamination...
2024-11-28 01:07:59.596835 INFO::io.R/writeFastQFiles: writing filename= /tmp/Rtmp246ESM/test.detectRRNA.paired_end.4c13d1e689e72/bams/rRNA_contam/input1.fastq
2024-11-28 01:07:59.598248 INFO::io.R/writeFastQFiles: writing filename= /tmp/Rtmp246ESM/test.detectRRNA.paired_end.4c13d1e689e72/bams/rRNA_contam/input2.fastq
2024-11-28 01:07:59.600267 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 /tmp/Rtmp246ESM/test.detectRRNA.paired_end.4c13d1e689e72/bams/rRNA_contam/test_pe /tmp/Rtmp246ESM/test.detectRRNA.paired_end.4c13d1e689e72/bams/rRNA_contam/input1.fastq -a paired /tmp/Rtmp246ESM/test.detectRRNA.paired_end.4c13d1e689e72/bams/rRNA_contam/input2.fastq 2>&1
2024-11-28 01:07:59.812091 INFO::detectRRNA.R/detectRRNA: contaminated fraction= 1
2024-11-28 01:07:59.813027 INFO::detectRRNA.R/detectRRNA: done
 done successfully.



Executing test function test.getRRNAIds  ... 2024-11-28 01:07:59.83094 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 /tmp/Rtmp246ESM/test_get_rRNA_idsvtyrhozd/test_pe /tmp/Rtmp246ESM/test_get_rRNA_idsvtyrhozd/1.fastq -a paired /tmp/Rtmp246ESM/test_get_rRNA_idsvtyrhozd/2.fastq 2>&1
 done successfully.



Executing test function test.getRRNAIds_random  ... 2024-11-28 01:08:00.060228 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 /tmp/Rtmp246ESM/test_get_rRNAIds_randomtcxjugsz/test_pe /tmp/Rtmp246ESM/test_get_rRNAIds_randomtcxjugsz/1.fastq 2>&1
 done successfully.



Executing test function test.filterByLength  ... 2024-11-28 01:08:00.286857 INFO::filterQuality.R/filterQuality: filterByLength...
2024-11-28 01:08:00.288167 INFO::filterQuality.R/filterByLength: fraction of filtered short reads= 0.5
2024-11-28 01:08:00.289031 INFO::filterQuality.R/filterByLength: done
2024-11-28 01:08:00.33197 INFO::filterQuality.R/filterQuality: filterByLength...
2024-11-28 01:08:00.332839 INFO::filterQuality.R/filterByLength: fraction of filtered short reads= 1
2024-11-28 01:08:00.333632 INFO::filterQuality.R/filterByLength: done
 done successfully.



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



Executing test function test.trimTailsByQuality  ... 2024-11-28 01:08:00.378779 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2024-11-28 01:08:00.386873 INFO::preprocessReads.R/preprocessReadsChunk: done
2024-11-28 01:08:00.387829 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2024-11-28 01:08:00.391794 INFO::preprocessReads.R/preprocessReadsChunk: done
2024-11-28 01:08:00.392668 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2024-11-28 01:08:00.396575 INFO::preprocessReads.R/preprocessReadsChunk: done
2024-11-28 01:08:00.39747 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2024-11-28 01:08:00.401335 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
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= //tmp/Rtmp246ESM/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2024-11-28 01:08:00.660184 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-11-28 01:08:00.662343 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
 done successfully.



Executing test function test.FastQStreamer.getReads.pefq.subsample  ... checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmp246ESM/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2024-11-28 01:08:01.709075 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-11-28 01:08:01.7659 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2024-11-28 01:08:01.768679 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-11-28 01:08:01.770894 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
 done successfully.



Executing test function test.FastQStreamer.getReads.segz  ... checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmp246ESM/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2024-11-28 01:08:01.932946 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/reads.fastq.gz
 done successfully.



Executing test function test.FastQStreamer.getReads.truncated  ... checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmp246ESM/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2024-11-28 01:08:02.056714 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/truncated.fastq.gz
 done successfully.



Executing test function test.FastQStreamer.subsampler.isdeterministic  ... checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmp246ESM/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2024-11-28 01:08:02.17304 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-11-28 01:08:02.204775 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2024-11-28 01:08:02.20707 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-11-28 01:08:02.209168 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmp246ESM/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2024-11-28 01:08:02.361105 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-11-28 01:08:02.393547 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2024-11-28 01:08:02.395821 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-11-28 01:08:02.397871 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
 done successfully.



