Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-04 11:40:38 -0400 (Sat, 04 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4753 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" | 4486 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" | 4519 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4479 |
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 989/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
HTSeqGenie 4.34.0 (landing page) Jens Reeder
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | ... NOT SUPPORTED ... | ||||||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
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. |
Package: HTSeqGenie |
Version: 4.34.0 |
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:HTSeqGenie.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings HTSeqGenie_4.34.0.tar.gz |
StartedAt: 2024-05-04 08:29:01 -0000 (Sat, 04 May 2024) |
EndedAt: 2024-05-04 08:43:52 -0000 (Sat, 04 May 2024) |
EllapsedTime: 891.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: HTSeqGenie.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:HTSeqGenie.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings HTSeqGenie_4.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/HTSeqGenie.Rcheck’ * using R version 4.4.0 beta (2024-04-15 r86425) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘HTSeqGenie/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘HTSeqGenie’ version ‘4.34.0’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘HTSeqGenie’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: ‘ShortRead:::.set_omp_threads’ ‘gmapR:::..gsnap’ ‘gmapR:::GeneGenome’ ‘gmapR:::checkPackageInstalled’ ‘gmapR:::getDefaultGmapGenomePath’ ‘gmapR:::getGeneRoi’ ‘gmapR:::subsetRegion’ ‘parallel:::mckill’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... NOTE Foreign function call to a different package: .Call(ShortRead:::.set_omp_threads, ...) See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual. * checking R code for possible problems ... NOTE .makePreprocessAlignPlots: no visible binding for global variable ‘data’ .plot.in.out.min.max.readlength: no visible global function definition for ‘median’ FastQStreamer.init: no visible binding for '<<-' assignment to ‘FastQStreamer.lfqs’ FastQStreamer.init: no visible binding for '<<-' assignment to ‘FastQStreamer.chunkid’ FastQStreamer.init: no visible binding for '<<-' assignment to ‘FastQStreamer.subsampling_filter’ FastQStreamer.init: no visible binding for '<<-' assignment to ‘FastQStreamer.max_nbchunks’ addHandler: no visible binding for '<<-' assignment to ‘logging.handlers’ addHandler: no visible binding for global variable ‘logging.handlers’ addHandler: no visible binding for '<<-' assignment to ‘logging.file’ buildAnyFastaGenome: no visible global function definition for ‘getSeq’ buildGenomicFeaturesFromTxDb: no visible global function definition for ‘gaps’ buildGenomicFeaturesFromTxDb: no visible global function definition for ‘ranges’ buildTP53FastaGenome: no visible global function definition for ‘getSeq’ buildTallyParam: no visible global function definition for ‘seqinfo’ computeCoverage: no visible global function definition for ‘resize’ computeCoverage: no visible global function definition for ‘coverage’ estimateCutoffs : <anonymous>: no visible binding for global variable ‘quantile’ getGenomeSegments: no visible global function definition for ‘seqinfo’ hashVariants: no visible global function definition for ‘ranges’ isAboveQualityThresh: no visible global function definition for ‘Views’ isAboveQualityThresh: no visible global function definition for ‘viewMeans’ listIterator.init: no visible binding for '<<-' assignment to ‘listIterator.n’ listIterator.init: no visible binding for '<<-' assignment to ‘listIterator.x’ logReset: no visible binding for '<<-' assignment to ‘logging.handlers’ logReset: no visible binding for '<<-' assignment to ‘logging.loglevel’ logReset: no visible binding for '<<-' assignment to ‘logging.file’ loglevel: no visible binding for global variable ‘logging.loglevel’ loglevel: no visible binding for global variable ‘logging.handlers’ processChunks : tracefun: no visible binding for global variable ‘sjobs’ processChunks : tracefun: no visible binding for global variable ‘chunkid’ setLevel: no visible binding for '<<-' assignment to ‘logging.loglevel’ statCountFeatures: no visible global function definition for ‘quantile’ truncateReads: no visible global function definition for ‘subseq’ vcfStat: no visible global function definition for ‘quantile’ writeToFile: no visible binding for global variable ‘logging.file’ Undefined global functions or variables: Views chunkid coverage data gaps getSeq logging.file logging.handlers logging.loglevel median quantile ranges resize seqinfo sjobs subseq viewMeans Consider adding importFrom("stats", "median", "quantile") importFrom("utils", "data") to your NAMESPACE file. * checking Rd files ... NOTE checkRd: (-1) calculateTargetLengths.Rd:17: Lost braces; missing escapes or markup? 17 | Target length table and writes two files in {save_dir}/reports/images/TargetLenghts.[pdf|png]" | ^ checkRd: (-1) initLog.Rd:18: Lost braces; missing escapes or markup? 18 | Setup logging file in {save_dir}/progress.log | ^ * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... NOTE Documented arguments not in \usage in Rd file 'findVariantFile.Rd': ‘dir_path’ Documented arguments not in \usage in Rd file 'logdebug.Rd': ‘...’ Documented arguments not in \usage in Rd file 'logerror.Rd': ‘...’ Documented arguments not in \usage in Rd file 'loginfo.Rd': ‘...’ Documented arguments not in \usage in Rd file 'logwarn.Rd': ‘...’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘doRUnit.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 7 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/HTSeqGenie.Rcheck/00check.log’ for details.
HTSeqGenie.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL HTSeqGenie ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/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)
HTSeqGenie.Rcheck/tests/doRUnit.Rout
R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library("HTSeqGenie") Loading required package: gmapR Loading required package: GenomeInfoDb Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Loading required package: GenomicRanges Loading required package: Rsamtools Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Loading required package: ShortRead Loading required package: BiocParallel Loading required package: GenomicAlignments Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians Loading required package: VariantAnnotation Attaching package: 'VariantAnnotation' The following object is masked from 'package:base': tabulate > > source(getPackageFile("unitTests/runTests.R")) Loading required package: GenomicFeatures Loading required package: AnnotationDbi did not source anything in dirname= ./R Executing test function test.alignReads ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpliomS5/tp53-config.txt checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt 2024-05-04 08:36:24.315782 INFO::preprocessReads.R/preprocessReads: starting... 2024-05-04 08:36:24.324976 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/test-data/unit_tests_1.fastq 2024-05-04 08:36:24.330283 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/test-data/unit_tests_2.fastq 2024-05-04 08:36:24.332993 DEBUG::tools.R/processChunks: starting... 2024-05-04 08:36:27.642496 DEBUG::tools.R/processChunks: waiting for chunkid=[ ] ... 2024-05-04 08:36:27.644524 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpliomS5/test.alignReads.1022237a878076/chunks/chunk_000001/logs/progress.log 2024-05-04 08:36:30.560914 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.049 minutes 2024-05-04 08:36:30.562848 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmpliomS5/test.alignReads.1022237a878076/chunks/chunk_000002/logs/progress.log 2024-05-04 08:36:33.431063 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.048 minutes 2024-05-04 08:36:33.432968 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmpliomS5/test.alignReads.1022237a878076/chunks/chunk_000003/logs/progress.log 2024-05-04 08:36:36.286195 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.048 minutes 2024-05-04 08:36:36.325797 DEBUG::tools.R/processChunks: done 2024-05-04 08:36:36.330989 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ... 