| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-14 11:48 -0500 (Tue, 14 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4767 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4487 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4450 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4405 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4398 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 977/2281 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Jens Reeder
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | TIMEOUT | |||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | ... NOT SUPPORTED ... | ||||||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | ... NOT SUPPORTED ... | ||||||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
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: 4.37.1 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:HTSeqGenie.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings HTSeqGenie_4.37.1.tar.gz |
| StartedAt: 2025-01-14 07:41:10 -0000 (Tue, 14 Jan 2025) |
| EndedAt: 2025-01-14 07:56:16 -0000 (Tue, 14 Jan 2025) |
| EllapsedTime: 906.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: HTSeqGenie.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:HTSeqGenie.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings HTSeqGenie_4.37.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/HTSeqGenie.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HTSeqGenie/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HTSeqGenie’ version ‘4.37.1’
* 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-3.21-bioc/meat/HTSeqGenie.Rcheck/00check.log’
for details.
HTSeqGenie.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL HTSeqGenie ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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 Warning in fun(libname, pkgname) : Package 'HTSeqGenie' is deprecated and will be removed from Bioconductor version 3.22 ** testing if installed package can be loaded from final location Warning in fun(libname, pkgname) : Package 'HTSeqGenie' is deprecated and will be removed from Bioconductor version 3.22 ** testing if installed package keeps a record of temporary installation path * DONE (HTSeqGenie)
HTSeqGenie.Rcheck/tests/doRUnit.Rout
R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library("HTSeqGenie")
Loading required package: gmapR
Loading required package: GenomeInfoDb
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: 'generics'
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: ShortRead
Loading required package: BiocParallel
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Loading required package: VariantAnnotation
Attaching package: 'VariantAnnotation'
The following object is masked from 'package:base':
tabulate
Warning message:
In fun(libname, pkgname) :
Package 'HTSeqGenie' is deprecated and will be removed from
Bioconductor version 3.22
>
> 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/Rtmp9exJFi/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt
2025-01-14 07:48:30.833845 INFO::preprocessReads.R/preprocessReads: starting...
2025-01-14 07:48:30.842699 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-14 07:48:30.848033 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-01-14 07:48:30.850657 DEBUG::tools.R/processChunks: starting...
2025-01-14 07:48:34.222669 DEBUG::tools.R/processChunks: waiting for chunkid=[ ] ...
2025-01-14 07:48:34.224854 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp9exJFi/test.alignReads.2d41873d595828/chunks/chunk_000001/logs/progress.log
2025-01-14 07:48:37.120521 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.048 minutes
2025-01-14 07:48:37.122409 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/Rtmp9exJFi/test.alignReads.2d41873d595828/chunks/chunk_000002/logs/progress.log
2025-01-14 07:48:40.009956 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.048 minutes
2025-01-14 07:48:40.012033 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/Rtmp9exJFi/test.alignReads.2d41873d595828/chunks/chunk_000003/logs/progress.log
2025-01-14 07:48:42.866989 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.048 minutes
2025-01-14 07:48:42.907094 DEBUG::tools.R/processChunks: done
2025-01-14 07:48:42.91195 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-01-14 07:48:42.915241 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.alignReads.2d41873d595828/results/test_pe.adapter_contaminated_1.RData
2025-01-14 07:48:42.919177 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-01-14 07:48:42.921829 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.alignReads.2d41873d595828/results/test_pe.adapter_contaminated_2.RData
2025-01-14 07:48:42.93442 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=26 highqual_reads=25 adapter_contam=1 read_length=75 rRNA_contam_reads=0 processed_reads=25 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-01-14 07:48:42.937518 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.alignReads.2d41873d595828/results/test_pe.summary_preprocess.tab
2025-01-14 07:48:42.941821 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp9exJFi/test.alignReads.2d41873d595828/bams/processed.aligner_input_1.fastq ...
2025-01-14 07:48:42.948413 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp9exJFi/test.alignReads.2d41873d595828/bams/processed.aligner_input_2.fastq ...
2025-01-14 07:48:42.953809 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp9exJFi/test.alignReads.2d41873d595828/reports/shortReadReport_1 ...
2025-01-14 07:48:44.825161 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp9exJFi/test.alignReads.2d41873d595828/reports/shortReadReport_2 ...
2025-01-14 07:48:47.851685 INFO::preprocessReads.R/preprocessReads: done
2025-01-14 07:48:47.909378 INFO::alignReads.R/alignReads: starting alignment...
2025-01-14 07:48:47.915655 DEBUG::tools.R/processChunks: starting...
2025-01-14 07:48:51.217483 DEBUG::tools.R/processChunks: waiting for chunkid=[ ] ...