Executing test function test.createTmpDir  ...  done successfully.



Executing test function test.detectQualityInFASTQFile  ...  done successfully.



Executing test function test.getObjectFilename  ...  done successfully.



Executing test function test.safeUnlink  ...  done successfully.



Executing test function test.writeAudit  ... checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmp246ESM/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
 done successfully.



Executing test function test.mergeLanes  ... checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmp246ESM/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2024-11-28 01:08:02.959505 INFO::preprocessReads.R/preprocessReads: starting...
2024-11-28 01:08:02.964871 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-11-28 01:08:02.967889 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2024-11-28 01:08:02.969849 DEBUG::tools.R/processChunks: starting...
2024-11-28 01:08:05.567136 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-11-28 01:08:05.568793 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/chunks/chunk_000001/logs/progress.log
2024-11-28 01:08:08.110627 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.042 minutes
2024-11-28 01:08:08.112111 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/chunks/chunk_000002/logs/progress.log
2024-11-28 01:08:10.629843 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.042 minutes
2024-11-28 01:08:10.632037 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/chunks/chunk_000003/logs/progress.log
2024-11-28 01:08:13.224391 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.043 minutes
2024-11-28 01:08:13.261446 DEBUG::tools.R/processChunks: done
2024-11-28 01:08:13.264147 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2024-11-28 01:08:13.265796 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/results/test_pe.adapter_contaminated_1.RData
2024-11-28 01:08:13.267801 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2024-11-28 01:08:13.269261 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/results/test_pe.adapter_contaminated_2.RData
2024-11-28 01:08:13.277222 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
2024-11-28 01:08:13.279018 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/results/test_pe.summary_preprocess.tab
2024-11-28 01:08:13.281395 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/bams/processed.aligner_input_1.fastq ...
2024-11-28 01:08:13.285307 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/bams/processed.aligner_input_2.fastq ...
2024-11-28 01:08:13.288372 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/reports/shortReadReport_1 ...
2024-11-28 01:08:14.545377 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/reports/shortReadReport_2 ...
2024-11-28 01:08:15.524863 INFO::preprocessReads.R/preprocessReads: done
2024-11-28 01:08:15.613864 INFO::alignReads.R/alignReads: starting alignment...
2024-11-28 01:08:15.617761 DEBUG::tools.R/processChunks: starting...
2024-11-28 01:08:18.136752 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-11-28 01:08:18.138345 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/chunks/chunk_000001/logs/progress.log
2024-11-28 01:08:20.697014 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.043 minutes
2024-11-28 01:08:20.698599 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/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.
2024-11-28 01:08:23.282403 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.043 minutes
2024-11-28 01:08:23.284079 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/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.
2024-11-28 01:08:25.868214 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.043 minutes
2024-11-28 01:08:25.871364 DEBUG::tools.R/processChunks: done
2024-11-28 01:08:25.873286 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.
2024-11-28 01:08:26.07189 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2024-11-28 01:08:26.079229 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/results/test_pe.summary_alignment.tab
2024-11-28 01:08:26.0857 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/results/test_pe.summary_analyzed_bamstats.tab
2024-11-28 01:08:26.087419 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2024-11-28 01:08:26.299031 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/results/test_pe.summary_target_lengths.tab
2024-11-28 01:08:26.343875 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2024-11-28 01:08:26.344851 INFO::alignReads.R/alignReads: done
2024-11-28 01:08:26.418408 INFO::countGenomicFeatures.R/countGenomicFeatures: starting...
2024-11-28 01:08:26.434361 DEBUG::tools.R/processChunks: starting...
2024-11-28 01:08:28.98015 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-11-28 01:08:28.981688 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/chunks/chunk_000001/logs/progress.log
2024-11-28 01:08:31.375798 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.04 minutes
2024-11-28 01:08:31.377188 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/chunks/chunk_000002/logs/progress.log
2024-11-28 01:08:33.753979 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.04 minutes
2024-11-28 01:08:33.755425 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/chunks/chunk_000003/logs/progress.log
2024-11-28 01:08:36.143602 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.04 minutes
2024-11-28 01:08:36.147239 DEBUG::tools.R/processChunks: done
2024-11-28 01:08:36.149586 INFO::countGenomicFeatures.R/mergeCounts: starting...
2024-11-28 01:08:36.169825 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/results/test_pe.counts_exon.tab
2024-11-28 01:08:36.186546 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/results/test_pe.counts_exon_disjoint.tab
2024-11-28 01:08:36.195711 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/results/test_pe.counts_gene.tab
2024-11-28 01:08:36.20191 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/results/test_pe.counts_gene_coding.tab
2024-11-28 01:08:36.207554 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/results/test_pe.counts_gene_exonic.tab
2024-11-28 01:08:36.21285 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/results/test_pe.counts_intergenic.tab
2024-11-28 01:08:36.221606 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/results/test_pe.counts_intron.tab
2024-11-28 01:08:36.223997 INFO::countGenomicFeatures.R/mergeCounts: done
2024-11-28 01:08:36.228805 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/results/test_pe.summary_counts.tab
2024-11-28 01:08:36.230131 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2024-11-28 01:08:36.517701 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2024-11-28 01:08:36.518571 INFO::countGenomicFeatures.R/countGenomicFeatures: done...