2024-05-04 08:36:36.334243 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.alignReads.1022237a878076/results/test_pe.adapter_contaminated_1.RData 2024-05-04 08:36:36.338289 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ... 2024-05-04 08:36:36.340916 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.alignReads.1022237a878076/results/test_pe.adapter_contaminated_2.RData 2024-05-04 08:36:36.353845 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 2024-05-04 08:36:36.356929 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.alignReads.1022237a878076/results/test_pe.summary_preprocess.tab 2024-05-04 08:36:36.361355 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpliomS5/test.alignReads.1022237a878076/bams/processed.aligner_input_1.fastq ... 2024-05-04 08:36:36.368045 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpliomS5/test.alignReads.1022237a878076/bams/processed.aligner_input_2.fastq ... 2024-05-04 08:36:36.373811 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpliomS5/test.alignReads.1022237a878076/reports/shortReadReport_1 ... 2024-05-04 08:36:38.21764 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpliomS5/test.alignReads.1022237a878076/reports/shortReadReport_2 ... 2024-05-04 08:36:39.717062 INFO::preprocessReads.R/preprocessReads: done 2024-05-04 08:36:39.776374 INFO::alignReads.R/alignReads: starting alignment... 2024-05-04 08:36:39.78328 DEBUG::tools.R/processChunks: starting... 2024-05-04 08:36:43.604064 DEBUG::tools.R/processChunks: waiting for chunkid=[ ] ... 2024-05-04 08:36:43.606324 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpliomS5/test.alignReads.1022237a878076/chunks/chunk_000001/logs/progress.log 2024-05-04 08:36:46.655905 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.051 minutes 2024-05-04 08:36:46.658174 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmpliomS5/test.alignReads.1022237a878076/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. 2024-05-04 08:36:49.391084 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.046 minutes 2024-05-04 08:36:49.393191 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmpliomS5/test.alignReads.1022237a878076/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. 2024-05-04 08:36:52.092095 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.045 minutes 2024-05-04 08:36:52.095324 DEBUG::tools.R/processChunks: done 2024-05-04 08:36:52.097117 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. 2024-05-04 08:36:52.422763 INFO::alignReads.R/mergeBAMsAcrossDirs: done 2024-05-04 08:36:52.434368 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.alignReads.1022237a878076/results/test_pe.summary_alignment.tab 2024-05-04 08:36:52.44502 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.alignReads.1022237a878076/results/test_pe.summary_analyzed_bamstats.tab 2024-05-04 08:36:52.447557 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report... 2024-05-04 08:36:52.72052 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.alignReads.1022237a878076/results/test_pe.summary_target_lengths.tab 2024-05-04 08:36:52.78125 INFO::reportPipelineQA.R/writePreprocessAlignReport: done 2024-05-04 08:36:52.782629 INFO::alignReads.R/alignReads: done done successfully. Executing test function test.alignReads.sparsechunks ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpliomS5/tp53-config.txt checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt 2024-05-04 08:36:53.077458 INFO::preprocessReads.R/preprocessReads: starting... 2024-05-04 08:36:53.080992 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/test-data/unit_tests_1.fastq 2024-05-04 08:36:53.162524 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 2 , totnbreads= 26 ) 2024-05-04 08:36:53.169398 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/test-data/unit_tests_1.fastq 2024-05-04 08:36:53.173807 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/test-data/unit_tests_2.fastq 2024-05-04 08:36:53.176492 DEBUG::tools.R/processChunks: starting... 2024-05-04 08:36:56.461686 DEBUG::tools.R/processChunks: waiting for chunkid=[ ] ... 2024-05-04 08:36:56.46368 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpliomS5/test.alignReads.sparsechunks.1022236478812/chunks/chunk_000001/logs/progress.log 2024-05-04 08:36:59.289714 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.047 minutes 2024-05-04 08:36:59.291546 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmpliomS5/test.alignReads.sparsechunks.1022236478812/chunks/chunk_000002/logs/progress.log 2024-05-04 08:37:02.092286 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.047 minutes 2024-05-04 08:37:02.094172 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmpliomS5/test.alignReads.sparsechunks.1022236478812/chunks/chunk_000003/logs/progress.log 2024-05-04 08:37:05.038079 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.049 minutes 2024-05-04 08:37:05.040075 DEBUG::tools.R/processChunks: starting chunkid= 4 ; see logfile= /home/biocbuild/tmp/RtmpliomS5/test.alignReads.sparsechunks.1022236478812/chunks/chunk_000004/logs/progress.log 2024-05-04 08:37:07.838371 DEBUG::tools.R/processChunks: done with chunkid= 4 ; elapsed.time= 0.047 minutes 2024-05-04 08:37:07.878324 DEBUG::tools.R/processChunks: done 2024-05-04 08:37:07.882777 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ... 2024-05-04 08:37:07.885932 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.alignReads.sparsechunks.1022236478812/results/test_pe.adapter_contaminated_1.RData 2024-05-04 08:37:07.890049 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ... 2024-05-04 08:37:07.892582 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.alignReads.sparsechunks.1022236478812/results/test_pe.adapter_contaminated_2.RData 2024-05-04 08:37:07.906143 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 2024-05-04 08:37:07.909095 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.alignReads.sparsechunks.1022236478812/results/test_pe.summary_preprocess.tab 2024-05-04 08:37:07.91378 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpliomS5/test.alignReads.sparsechunks.1022236478812/bams/processed.aligner_input_1.fastq ... 2024-05-04 08:37:07.92076 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpliomS5/test.alignReads.sparsechunks.1022236478812/bams/processed.aligner_input_2.fastq ... 2024-05-04 08:37:07.926439 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpliomS5/test.alignReads.sparsechunks.1022236478812/reports/shortReadReport_1 ... 2024-05-04 08:37:09.716796 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpliomS5/test.alignReads.sparsechunks.1022236478812/reports/shortReadReport_2 ... 2024-05-04 08:37:11.175257 INFO::preprocessReads.R/preprocessReads: done done successfully. Executing test function test.alignReadsOneSingleEnd ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpliomS5/tp53-config.txt checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt 2024-05-04 08:37:11.368275 INFO::alignReads.R/alignReadsChunk: running gsnap... 2024-05-04 08:37:11.374231 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/RtmpliomS5/test.alignReadsOneSingleEnd.102223370d26c/bams/test.alignReads /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/test-data/unit_tests_1.fastq 2>&1 2024-05-04 08:37:11.523301 INFO::alignReads.R/createSummaryAlignment: counting unique bam reads... 2024-05-04 08:37:11.657328 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.alignReadsOneSingleEnd.102223370d26c/results/test.alignReads.summary_alignment.tab 2024-05-04 08:37:11.705012 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.alignReadsOneSingleEnd.102223370d26c/results/test.alignReads.summary_analyzed_bamstats.tab 2024-05-04 08:37:11.70703 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/RtmpliomS5/tp53-config.txt checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt 2024-05-04 08:37:12.103226 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.genotype.1022235ee3487a/results/test_pe.coverage.RData 2024-05-04 08:37:12.105597 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/RtmpliomS5/test.genotype.1022235ee3487a/results/test_pe.coverage.bw 2024-05-04 08:37:12.28023 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.genotype.1022235ee3487a/results/test_pe.summary_coverage.tab 2024-05-04 08:37:12.282445 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants... 2024-05-04 08:37:25.239973 INFO::analyzeVariants.R/wrap.callVariants: calling variants... 