2025-01-14 07:48:51.219581 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp9exJFi/test.alignReads.2d41873d595828/chunks/chunk_000001/logs/progress.log
2025-01-14 07:48:54.398941 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.053 minutes
2025-01-14 07:48:54.401213 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/Rtmp9exJFi/test.alignReads.2d41873d595828/chunks/chunk_000002/logs/progress.log
[bam_translate] PG tag "A" on read "highqualPEsInManyTxsOfMultiTxGene:1:1:1:16#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1MicrobialPE2MultimappingIntergenic:1:1:1:19#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInOneTxOfMultiTxGene:1:1:1:15#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1UniqueUtrPE2MultimappingIntergenic:1:1:1:18#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-01-14 07:48:57.127763 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.045 minutes
2025-01-14 07:48:57.130143 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/Rtmp9exJFi/test.alignReads.2d41873d595828/chunks/chunk_000003/logs/progress.log
[bam_translate] PG tag "A" on read "highqualPE1GeneFusionMidExonDiffChrPE2MultimappingIntergenic:1:1:1:25#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-01-14 07:48:59.846831 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.045 minutes
2025-01-14 07:48:59.850346 DEBUG::tools.R/processChunks: done
2025-01-14 07:48:59.85237 INFO::alignReads.R/mergeBAMsAcrossDirs: starting...
[bam_translate] PG tag "A" on read "highqualAdapterContamIn3PrimeEnd:1:1:1:7#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInManyTxsOfMultiTxGene:1:1:1:16#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1MicrobialPE2MultimappingIntergenic:1:1:1:19#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1GeneFusionMidExonDiffChrPE2MultimappingIntergenic:1:1:1:25#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1UniqueUtrPE2MultimappingIntergenic:1:1:1:18#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInOneTxOfMultiTxGene:1:1:1:15#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-01-14 07:49:00.190715 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-01-14 07:49:00.202401 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.alignReads.2d41873d595828/results/test_pe.summary_alignment.tab
2025-01-14 07:49:00.212974 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.alignReads.2d41873d595828/results/test_pe.summary_analyzed_bamstats.tab
2025-01-14 07:49:00.215426 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-01-14 07:49:00.5016 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.alignReads.2d41873d595828/results/test_pe.summary_target_lengths.tab
2025-01-14 07:49:00.564146 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-01-14 07:49:00.565495 INFO::alignReads.R/alignReads: done
done successfully.
Executing test function test.alignReads.sparsechunks ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp9exJFi/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt
2025-01-14 07:49:00.906613 INFO::preprocessReads.R/preprocessReads: starting...
2025-01-14 07:49:00.910158 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-14 07:49:00.99174 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 2 , totnbreads= 26 )
2025-01-14 07:49:00.998293 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-14 07:49:01.002506 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-01-14 07:49:01.005147 DEBUG::tools.R/processChunks: starting...
2025-01-14 07:49:04.420286 DEBUG::tools.R/processChunks: waiting for chunkid=[ ] ...
2025-01-14 07:49:04.422263 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp9exJFi/test.alignReads.sparsechunks.2d41877ed6f01/chunks/chunk_000001/logs/progress.log
2025-01-14 07:49:07.260703 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.047 minutes
2025-01-14 07:49:07.262563 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/Rtmp9exJFi/test.alignReads.sparsechunks.2d41877ed6f01/chunks/chunk_000002/logs/progress.log
2025-01-14 07:49:10.085195 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.047 minutes
2025-01-14 07:49:10.08711 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/Rtmp9exJFi/test.alignReads.sparsechunks.2d41877ed6f01/chunks/chunk_000003/logs/progress.log
2025-01-14 07:49:12.991816 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.048 minutes
2025-01-14 07:49:12.993762 DEBUG::tools.R/processChunks: starting chunkid= 4 ; see logfile= /home/biocbuild/tmp/Rtmp9exJFi/test.alignReads.sparsechunks.2d41877ed6f01/chunks/chunk_000004/logs/progress.log
2025-01-14 07:49:15.815441 DEBUG::tools.R/processChunks: done with chunkid= 4 ; elapsed.time= 0.047 minutes
2025-01-14 07:49:15.858879 DEBUG::tools.R/processChunks: done
2025-01-14 07:49:15.863453 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-01-14 07:49:15.866658 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.alignReads.sparsechunks.2d41877ed6f01/results/test_pe.adapter_contaminated_1.RData
2025-01-14 07:49:15.870744 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-01-14 07:49:15.873326 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.alignReads.sparsechunks.2d41877ed6f01/results/test_pe.adapter_contaminated_2.RData
2025-01-14 07:49:15.888169 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=2 highqual_reads=1 adapter_contam=0 read_length=75 rRNA_contam_reads=0 processed_reads=1 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-01-14 07:49:15.891793 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.alignReads.sparsechunks.2d41877ed6f01/results/test_pe.summary_preprocess.tab
2025-01-14 07:49:15.897648 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp9exJFi/test.alignReads.sparsechunks.2d41877ed6f01/bams/processed.aligner_input_1.fastq ...