2024-11-28 01:08:36.621478 INFO::coverage.R/calculateCoverage: starting...
2024-11-28 01:08:36.625561 DEBUG::tools.R/processChunks: starting...
2024-11-28 01:08:39.223289 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-11-28 01:08:39.224845 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/chunks/chunk_000001/logs/progress.log
2024-11-28 01:08:41.37464 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.036 minutes
2024-11-28 01:08:41.376049 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/chunks/chunk_000002/logs/progress.log
2024-11-28 01:08:43.539067 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.036 minutes
2024-11-28 01:08:43.54072 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/chunks/chunk_000003/logs/progress.log
2024-11-28 01:08:45.7043 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.036 minutes
2024-11-28 01:08:45.706731 DEBUG::tools.R/processChunks: done
2024-11-28 01:08:47.467716 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/results/test_pe.coverage.RData
2024-11-28 01:08:47.46926 INFO::coverage.R/saveCoverage: saving file= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/results/test_pe.coverage.bw
2024-11-28 01:08:47.480524 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/results/test_pe.summary_coverage.tab
2024-11-28 01:08:47.481697 INFO::coverage.R/calculateCoverage: done
2024-11-28 01:08:47.489114 INFO::analyzeVariants/analyzeVariants: starting ...
2024-11-28 01:08:47.613138 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2024-11-28 01:08:50.279092 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2024-11-28 01:08:50.345745 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2024-11-28 01:08:50.360732 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2024-11-28 01:08:50.36196 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/results/test_pe.raw_variants.RData
2024-11-28 01:08:50.36347 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/results/test_pe.filtered_variants.RData
2024-11-28 01:08:50.36464 INFO::analyzeVariants.R/wrap.callVariants: ...done
2024-11-28 01:08:50.365557 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2024-11-28 01:08:50.560436 INFO::analyzeVariants.R/writeVCF: ...done
2024-11-28 01:08:50.651162 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/results/test_pe.summary_variants.tab
2024-11-28 01:08:50.653222 INFO::analyzeVariants/analyzeVariants: done
2024-11-28 01:08:50.657006 INFO::Pipeline run successful.
2024-11-28 01:08:50.807172 INFO::mergeLanes.R/doMergeLanes: starting...
2024-11-28 01:08:50.81181 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2024-11-28 01:08:50.813953 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/merged/results/merged.adapter_contaminated_1.RData
2024-11-28 01:08:50.81663 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2024-11-28 01:08:50.818476 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/merged/results/merged.adapter_contaminated_2.RData
2024-11-28 01:08:50.882599 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
2024-11-28 01:08:50.885012 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/merged/results/merged.summary_preprocess.tab
2024-11-28 01:08:50.887098 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.
2024-11-28 01:08:51.105598 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2024-11-28 01:08:51.112052 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/merged/results/merged.summary_alignment.tab
2024-11-28 01:08:51.119424 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/merged/results/merged.summary_analyzed_bamstats.tab
2024-11-28 01:08:51.12134 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2024-11-28 01:08:51.350128 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/merged/results/merged.summary_target_lengths.tab
2024-11-28 01:08:51.398988 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2024-11-28 01:08:51.445582 INFO::countGenomicFeatures.R/mergeCounts: starting...
2024-11-28 01:08:51.465554 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/merged/results/merged.counts_exon.tab
2024-11-28 01:08:51.476491 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/merged/results/merged.counts_exon_disjoint.tab
2024-11-28 01:08:51.483025 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/merged/results/merged.counts_gene.tab
2024-11-28 01:08:51.488568 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/merged/results/merged.counts_gene_coding.tab
2024-11-28 01:08:51.493874 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/merged/results/merged.counts_gene_exonic.tab
2024-11-28 01:08:51.499388 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/merged/results/merged.counts_intergenic.tab
2024-11-28 01:08:51.510253 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/merged/results/merged.counts_intron.tab
2024-11-28 01:08:51.512881 INFO::countGenomicFeatures.R/mergeCounts: done
2024-11-28 01:08:51.519086 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/merged/results/merged.summary_counts.tab
2024-11-28 01:08:51.520769 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2024-11-28 01:08:51.756423 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2024-11-28 01:08:53.520941 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/merged/results/merged.coverage.RData
2024-11-28 01:08:53.522735 INFO::coverage.R/saveCoverage: saving file= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/merged/results/merged.coverage.bw
2024-11-28 01:08:53.533456 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/merged/results/merged.summary_coverage.tab
2024-11-28 01:08:53.575323 INFO::analyzeVariants/analyzeVariants: starting ...
2024-11-28 01:08:53.655777 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2024-11-28 01:08:56.376447 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2024-11-28 01:08:56.44201 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2024-11-28 01:08:56.456455 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2024-11-28 01:08:56.457744 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/merged/results/merged.raw_variants.RData
2024-11-28 01:08:56.459211 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/merged/results/merged.filtered_variants.RData
2024-11-28 01:08:56.460359 INFO::analyzeVariants.R/wrap.callVariants: ...done
2024-11-28 01:08:56.46127 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2024-11-28 01:08:56.655232 INFO::analyzeVariants.R/writeVCF: ...done
2024-11-28 01:08:56.743844 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.mergeLanes.4c13d5c0a02ab/merged/results/merged.summary_variants.tab
2024-11-28 01:08:56.745883 INFO::analyzeVariants/analyzeVariants: done
2024-11-28 01:08:56.748881 INFO::mergeLanes.R/doMergeLanes: merge lanes successful.
 done successfully.