2024-05-04 08:37:25.372661 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants... 2024-05-04 08:37:25.399377 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants... 2024-05-04 08:37:25.401684 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.genotype.1022235ee3487a/results/test_pe.raw_variants.RData 2024-05-04 08:37:25.405155 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.genotype.1022235ee3487a/results/test_pe.filtered_variants.RData 2024-05-04 08:37:25.407385 INFO::analyzeVariants.R/wrap.callVariants: ...done 2024-05-04 08:37:25.409378 INFO::analyzeVariants.R/writeVCF: writing vcf file... 2024-05-04 08:37:25.995872 INFO::analyzeVariants.R/writeVCF: ...done 2024-05-04 08:37:25.997602 INFO::analyzeVariants.R/.callGenotypes: calling genotypes... 2024-05-04 08:38:50.533031 INFO::analyzeVariants.R/writeVCF: writing vcf file... 2024-05-04 08:38:51.178023 INFO::analyzeVariants.R/writeVCF: ...done 2024-05-04 08:38:51.1794 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/RtmpliomS5/tp53-config.txt checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt 2024-05-04 08:38:51.79449 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants... 2024-05-04 08:39:04.754938 INFO::analyzeVariants.R/wrap.callVariants: calling variants... 2024-05-04 08:39:04.884055 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants... 2024-05-04 08:39:04.909842 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants... 2024-05-04 08:39:04.911892 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.wrap.callVariants.1022235ae5bc5c/results/test_pe.raw_variants.RData 2024-05-04 08:39:04.915214 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.wrap.callVariants.1022235ae5bc5c/results/test_pe.filtered_variants.RData 2024-05-04 08:39:04.917328 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/RtmpliomS5/tp53-config.txt checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt 2024-05-04 08:39:05.110667 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants... 2024-05-04 08:39:18.285363 INFO::analyzeVariants.R/wrap.callVariants: calling variants... 2024-05-04 08:39:18.374704 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants... 2024-05-04 08:39:18.399782 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants... 2024-05-04 08:39:18.401701 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.wrap.callVariants.filters.10222364d4bdf0/results/test_pe.raw_variants.RData 2024-05-04 08:39:18.404838 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.wrap.callVariants.filters.10222364d4bdf0/results/test_pe.filtered_variants.RData 2024-05-04 08:39:18.406699 INFO::analyzeVariants.R/wrap.callVariants: ...done 2024-05-04 08:39:18.408778 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants... 2024-05-04 08:39:31.524792 INFO::analyzeVariants.R/wrap.callVariants: calling variants... 2024-05-04 08:39:31.581686 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants... 2024-05-04 08:39:31.606698 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants... 2024-05-04 08:39:31.608653 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.wrap.callVariants.filters.10222364d4bdf0/results/test_pe.raw_variants.RData 2024-05-04 08:39:31.611921 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.wrap.callVariants.filters.10222364d4bdf0/results/test_pe.filtered_variants.RData 2024-05-04 08:39:31.614543 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/RtmpliomS5/tp53-config.txt checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt 2024-05-04 08:39:31.973187 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants... 2024-05-04 08:39:31.975337 INFO::analyzeVariants.R/buildTallyParam: restricting variant calls using 'which' 2024-05-04 08:39:35.792132 INFO::analyzeVariants.R/wrap.callVariants: calling variants... 2024-05-04 08:39:35.91277 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants... 2024-05-04 08:39:35.940068 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants... 2024-05-04 08:39:35.942071 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.wrap.callVariants.which.1022233645cf9/results/test_pe.raw_variants.RData 2024-05-04 08:39:35.944589 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.wrap.callVariants.which.1022233645cf9/results/test_pe.filtered_variants.RData 2024-05-04 08:39:35.946547 INFO::analyzeVariants.R/wrap.callVariants: ...done done successfully. Executing test function test.writeVCF.NULL ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpliomS5/tp53-config.txt checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt 2024-05-04 08:39:36.154551 INFO::analyzeVariants.R/writeVCF: writing vcf file... 2024-05-04 08:39:36.156389 INFO::analyzeVariants.R/writeVCF: ...done done successfully. Executing test function test.writeVCF.vcfStat ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpliomS5/tp53-config.txt checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt 2024-05-04 08:39:38.154188 INFO::analyzeVariants.R/writeVCF: writing vcf file... 2024-05-04 08:39:38.455357 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 ... 2024-05-04 08:40:49.548537 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/vzuqyoxr/merged/results/bla.coverage.RData 2024-05-04 08:40:49.552839 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/RtmpliomS5/vzuqyoxr/merged/results/bla.coverage.bw 2024-05-04 08:40:49.676373 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/vzuqyoxr/merged/results/bla.summary_coverage.tab done successfully. Executing test function test.mergeCoverage.sparse ... 2024-05-04 08:40:51.042982 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/xecandtb/merged/results/bla.coverage.RData 2024-05-04 08:40:51.044894 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/RtmpliomS5/xecandtb/merged/results/bla.coverage.bw 2024-05-04 08:40:51.059469 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/xecandtb/merged/results/bla.summary_coverage.tab done successfully. Executing test function test.checkConfig.analyzeVariants ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpliomS5/tp53-config.txt checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/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/RtmpliomS5/tp53-config.txt checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpliomS5/tp53-config.txt checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpliomS5/tp53-config.txt checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpliomS5/tp53-config.txt checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/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/RtmpliomS5/tp53-config.txt checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpliomS5/tp53-config.txt checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpliomS5/tp53-config.txt checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpliomS5/tp53-config.txt checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/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/RtmpliomS5/tp53-config.txt checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt 2024-05-04 08:40:52.617246 INFO::detectRRNA.R/detectRRNA: searching for rRNA contamination... 2024-05-04 08:40:52.618818 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/tmp/RtmpliomS5/test.detectRRNA.102223733e5040/bams/rRNA_contam/input1.fastq 2024-05-04 08:40:52.623455 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/RtmpliomS5/test.detectRRNA.102223733e5040/bams/rRNA_contam/test_se /home/biocbuild/tmp/RtmpliomS5/test.detectRRNA.102223733e5040/bams/rRNA_contam/input1.fastq 2>&1 2024-05-04 08:40:52.731819 INFO::detectRRNA.R/detectRRNA: contaminated fraction= 1 2024-05-04 08:40:52.733178 INFO::detectRRNA.R/detectRRNA: done done successfully. Executing test function test.detectRRNA.paired_end ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpliomS5/tp53-config.txt checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt 2024-05-04 08:40:52.92256 INFO::detectRRNA.R/detectRRNA: searching for rRNA contamination... 2024-05-04 08:40:52.924743 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/tmp/RtmpliomS5/test.detectRRNA.paired_end.1022236252aedb/bams/rRNA_contam/input1.fastq 2024-05-04 08:40:52.926919 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/tmp/RtmpliomS5/test.detectRRNA.paired_end.1022236252aedb/bams/rRNA_contam/input2.fastq 2024-05-04 08:40:52.93015 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/RtmpliomS5/test.detectRRNA.paired_end.1022236252aedb/bams/rRNA_contam/test_pe /home/biocbuild/tmp/RtmpliomS5/test.detectRRNA.paired_end.1022236252aedb/bams/rRNA_contam/input1.fastq -a paired /home/biocbuild/tmp/RtmpliomS5/test.detectRRNA.paired_end.1022236252aedb/bams/rRNA_contam/input2.fastq 2>&1 2024-05-04 08:40:53.189312 INFO::detectRRNA.R/detectRRNA: contaminated fraction= 1 2024-05-04 08:40:53.191114 INFO::detectRRNA.R/detectRRNA: done done successfully. Executing test function test.getRRNAIds ... 2024-05-04 08:40:53.220526 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/RtmpliomS5/test_get_rRNA_idskpsfzang/test_pe /home/biocbuild/tmp/RtmpliomS5/test_get_rRNA_idskpsfzang/1.fastq -a paired /home/biocbuild/tmp/RtmpliomS5/test_get_rRNA_idskpsfzang/2.fastq 2>&1 done successfully. Executing test function test.getRRNAIds_random ... 2024-05-04 08:40:53.516361 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/RtmpliomS5/test_get_rRNAIds_randomogsxprcq/test_pe /home/biocbuild/tmp/RtmpliomS5/test_get_rRNAIds_randomogsxprcq/1.fastq 2>&1 done successfully. Executing test function test.filterByLength ... 2024-05-04 08:40:53.695609 INFO::filterQuality.R/filterQuality: filterByLength... 2024-05-04 08:40:53.697574 INFO::filterQuality.R/filterByLength: fraction of filtered short reads= 0.5 2024-05-04 08:40:53.698834 INFO::filterQuality.R/filterByLength: done 2024-05-04 08:40:53.767222 INFO::filterQuality.R/filterQuality: filterByLength... 2024-05-04 08:40:53.768511 INFO::filterQuality.R/filterByLength: fraction of filtered short reads= 1 2024-05-04 08:40:53.769732 INFO::filterQuality.R/filterByLength: done done successfully. Executing test function test.isAboveQualityThresh ... done successfully. Executing test function test.trimTailsByQuality ... 2024-05-04 08:40:53.845237 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ... 2024-05-04 08:40:53.858076 INFO::preprocessReads.R/preprocessReadsChunk: done 2024-05-04 08:40:53.859685 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ... 2024-05-04 08:40:53.866333 INFO::preprocessReads.R/preprocessReadsChunk: done 2024-05-04 08:40:53.867873 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ... 2024-05-04 08:40:53.87447 INFO::preprocessReads.R/preprocessReadsChunk: done 2024-05-04 08:40:53.876011 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ... 2024-05-04 08:40:53.882702 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= //home/biocbuild/tmp/RtmpliomS5/tp53-config.txt checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt 2024-05-04 08:40:54.246944 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/test-data/unit_tests_1.fastq 2024-05-04 08:40:54.250204 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-beta-2024-04-15_r86425/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/RtmpliomS5/tp53-config.txt checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt 2024-05-04 08:40:54.478822 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/test-data/unit_tests_1.fastq 2024-05-04 08:40:54.574478 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 ) 2024-05-04 08:40:54.578336 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/test-data/unit_tests_1.fastq 2024-05-04 08:40:54.581525 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-beta-2024-04-15_r86425/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/RtmpliomS5/tp53-config.txt checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt 2024-05-04 08:40:54.833388 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-beta-2024-04-15_r86425/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/RtmpliomS5/tp53-config.txt checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt 2024-05-04 08:40:55.017545 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-beta-2024-04-15_r86425/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/RtmpliomS5/tp53-config.txt checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt 2024-05-04 08:40:55.185075 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/test-data/unit_tests_1.fastq 2024-05-04 08:40:55.240795 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 ) 2024-05-04 08:40:55.244333 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/test-data/unit_tests_1.fastq 2024-05-04 08:40:55.247521 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/test-data/unit_tests_2.fastq checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpliomS5/tp53-config.txt checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt 2024-05-04 08:40:55.482044 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/test-data/unit_tests_1.fastq 2024-05-04 08:40:55.537703 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 ) 2024-05-04 08:40:55.541179 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/test-data/unit_tests_1.fastq 2024-05-04 08:40:55.544599 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-beta-2024-04-15_r86425/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/RtmpliomS5/tp53-config.txt checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt done successfully. Executing test function test.mergeLanes ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpliomS5/tp53-config.txt checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt 2024-05-04 08:40:56.397774 INFO::preprocessReads.R/preprocessReads: starting... 2024-05-04 08:40:56.404968 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/test-data/unit_tests_1.fastq 2024-05-04 08:40:56.409833 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/test-data/unit_tests_2.fastq 2024-05-04 08:40:56.412955 DEBUG::tools.R/processChunks: starting... 2024-05-04 08:41:01.270757 DEBUG::tools.R/processChunks: waiting for chunkid=[ ] ... 2024-05-04 08:41:01.272853 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/chunks/chunk_000001/logs/progress.log 2024-05-04 08:41:03.981021 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.045 minutes 2024-05-04 08:41:03.983005 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/chunks/chunk_000002/logs/progress.log 2024-05-04 08:41:06.725147 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.046 minutes 2024-05-04 08:41:06.727217 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/chunks/chunk_000003/logs/progress.log 2024-05-04 08:41:09.510745 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.046 minutes 2024-05-04 08:41:09.562871 DEBUG::tools.R/processChunks: done 2024-05-04 08:41:09.566721 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ... 2024-05-04 08:41:09.569169 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/results/test_pe.adapter_contaminated_1.RData 2024-05-04 08:41:09.572258 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ... 2024-05-04 08:41:09.574546 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/results/test_pe.adapter_contaminated_2.RData 2024-05-04 08:41:09.585537 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 2024-05-04 08:41:09.588255 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/results/test_pe.summary_preprocess.tab 2024-05-04 08:41:09.591853 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/bams/processed.aligner_input_1.fastq ... 2024-05-04 08:41:09.598778 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/bams/processed.aligner_input_2.fastq ... 2024-05-04 08:41:09.604686 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/reports/shortReadReport_1 ... 2024-05-04 08:41:11.481674 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/reports/shortReadReport_2 ... 2024-05-04 08:41:12.997846 INFO::preprocessReads.R/preprocessReads: done 2024-05-04 08:41:13.075587 INFO::alignReads.R/alignReads: starting alignment... 2024-05-04 08:41:13.080633 DEBUG::tools.R/processChunks: starting... 2024-05-04 08:41:18.407449 DEBUG::tools.R/processChunks: waiting for chunkid=[ ] ... 2024-05-04 08:41:18.409899 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/chunks/chunk_000001/logs/progress.log 2024-05-04 08:41:21.028505 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.044 minutes 2024-05-04 08:41:21.030758 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/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. 2024-05-04 08:41:23.709662 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.045 minutes 2024-05-04 08:41:23.71209 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/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. 2024-05-04 08:41:26.348518 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.044 minutes 2024-05-04 08:41:26.351836 DEBUG::tools.R/processChunks: done 2024-05-04 08:41:26.353679 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. 