Executing test function test.markDuplicates  ... Timing stopped at: 0 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= //tmp/Rtmp246ESM/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2024-11-28 01:08:57.009836 INFO::preprocessReads.R/preprocessReads: starting...
2024-11-28 01:08:57.017273 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-11-28 01:08:57.020607 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2024-11-28 01:08:57.022772 DEBUG::tools.R/processChunks: starting...
2024-11-28 01:08:59.928346 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-11-28 01:08:59.929722 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /tmp/Rtmp246ESM/test.preprocessReads.4c13d6f89ccdc/chunks/chunk_000001/logs/progress.log
2024-11-28 01:09:02.505439 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.043 minutes
2024-11-28 01:09:02.541301 DEBUG::tools.R/processChunks: done
2024-11-28 01:09:02.543542 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2024-11-28 01:09:02.544993 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.preprocessReads.4c13d6f89ccdc/results/test_pe.adapter_contaminated_1.RData
2024-11-28 01:09:02.546542 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2024-11-28 01:09:02.547813 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.preprocessReads.4c13d6f89ccdc/results/test_pe.adapter_contaminated_2.RData
2024-11-28 01:09:02.553653 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
2024-11-28 01:09:02.555241 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.preprocessReads.4c13d6f89ccdc/results/test_pe.summary_preprocess.tab
2024-11-28 01:09:02.557095 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/Rtmp246ESM/test.preprocessReads.4c13d6f89ccdc/bams/processed.aligner_input_1.fastq ...
2024-11-28 01:09:02.561257 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/Rtmp246ESM/test.preprocessReads.4c13d6f89ccdc/bams/processed.aligner_input_2.fastq ...
2024-11-28 01:09:02.564182 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/Rtmp246ESM/test.preprocessReads.4c13d6f89ccdc/reports/shortReadReport_1 ...
2024-11-28 01:09:03.856925 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/Rtmp246ESM/test.preprocessReads.4c13d6f89ccdc/reports/shortReadReport_2 ...
2024-11-28 01:09:04.926584 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