2024-05-04 08:41:26.638465 INFO::alignReads.R/mergeBAMsAcrossDirs: done 2024-05-04 08:41:26.648561 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/results/test_pe.summary_alignment.tab 2024-05-04 08:41:26.658331 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/results/test_pe.summary_analyzed_bamstats.tab 2024-05-04 08:41:26.660891 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report... 2024-05-04 08:41:26.906336 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/results/test_pe.summary_target_lengths.tab 2024-05-04 08:41:26.965015 INFO::reportPipelineQA.R/writePreprocessAlignReport: done 2024-05-04 08:41:26.966307 INFO::alignReads.R/alignReads: done 2024-05-04 08:41:27.047169 INFO::countGenomicFeatures.R/countGenomicFeatures: starting... 2024-05-04 08:41:27.067413 DEBUG::tools.R/processChunks: starting... 2024-05-04 08:41:31.262822 DEBUG::tools.R/processChunks: waiting for chunkid=[ ] ... 2024-05-04 08:41:31.265136 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/chunks/chunk_000001/logs/progress.log 2024-05-04 08:41:33.860271 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.043 minutes 2024-05-04 08:41:33.862679 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/chunks/chunk_000002/logs/progress.log 2024-05-04 08:41:36.442657 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.043 minutes 2024-05-04 08:41:36.444945 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/chunks/chunk_000003/logs/progress.log 2024-05-04 08:41:39.000922 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.043 minutes 2024-05-04 08:41:39.004229 DEBUG::tools.R/processChunks: done 2024-05-04 08:41:39.006371 INFO::countGenomicFeatures.R/mergeCounts: starting... 2024-05-04 08:41:39.023261 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/results/test_pe.counts_exon.tab 2024-05-04 08:41:39.037354 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/results/test_pe.counts_exon_disjoint.tab 2024-05-04 08:41:39.04629 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/results/test_pe.counts_gene.tab 2024-05-04 08:41:39.053608 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/results/test_pe.counts_gene_coding.tab 2024-05-04 08:41:39.060757 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/results/test_pe.counts_gene_exonic.tab 2024-05-04 08:41:39.068143 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/results/test_pe.counts_intergenic.tab 2024-05-04 08:41:39.079975 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/results/test_pe.counts_intron.tab 2024-05-04 08:41:39.083635 INFO::countGenomicFeatures.R/mergeCounts: done 2024-05-04 08:41:39.091188 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/results/test_pe.summary_counts.tab 2024-05-04 08:41:39.093472 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts... 2024-05-04 08:41:39.43887 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done 2024-05-04 08:41:39.440183 INFO::countGenomicFeatures.R/countGenomicFeatures: done... 2024-05-04 08:41:39.518199 INFO::coverage.R/calculateCoverage: starting... 2024-05-04 08:41:39.522862 DEBUG::tools.R/processChunks: starting... 2024-05-04 08:41:44.153967 DEBUG::tools.R/processChunks: waiting for chunkid=[ ] ... 2024-05-04 08:41:44.156407 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/chunks/chunk_000001/logs/progress.log 2024-05-04 08:41:46.343653 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.036 minutes 2024-05-04 08:41:46.345651 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/chunks/chunk_000002/logs/progress.log 2024-05-04 08:41:48.543295 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.037 minutes 2024-05-04 08:41:48.54554 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/chunks/chunk_000003/logs/progress.log 2024-05-04 08:41:50.755467 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.037 minutes 2024-05-04 08:41:50.759334 DEBUG::tools.R/processChunks: done 2024-05-04 08:41:52.576793 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/results/test_pe.coverage.RData 2024-05-04 08:41:52.578868 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/results/test_pe.coverage.bw 2024-05-04 08:41:52.595731 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/results/test_pe.summary_coverage.tab 2024-05-04 08:41:52.597712 INFO::coverage.R/calculateCoverage: done 2024-05-04 08:41:52.600063 INFO::analyzeVariants/analyzeVariants: starting ... 2024-05-04 08:41:52.68485 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants... 2024-05-04 08:41:56.553287 INFO::analyzeVariants.R/wrap.callVariants: calling variants... 2024-05-04 08:41:56.671934 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants... 2024-05-04 08:41:56.699084 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants... 2024-05-04 08:41:56.701102 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/results/test_pe.raw_variants.RData 2024-05-04 08:41:56.703839 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/results/test_pe.filtered_variants.RData 2024-05-04 08:41:56.705736 INFO::analyzeVariants.R/wrap.callVariants: ...done 2024-05-04 08:41:56.707263 INFO::analyzeVariants.R/writeVCF: writing vcf file... 2024-05-04 08:41:57.022634 INFO::analyzeVariants.R/writeVCF: ...done 2024-05-04 08:41:57.161308 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/results/test_pe.summary_variants.tab 2024-05-04 08:41:57.163839 INFO::analyzeVariants/analyzeVariants: done 2024-05-04 08:41:57.167748 INFO::Pipeline run successful. 2024-05-04 08:41:57.34887 INFO::mergeLanes.R/doMergeLanes: starting... 2024-05-04 08:41:57.354604 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ... 2024-05-04 08:41:57.357723 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/merged/results/merged.adapter_contaminated_1.RData 2024-05-04 08:41:57.361876 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ... 2024-05-04 08:41:57.364978 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/merged/results/merged.adapter_contaminated_2.RData 2024-05-04 08:41:57.380082 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 2024-05-04 08:41:57.383354 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/merged/results/merged.summary_preprocess.tab 2024-05-04 08:41:57.386388 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. 2024-05-04 08:41:57.725526 INFO::alignReads.R/mergeBAMsAcrossDirs: done 2024-05-04 08:41:57.734983 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/merged/results/merged.summary_alignment.tab 2024-05-04 08:41:57.746157 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/merged/results/merged.summary_analyzed_bamstats.tab 2024-05-04 08:41:57.748998 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report... 2024-05-04 08:41:58.007559 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/merged/results/merged.summary_target_lengths.tab 2024-05-04 08:41:58.070862 INFO::reportPipelineQA.R/writePreprocessAlignReport: done 2024-05-04 08:41:58.112677 INFO::countGenomicFeatures.R/mergeCounts: starting... 2024-05-04 08:41:58.135967 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/merged/results/merged.counts_exon.tab 2024-05-04 08:41:58.152465 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/merged/results/merged.counts_exon_disjoint.tab 2024-05-04 08:41:58.161751 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/merged/results/merged.counts_gene.tab 2024-05-04 08:41:58.169572 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/merged/results/merged.counts_gene_coding.tab 2024-05-04 08:41:58.177284 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/merged/results/merged.counts_gene_exonic.tab 2024-05-04 08:41:58.185732 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/merged/results/merged.counts_intergenic.tab 2024-05-04 08:41:58.199789 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/merged/results/merged.counts_intron.tab 2024-05-04 08:41:58.203511 INFO::countGenomicFeatures.R/mergeCounts: done 2024-05-04 08:41:58.212236 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/merged/results/merged.summary_counts.tab 2024-05-04 08:41:58.21475 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts... 2024-05-04 08:41:58.499008 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done 2024-05-04 08:42:00.697974 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/merged/results/merged.coverage.RData 2024-05-04 08:42:00.700974 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/merged/results/merged.coverage.bw 2024-05-04 08:42:00.716113 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/merged/results/merged.summary_coverage.tab 2024-05-04 08:42:00.755651 INFO::analyzeVariants/analyzeVariants: starting ... 2024-05-04 08:42:00.834066 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants... 2024-05-04 08:42:04.526232 INFO::analyzeVariants.R/wrap.callVariants: calling variants... 2024-05-04 08:42:04.639954 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants... 2024-05-04 08:42:04.66502 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants... 2024-05-04 08:42:04.666964 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/merged/results/merged.raw_variants.RData 2024-05-04 08:42:04.669236 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/merged/results/merged.filtered_variants.RData 2024-05-04 08:42:04.670979 INFO::analyzeVariants.R/wrap.callVariants: ...done 2024-05-04 08:42:04.672465 INFO::analyzeVariants.R/writeVCF: writing vcf file... 2024-05-04 08:42:04.995186 INFO::analyzeVariants.R/writeVCF: ...done 2024-05-04 08:42:05.138575 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.mergeLanes.102223437af92c/merged/results/merged.summary_variants.tab 2024-05-04 08:42:05.14127 INFO::analyzeVariants/analyzeVariants: done 2024-05-04 08:42:05.144341 INFO::mergeLanes.R/doMergeLanes: merge lanes successful. done successfully. Executing test function test.markDuplicates ... Timing stopped at: 0 0 0.001 Error in DEACTIVATED("Skipped markDuplicates() test") : Skipped markDuplicates() test In addition: There were 28 warnings (use warnings() to see them) done successfully. Executing test function test.markDuplicates_w_outfile ... Timing stopped at: 0 0 0 Error in DEACTIVATED("Skipped markDuplicates() test") : Skipped markDuplicates() test done successfully. Executing test function test.preprocessReads ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpliomS5/tp53-config.txt checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt 2024-05-04 08:42:05.496858 INFO::preprocessReads.R/preprocessReads: starting... 2024-05-04 08:42:05.518412 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/test-data/unit_tests_1.fastq 2024-05-04 08:42:05.538213 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/test-data/unit_tests_2.fastq 2024-05-04 08:42:05.541321 DEBUG::tools.R/processChunks: starting... 2024-05-04 08:42:08.990317 DEBUG::tools.R/processChunks: waiting for chunkid=[ ] ... 2024-05-04 08:42:08.992461 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpliomS5/test.preprocessReads.10222310b0c056/chunks/chunk_000001/logs/progress.log 2024-05-04 08:42:11.743628 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.046 minutes 2024-05-04 08:42:11.795393 DEBUG::tools.R/processChunks: done 2024-05-04 08:42:11.798174 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ... 2024-05-04 08:42:11.80018 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.preprocessReads.10222310b0c056/results/test_pe.adapter_contaminated_1.RData 2024-05-04 08:42:11.802873 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ... 2024-05-04 08:42:11.804924 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.preprocessReads.10222310b0c056/results/test_pe.adapter_contaminated_2.RData 2024-05-04 08:42:11.813262 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 2024-05-04 08:42:11.815742 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.preprocessReads.10222310b0c056/results/test_pe.summary_preprocess.tab 2024-05-04 08:42:11.818549 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpliomS5/test.preprocessReads.10222310b0c056/bams/processed.aligner_input_1.fastq ... 2024-05-04 08:42:11.824426 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpliomS5/test.preprocessReads.10222310b0c056/bams/processed.aligner_input_2.fastq ... 2024-05-04 08:42:11.83025 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpliomS5/test.preprocessReads.10222310b0c056/reports/shortReadReport_1 ... 2024-05-04 08:42:13.711793 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpliomS5/test.preprocessReads.10222310b0c056/reports/shortReadReport_2 ... 2024-05-04 08:42:15.217861 INFO::preprocessReads.R/preprocessReads: done done successfully. Executing test function test.preprocessReads.minichunks ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpliomS5/tp53-config.txt checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt 2024-05-04 08:42:15.507963 INFO::preprocessReads.R/preprocessReads: starting... 2024-05-04 08:42:15.514885 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/test-data/unit_tests_1.fastq 2024-05-04 08:42:15.520035 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/test-data/unit_tests_2.fastq 2024-05-04 08:42:15.523155 DEBUG::tools.R/processChunks: starting... 2024-05-04 08:42:18.866406 DEBUG::tools.R/processChunks: waiting for chunkid=[ ] ... 2024-05-04 08:42:18.86841 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpliomS5/test.preprocessReads.minichunks.10222319c2628d/chunks/chunk_000001/logs/progress.log 2024-05-04 08:42:21.643982 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.046 minutes 2024-05-04 08:42:21.646101 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmpliomS5/test.preprocessReads.minichunks.10222319c2628d/chunks/chunk_000002/logs/progress.log 2024-05-04 08:42:24.479309 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.047 minutes 2024-05-04 08:42:24.48152 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmpliomS5/test.preprocessReads.minichunks.10222319c2628d/chunks/chunk_000003/logs/progress.log 2024-05-04 08:42:27.301777 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.047 minutes 2024-05-04 08:42:27.354773 DEBUG::tools.R/processChunks: done 2024-05-04 08:42:27.35842 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ... 2024-05-04 08:42:27.360787 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.preprocessReads.minichunks.10222319c2628d/results/test_pe.adapter_contaminated_1.RData 2024-05-04 08:42:27.363807 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ... 2024-05-04 08:42:27.366027 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.preprocessReads.minichunks.10222319c2628d/results/test_pe.adapter_contaminated_2.RData 2024-05-04 08:42:27.377186 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 2024-05-04 08:42:27.379905 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.preprocessReads.minichunks.10222319c2628d/results/test_pe.summary_preprocess.tab 2024-05-04 08:42:27.383652 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpliomS5/test.preprocessReads.minichunks.10222319c2628d/bams/processed.aligner_input_1.fastq ... 2024-05-04 08:42:27.390555 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpliomS5/test.preprocessReads.minichunks.10222319c2628d/bams/processed.aligner_input_2.fastq ... 2024-05-04 08:42:27.396284 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpliomS5/test.preprocessReads.minichunks.10222319c2628d/reports/shortReadReport_1 ... 2024-05-04 08:42:29.307747 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpliomS5/test.preprocessReads.minichunks.10222319c2628d/reports/shortReadReport_2 ... 2024-05-04 08:42:30.842263 INFO::preprocessReads.R/preprocessReads: done done successfully. Executing test function test.preprocessReads_single_end ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpliomS5/tp53-config.txt checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt 2024-05-04 08:42:31.08989 INFO::preprocessReads.R/preprocessReads: starting... 2024-05-04 08:42:31.111917 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/test-data/unit_tests_1.fastq 2024-05-04 08:42:31.11506 DEBUG::tools.R/processChunks: starting... 2024-05-04 08:42:34.53991 DEBUG::tools.R/processChunks: waiting for chunkid=[ ] ... 2024-05-04 08:42:34.541921 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpliomS5/test.preprocessReads_single_end.1022237b5e4988/chunks/chunk_000001/logs/progress.log 2024-05-04 08:42:36.982468 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.041 minutes 2024-05-04 08:42:37.024809 DEBUG::tools.R/processChunks: done 2024-05-04 08:42:37.028144 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ... 2024-05-04 08:42:37.030771 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.preprocessReads_single_end.1022237b5e4988/results/test_se.adapter_contaminated_1.RData 2024-05-04 08:42:37.039454 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 2024-05-04 08:42:37.041907 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.preprocessReads_single_end.1022237b5e4988/results/test_se.summary_preprocess.tab 2024-05-04 08:42:37.044702 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpliomS5/test.preprocessReads_single_end.1022237b5e4988/bams/processed.aligner_input_1.fastq ... 