Executing test function test.preprocessReads.minichunks  ... checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmp246ESM/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2024-11-28 01:09:05.182889 INFO::preprocessReads.R/preprocessReads: starting...
2024-11-28 01:09:05.188811 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-11-28 01:09:05.192215 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2024-11-28 01:09:05.194531 DEBUG::tools.R/processChunks: starting...
2024-11-28 01:09:07.702548 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-11-28 01:09:07.703894 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /tmp/Rtmp246ESM/test.preprocessReads.minichunks.4c13d7290a127/chunks/chunk_000001/logs/progress.log
2024-11-28 01:09:10.240618 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.042 minutes
2024-11-28 01:09:10.242067 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /tmp/Rtmp246ESM/test.preprocessReads.minichunks.4c13d7290a127/chunks/chunk_000002/logs/progress.log
2024-11-28 01:09:12.819779 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.043 minutes
2024-11-28 01:09:12.821186 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /tmp/Rtmp246ESM/test.preprocessReads.minichunks.4c13d7290a127/chunks/chunk_000003/logs/progress.log
2024-11-28 01:09:15.371704 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.042 minutes
2024-11-28 01:09:15.401146 DEBUG::tools.R/processChunks: done
2024-11-28 01:09:15.403545 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2024-11-28 01:09:15.40501 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.preprocessReads.minichunks.4c13d7290a127/results/test_pe.adapter_contaminated_1.RData
2024-11-28 01:09:15.406842 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2024-11-28 01:09:15.408238 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.preprocessReads.minichunks.4c13d7290a127/results/test_pe.adapter_contaminated_2.RData
2024-11-28 01:09:15.415205 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
2024-11-28 01:09:15.416842 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.preprocessReads.minichunks.4c13d7290a127/results/test_pe.summary_preprocess.tab
2024-11-28 01:09:15.418983 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/Rtmp246ESM/test.preprocessReads.minichunks.4c13d7290a127/bams/processed.aligner_input_1.fastq ...
2024-11-28 01:09:15.424033 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/Rtmp246ESM/test.preprocessReads.minichunks.4c13d7290a127/bams/processed.aligner_input_2.fastq ...
2024-11-28 01:09:15.428246 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/Rtmp246ESM/test.preprocessReads.minichunks.4c13d7290a127/reports/shortReadReport_1 ...
2024-11-28 01:09:16.640668 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/Rtmp246ESM/test.preprocessReads.minichunks.4c13d7290a127/reports/shortReadReport_2 ...
2024-11-28 01:09:17.629678 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



Executing test function test.preprocessReads_single_end  ... checkConfig.R/checkConfig.template: loading template config= //tmp/Rtmp246ESM/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2024-11-28 01:09:17.896666 INFO::preprocessReads.R/preprocessReads: starting...
2024-11-28 01:09:17.903455 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2024-11-28 01:09:17.905853 DEBUG::tools.R/processChunks: starting...
2024-11-28 01:09:20.765799 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-11-28 01:09:20.767147 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /tmp/Rtmp246ESM/test.preprocessReads_single_end.4c13d76843937/chunks/chunk_000001/logs/progress.log
2024-11-28 01:09:23.120546 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.039 minutes
2024-11-28 01:09:23.153109 DEBUG::tools.R/processChunks: done
2024-11-28 01:09:23.155631 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2024-11-28 01:09:23.157291 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.preprocessReads_single_end.4c13d76843937/results/test_se.adapter_contaminated_1.RData
2024-11-28 01:09:23.163767 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
2024-11-28 01:09:23.165514 INFO::io.R/saveWithID: saving file= /tmp/Rtmp246ESM/test.preprocessReads_single_end.4c13d76843937/results/test_se.summary_preprocess.tab
2024-11-28 01:09:23.167309 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /tmp/Rtmp246ESM/test.preprocessReads_single_end.4c13d76843937/bams/processed.aligner_input_1.fastq ...
2024-11-28 01:09:23.171757 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /tmp/Rtmp246ESM/test.preprocessReads_single_end.4c13d76843937/reports/shortReadReport_1 ...
2024-11-28 01:09:24.484853 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