2024-05-04 08:42:37.050643 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpliomS5/test.preprocessReads_single_end.1022237b5e4988/reports/shortReadReport_1 ... 2024-05-04 08:42:38.879553 INFO::preprocessReads.R/preprocessReads: done done successfully. Executing test function test.readRNASeqEnds ... done successfully. Executing test function test.readRNASeqEnds.dupmark ... done successfully. Executing test function test.how_many ... done successfully. Executing test function test.plotDF ... done successfully. Executing test function test.relativeBarPlot ... done successfully. Executing test function test.runPipeline ... checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt 2024-05-04 08:42:39.615806 INFO::preprocessReads.R/preprocessReads: starting... 2024-05-04 08:42:39.636873 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/extdata/H1993_TP53_subset2500_1.fastq.gz 2024-05-04 08:42:39.656773 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/extdata/H1993_TP53_subset2500_2.fastq.gz 2024-05-04 08:42:39.659638 DEBUG::tools.R/processChunks: starting... 2024-05-04 08:42:43.145631 DEBUG::tools.R/processChunks: waiting for chunkid=[ ] ... 2024-05-04 08:42:43.147636 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= test/chunks/chunk_000001/logs/progress.log 2024-05-04 08:42:46.159414 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.05 minutes 2024-05-04 08:42:46.210186 DEBUG::tools.R/processChunks: done 2024-05-04 08:42:46.213161 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ... 2024-05-04 08:42:46.215197 INFO::io.R/saveWithID: saving file= test/results/test.adapter_contaminated_1.RData 2024-05-04 08:42:46.217391 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ... 2024-05-04 08:42:46.21931 INFO::io.R/saveWithID: saving file= test/results/test.adapter_contaminated_2.RData 2024-05-04 08:42:46.227113 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 2024-05-04 08:42:46.229494 INFO::io.R/saveWithID: saving file= test/results/test.summary_preprocess.tab 2024-05-04 08:42:46.232314 INFO::preprocessReads.R/mergePreprocessedReads: merging file= test/bams/processed.aligner_input_1.fastq ... 2024-05-04 08:42:46.23935 INFO::preprocessReads.R/mergePreprocessedReads: merging file= test/bams/processed.aligner_input_2.fastq ... 2024-05-04 08:42:46.246112 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= test/reports/shortReadReport_1 ... 2024-05-04 08:42:48.329839 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= test/reports/shortReadReport_2 ... 2024-05-04 08:42:50.090041 INFO::preprocessReads.R/preprocessReads: done 2024-05-04 08:42:50.171115 INFO::alignReads.R/alignReads: starting alignment... 2024-05-04 08:42:50.175834 DEBUG::tools.R/processChunks: starting... 2024-05-04 08:42:53.628448 DEBUG::tools.R/processChunks: waiting for chunkid=[ ] ... 2024-05-04 08:42:53.631137 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= test/chunks/chunk_000001/logs/progress.log [bam_translate] PG tag "A" on read "HISEQ1:109:D093LACXX:4:2205:16499:6611" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID. [bam_translate] PG tag "A" on read "HISEQ1:109:D093LACXX:4:1206:17367:135118" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID. [bam_translate] PG tag "A" on read "HISEQ1:109:D093LACXX:4:1304:1838:53573" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID. [bam_translate] PG tag "A" on read "HISEQ1:109:D093LACXX:4:2303:2956:116587" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID. [bam_translate] PG tag "M" on read "HISEQ1:109:D093LACXX:4:2205:16499:6611" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID. [bam_translate] PG tag "T" on read "HISEQ1:109:D093LACXX:4:1206:20028:108227" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID. [bam_translate] PG tag "T" on read "HISEQ1:109:D093LACXX:4:1207:19518:143960" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID. [bam_translate] PG tag "T" on read "HISEQ1:109:D093LACXX:4:2207:4065:173048" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID. 2024-05-04 08:42:59.488415 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.098 minutes 2024-05-04 08:42:59.491634 DEBUG::tools.R/processChunks: done 2024-05-04 08:42:59.493486 INFO::alignReads.R/mergeBAMsAcrossDirs: starting... 2024-05-04 08:42:59.528812 INFO::alignReads.R/mergeBAMsAcrossDirs: done 2024-05-04 08:42:59.537069 INFO::io.R/saveWithID: saving file= test/results/test.summary_alignment.tab 2024-05-04 08:42:59.544945 INFO::io.R/saveWithID: saving file= test/results/test.summary_analyzed_bamstats.tab 2024-05-04 08:42:59.547888 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report... 2024-05-04 08:42:59.73798 INFO::io.R/saveWithID: saving file= test/results/test.summary_target_lengths.tab 2024-05-04 08:42:59.797008 INFO::reportPipelineQA.R/writePreprocessAlignReport: done 2024-05-04 08:42:59.798398 INFO::alignReads.R/alignReads: done 2024-05-04 08:42:59.880758 INFO::countGenomicFeatures.R/countGenomicFeatures: starting... 2024-05-04 08:42:59.899372 DEBUG::tools.R/processChunks: starting... 2024-05-04 08:43:04.670649 DEBUG::tools.R/processChunks: waiting for chunkid=[ ] ... 2024-05-04 08:43:04.672967 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= test/chunks/chunk_000001/logs/progress.log 2024-05-04 08:43:07.29358 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.044 minutes 2024-05-04 08:43:07.297196 DEBUG::tools.R/processChunks: done 2024-05-04 08:43:07.299406 INFO::countGenomicFeatures.R/mergeCounts: starting... 2024-05-04 08:43:07.311414 INFO::io.R/saveWithID: saving file= test/results/test.counts_exon.tab 2024-05-04 08:43:07.322083 INFO::io.R/saveWithID: saving file= test/results/test.counts_exon_disjoint.tab 2024-05-04 08:43:07.329767 INFO::io.R/saveWithID: saving file= test/results/test.counts_gene.tab 2024-05-04 08:43:07.335262 INFO::io.R/saveWithID: saving file= test/results/test.counts_gene_coding.tab 2024-05-04 08:43:07.340579 INFO::io.R/saveWithID: saving file= test/results/test.counts_gene_exonic.tab 2024-05-04 08:43:07.345858 INFO::io.R/saveWithID: saving file= test/results/test.counts_intergenic.tab 2024-05-04 08:43:07.353595 INFO::io.R/saveWithID: saving file= test/results/test.counts_intron.tab 2024-05-04 08:43:07.357655 INFO::countGenomicFeatures.R/mergeCounts: done 2024-05-04 08:43:07.362648 INFO::io.R/saveWithID: saving file= test/results/test.summary_counts.tab 2024-05-04 08:43:07.365037 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts... 2024-05-04 08:43:07.633293 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done 2024-05-04 08:43:07.634618 INFO::countGenomicFeatures.R/countGenomicFeatures: done... 2024-05-04 08:43:07.715472 INFO::coverage.R/calculateCoverage: starting... 2024-05-04 08:43:07.719738 DEBUG::tools.R/processChunks: starting... 2024-05-04 08:43:12.746503 DEBUG::tools.R/processChunks: waiting for chunkid=[ ] ... 2024-05-04 08:43:12.748919 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= test/chunks/chunk_000001/logs/progress.log 2024-05-04 08:43:15.149107 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.04 minutes 2024-05-04 08:43:15.152355 DEBUG::tools.R/processChunks: done 2024-05-04 08:43:16.843105 INFO::io.R/saveWithID: saving file= test/results/test.coverage.RData 2024-05-04 08:43:16.845027 INFO::coverage.R/saveCoverage: saving file= test/results/test.coverage.bw 2024-05-04 08:43:16.948266 INFO::io.R/saveWithID: saving file= test/results/test.summary_coverage.tab 2024-05-04 08:43:16.950074 INFO::coverage.R/calculateCoverage: done 2024-05-04 08:43:16.951675 INFO::analyzeVariants/analyzeVariants: starting ... 2024-05-04 08:43:17.033181 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants... 2024-05-04 08:43:30.693554 INFO::analyzeVariants.R/wrap.callVariants: calling variants... 