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



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



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



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



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



Executing test function test.runPipeline  ... checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/config/default-config.txt 
2024-11-28 01:09:25.051387 INFO::preprocessReads.R/preprocessReads: starting...
2024-11-28 01:09:25.057166 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/extdata/H1993_TP53_subset2500_1.fastq.gz
2024-11-28 01:09:25.061171 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/bbs-3.21-bioc/R/site-library/HTSeqGenie/extdata/H1993_TP53_subset2500_2.fastq.gz
2024-11-28 01:09:25.063268 DEBUG::tools.R/processChunks: starting...
2024-11-28 01:09:27.660963 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-11-28 01:09:27.662342 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= test/chunks/chunk_000001/logs/progress.log
2024-11-28 01:09:30.421228 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.046 minutes
2024-11-28 01:09:30.456346 DEBUG::tools.R/processChunks: done
2024-11-28 01:09:30.458681 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2024-11-28 01:09:30.460142 INFO::io.R/saveWithID: saving file= test/results/test.adapter_contaminated_1.RData
2024-11-28 01:09:30.461801 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2024-11-28 01:09:30.463114 INFO::io.R/saveWithID: saving file= test/results/test.adapter_contaminated_2.RData
2024-11-28 01:09:30.468931 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
2024-11-28 01:09:30.470549 INFO::io.R/saveWithID: saving file= test/results/test.summary_preprocess.tab
2024-11-28 01:09:30.472531 INFO::preprocessReads.R/mergePreprocessedReads: merging file= test/bams/processed.aligner_input_1.fastq ...
2024-11-28 01:09:30.476875 INFO::preprocessReads.R/mergePreprocessedReads: merging file= test/bams/processed.aligner_input_2.fastq ...
2024-11-28 01:09:30.48052 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= test/reports/shortReadReport_1 ...
2024-11-28 01:10:25.080935 DEBUG::tools.R/traceMem: wired.mem=25.176834 GiB
2024-11-28 01:11:25.088428 DEBUG::tools.R/traceMem: wired.mem=28.804801 GiB
2024-11-28 01:12:25.154149 DEBUG::tools.R/traceMem: wired.mem=23.876329 GiB
2024-11-28 01:13:25.221725 DEBUG::tools.R/traceMem: wired.mem=24.787419 GiB
2024-11-28 01:14:25.301754 DEBUG::tools.R/traceMem: wired.mem=95.408833 GiB
2024-11-28 01:15:25.386895 DEBUG::tools.R/traceMem: wired.mem=20.638302 GiB
2024-11-28 01:16:25.484866 DEBUG::tools.R/traceMem: wired.mem=20.313211 GiB
2024-11-28 01:17:25.558133 DEBUG::tools.R/traceMem: wired.mem=23.145439 GiB
2024-11-28 01:18:25.625772 DEBUG::tools.R/traceMem: wired.mem=21.187191 GiB
2024-11-28 01:19:25.697255 DEBUG::tools.R/traceMem: wired.mem=27.512766 GiB
2024-11-28 01:20:25.767231 DEBUG::tools.R/traceMem: wired.mem=32.672096 GiB
2024-11-28 01:21:25.784276 DEBUG::tools.R/traceMem: wired.mem=32.835707 GiB
2024-11-28 01:22:25.84287 DEBUG::tools.R/traceMem: wired.mem=28.267799 GiB
2024-11-28 01:23:25.911861 DEBUG::tools.R/traceMem: wired.mem=22.337454 GiB
2024-11-28 01:24:25.981102 DEBUG::tools.R/traceMem: wired.mem=25.328296 GiB
2024-11-28 01:25:26.050893 DEBUG::tools.R/traceMem: wired.mem=27.823161 GiB
2024-11-28 01:26:26.12034 DEBUG::tools.R/traceMem: wired.mem=23.485432 GiB
2024-11-28 01:27:26.15514 DEBUG::tools.R/traceMem: wired.mem=35.723657 GiB
2024-11-28 01:28:26.224024 DEBUG::tools.R/traceMem: wired.mem=40.523710 GiB
2024-11-28 01:29:26.292922 DEBUG::tools.R/traceMem: wired.mem=27.496399 GiB
2024-11-28 01:30:26.361174 DEBUG::tools.R/traceMem: wired.mem=30.342775 GiB
2024-11-28 01:31:26.429367 DEBUG::tools.R/traceMem: wired.mem=22.895370 GiB
2024-11-28 01:32:26.499181 DEBUG::tools.R/traceMem: wired.mem=22.935044 GiB
2024-11-28 01:33:26.568156 DEBUG::tools.R/traceMem: wired.mem=26.406076 GiB
2024-11-28 01:34:26.636291 DEBUG::tools.R/traceMem: wired.mem=34.543763 GiB
2024-11-28 01:35:26.70481 DEBUG::tools.R/traceMem: wired.mem=32.989061 GiB

Example timings

HTSeqGenie.Rcheck/HTSeqGenie-Ex.timings

nameusersystemelapsed
HTSeqGenie000
buildGenomicFeaturesFromTxDb0.0000.0000.001
runPipeline0.0000.0010.001