2024-05-04 08:43:30.805487 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants... 2024-05-04 08:43:30.830034 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants... 2024-05-04 08:43:30.831976 INFO::io.R/saveWithID: saving file= test/results/test.raw_variants.RData 2024-05-04 08:43:30.835066 INFO::io.R/saveWithID: saving file= test/results/test.filtered_variants.RData 2024-05-04 08:43:30.836941 INFO::analyzeVariants.R/wrap.callVariants: ...done 2024-05-04 08:43:30.838363 INFO::analyzeVariants.R/writeVCF: writing vcf file... 2024-05-04 08:43:31.159365 INFO::analyzeVariants.R/writeVCF: ...done 2024-05-04 08:43:31.300931 INFO::io.R/saveWithID: saving file= test/results/test.summary_variants.tab 2024-05-04 08:43:31.303438 INFO::analyzeVariants/analyzeVariants: done 2024-05-04 08:43:31.308905 INFO::Pipeline run successful. done successfully. Executing test function test.calculateTargetLength ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpliomS5/tp53-config.txt checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/config/default-config.txt 2024-05-04 08:43:31.58483 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpliomS5/test.calcTargetLengths.102223696c1c19/results/test_pe.summary_target_lengths.tab done successfully. Executing test function test.sclapply ... done successfully. Executing test function test.tryKeepTraceback ... done successfully. Executing test function test.truncateReads ... done successfully. Executing test function test.truncateReads.trim5 ... done successfully. RUNIT TEST PROTOCOL -- Sat May 4 08:43:46 2024 *********************************************** Number of test functions: 61 Number of deactivated test functions: 10 Number of errors: 0 Number of failures: 0 1 Test Suite : HTSeqGenie unit testing - 61 test functions, 0 errors, 0 failures Details *************************** Test Suite: HTSeqGenie unit testing Test function regexp: ^test.+ Test file regexp: ^runit.+\.[rR]$ Involved directory: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/unitTests --------------------------- Test file: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/unitTests/runit.alignReads.R test.alignReads: (2 checks) ... OK (30.19 seconds) test.alignReads.sparsechunks: (2 checks) ... OK (18.38 seconds) test.alignReadsOneSingleEnd: (2 checks) ... OK (0.53 seconds) --------------------------- Test file: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/unitTests/runit.analyzeVariants.R test.annotateVariants : DEACTIVATED, Skipped annotateVariants() test test.callVariantsVariantTools.genotype: (2 checks) ... OK (99.91 seconds) test.wrap.callVariants: (4 checks) ... OK (13.29 seconds) test.wrap.callVariants.filters: (2 checks) ... OK (26.69 seconds) test.wrap.callVariants.which: (1 checks) ... OK (4.33 seconds) test.writeVCF.NULL: (1 checks) ... OK (0.21 seconds) test.writeVCF.vcfStat: (4 checks) ... OK (2.43 seconds) --------------------------- Test file: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/unitTests/runit.bamUtils.R test.isFirstFragment: (5 checks) ... OK (0 seconds) --------------------------- Test file: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/unitTests/runit.buildGenomicFeatures.R test.buildCountsGRangesList: (3 checks) ... OK (37.79 seconds) test.generateSingleGeneDERs: (4 checks) ... OK (30.39 seconds) --------------------------- Test file: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/unitTests/runit.calculateCoverage.R test.computeCoverage: (9 checks) ... OK (0.95 seconds) test.isSparse: (5 checks) ... OK (0.13 seconds) test.mergeCoverage: (1 checks) ... OK (1.81 seconds) test.mergeCoverage.sparse: (2 checks) ... OK (1.41 seconds) --------------------------- Test file: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/unitTests/runit.checkConfig.R test.checkConfig.analyzeVariants: (5 checks) ... OK (0.19 seconds) test.findTemplate: (5 checks) ... OK (0.01 seconds) --------------------------- Test file: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/unitTests/runit.config.R test.checkConfig: (5 checks) ... OK (0.38 seconds) test.checkConfig.alignReads: (5 checks) ... OK (0.43 seconds) test.getConfig: (14 checks) ... OK (0 seconds) test.loadConfig: (2 checks) ... OK (0 seconds) test.parseDCF: (7 checks) ... OK (0 seconds) test.updateConfig: (1 checks) ... OK (0 seconds) --------------------------- Test file: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/unitTests/runit.detectAdapterContam.R test.getAdapterSeqs: (5 checks) ... OK (0.05 seconds) test.isAdapter: (5 checks) ... OK (0.16 seconds) test.isAdapter3.primeEnd: (1 checks) ... OK (0.12 seconds) --------------------------- Test file: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/unitTests/runit.detectRRNA.R test.detectRRNA: (1 checks) ... OK (0.3 seconds) test.detectRRNA.paired_end: (1 checks) ... OK (0.46 seconds) test.getRRNAIds: (1 checks) ... OK (0.29 seconds) test.getRRNAIds_random: (1 checks) ... OK (0.2 seconds) --------------------------- Test file: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/unitTests/runit.filterQuality.R test.filterByLength: (2 checks) ... OK (0.08 seconds) test.isAboveQualityThresh: (3 checks) ... OK (0.06 seconds) test.trimTailsByQuality: (4 checks) ... OK (0.05 seconds) --------------------------- Test file: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/unitTests/runit.gatk.R test.callVariantsGATK : DEACTIVATED, callVariantsGATK() tests need gatk.path option set test.callVariantsGATK.withFiltering : DEACTIVATED, callVariantsGATK() tests need gatk.path option set test.checkGATKJar : DEACTIVATED, checkGATKJar() test needs gatk.path option set test.excludeVariantsByRegion: (3 checks) ... OK (0.21 seconds) test.gatk : DEACTIVATED, gatk() tests need gatk.path option set test.realignIndels : DEACTIVATED, test.realignIndels() tests need gatk.path option set test.realignIndelsGATK : DEACTIVATED, realignIndelsGATK() tests need gatk.path option set test.realignIndelsGATK.parallel : DEACTIVATED, realignIndelsGATK() tests need gatk.path option set test_zipUp: (3 checks) ... OK (0 seconds) --------------------------- Test file: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/unitTests/runit.io.R test.FastQStreamer.getReads.pefq: (1 checks) ... OK (0.2 seconds) test.FastQStreamer.getReads.pefq.subsample: (1 checks) ... OK (0.35 seconds) test.FastQStreamer.getReads.segz: (1 checks) ... OK (0.19 seconds) test.FastQStreamer.getReads.truncated: (1 checks) ... OK (0.21 seconds) test.FastQStreamer.subsampler.isdeterministic: (3 checks) ... OK (0.59 seconds) test.createTmpDir: (4 checks) ... OK (0 seconds) test.detectQualityInFASTQFile: (3 checks) ... OK (0.14 seconds) test.getObjectFilename: (4 checks) ... OK (0.01 seconds) test.safeUnlink: (2 checks) ... OK (0.01 seconds) test.writeAudit: (0 checks) ... OK (0.22 seconds) --------------------------- Test file: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/unitTests/runit.mergeLanes.R test.mergeLanes: (6 checks) ... OK (69.16 seconds) --------------------------- Test file: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/unitTests/runit.picard.R test.markDuplicates : DEACTIVATED, Skipped markDuplicates() test test.markDuplicates_w_outfile : DEACTIVATED, Skipped markDuplicates() test --------------------------- Test file: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/unitTests/runit.preprocessReads.R test.preprocessReads: (5 checks) ... OK (10.03 seconds) test.preprocessReads.minichunks: (5 checks) ... OK (15.62 seconds) test.preprocessReads_single_end: (5 checks) ... OK (8.04 seconds) --------------------------- Test file: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/unitTests/runit.readRNASeqEnds.R test.readRNASeqEnds: (6 checks) ... OK (0.17 seconds) test.readRNASeqEnds.dupmark: (2 checks) ... OK (0.13 seconds) --------------------------- Test file: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/unitTests/runit.reportPipelineQA.R test.how_many: (3 checks) ... OK (0 seconds) test.plotDF: (3 checks) ... OK (0.13 seconds) test.relativeBarPlot: (2 checks) ... OK (0.05 seconds) --------------------------- Test file: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/unitTests/runit.runPipeline.R test.runPipeline: (1 checks) ... OK (51.93 seconds) --------------------------- Test file: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/unitTests/runit.targetLengths.R test.calculateTargetLength: (4 checks) ... OK (0.28 seconds) --------------------------- Test file: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/unitTests/runit.tools.R test.sclapply: (10 checks) ... OK (14.49 seconds) test.tryKeepTraceback: (3 checks) ... OK (0.01 seconds) --------------------------- Test file: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/HTSeqGenie/unitTests/runit.trimReads.R test.truncateReads: (7 checks) ... OK (0.08 seconds) test.truncateReads.trim5: (15 checks) ... OK (0.24 seconds) runTests.R: OK ! There were 50 or more warnings (use warnings() to see the first 50) > > proc.time() user system elapsed 314.367 105.885 464.819
HTSeqGenie.Rcheck/HTSeqGenie-Ex.timings
name | user | system | elapsed | |
HTSeqGenie | 0 | 0 | 0 | |
buildGenomicFeaturesFromTxDb | 0 | 0 | 0 | |
runPipeline | 0.000 | 0.000 | 0.001 | |