2025-01-14 07:49:15.905535 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp9exJFi/test.alignReads.sparsechunks.2d41877ed6f01/bams/processed.aligner_input_2.fastq ...
2025-01-14 07:49:15.911574 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp9exJFi/test.alignReads.sparsechunks.2d41877ed6f01/reports/shortReadReport_1 ...
2025-01-14 07:49:17.891192 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp9exJFi/test.alignReads.sparsechunks.2d41877ed6f01/reports/shortReadReport_2 ...
2025-01-14 07:49:21.006343 INFO::preprocessReads.R/preprocessReads: done
done successfully.
Executing test function test.alignReadsOneSingleEnd ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp9exJFi/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt
2025-01-14 07:49:21.226383 INFO::alignReads.R/alignReadsChunk: running gsnap...
2025-01-14 07:49:21.232464 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/Rtmp9exJFi/test.alignReadsOneSingleEnd.2d41871023f4b8/bams/test.alignReads /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_1.fastq 2>&1
2025-01-14 07:49:21.382672 INFO::alignReads.R/createSummaryAlignment: counting unique bam reads...
2025-01-14 07:49:21.521831 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.alignReadsOneSingleEnd.2d41871023f4b8/results/test.alignReads.summary_alignment.tab
2025-01-14 07:49:21.573941 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.alignReadsOneSingleEnd.2d41871023f4b8/results/test.alignReads.summary_analyzed_bamstats.tab
2025-01-14 07:49:21.576123 INFO::alignReads.R/alignReadsChunk: done
done successfully.
Executing test function test.annotateVariants ... Timing stopped at: 0.003 0.001 0.004
Error in DEACTIVATED("Skipped annotateVariants() test") :
Skipped annotateVariants() test
In addition: There were 11 warnings (use warnings() to see them)
done successfully.
Executing test function test.callVariantsVariantTools.genotype ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp9exJFi/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt
2025-01-14 07:49:21.995249 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.genotype.2d41873f5e78cf/results/test_pe.coverage.RData
2025-01-14 07:49:21.997625 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.genotype.2d41873f5e78cf/results/test_pe.coverage.bw
2025-01-14 07:49:22.181219 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.genotype.2d41873f5e78cf/results/test_pe.summary_coverage.tab
2025-01-14 07:49:22.183549 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-01-14 07:49:36.025592 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-01-14 07:49:36.159981 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-01-14 07:49:36.186311 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-01-14 07:49:36.188406 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.genotype.2d41873f5e78cf/results/test_pe.raw_variants.RData
2025-01-14 07:49:36.191605 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.genotype.2d41873f5e78cf/results/test_pe.filtered_variants.RData
2025-01-14 07:49:36.193597 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-01-14 07:49:36.195317 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-01-14 07:49:36.818822 INFO::analyzeVariants.R/writeVCF: ...done
2025-01-14 07:49:36.821037 INFO::analyzeVariants.R/.callGenotypes: calling genotypes...
2025-01-14 07:51:07.174581 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-01-14 07:51:07.813711 INFO::analyzeVariants.R/writeVCF: ...done
2025-01-14 07:51:07.815252 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/Rtmp9exJFi/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt
2025-01-14 07:51:08.445252 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-01-14 07:51:21.747877 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-01-14 07:51:21.898874 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-01-14 07:51:21.932475 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-01-14 07:51:21.935017 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.wrap.callVariants.2d41873cb9bd36/results/test_pe.raw_variants.RData
2025-01-14 07:51:21.939103 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.wrap.callVariants.2d41873cb9bd36/results/test_pe.filtered_variants.RData
2025-01-14 07:51:21.941525 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/Rtmp9exJFi/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt
2025-01-14 07:51:22.248365 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-01-14 07:51:36.524649 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-01-14 07:51:36.623087 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-01-14 07:51:36.650241 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-01-14 07:51:36.652419 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.wrap.callVariants.filters.2d418774df9058/results/test_pe.raw_variants.RData
2025-01-14 07:51:36.656287 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.wrap.callVariants.filters.2d418774df9058/results/test_pe.filtered_variants.RData
2025-01-14 07:51:36.659019 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-01-14 07:51:36.661579 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-01-14 07:51:50.176887 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-01-14 07:51:50.244097 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-01-14 07:51:50.271879 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-01-14 07:51:50.27398 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.wrap.callVariants.filters.2d418774df9058/results/test_pe.raw_variants.RData
2025-01-14 07:51:50.2774 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.wrap.callVariants.filters.2d418774df9058/results/test_pe.filtered_variants.RData
2025-01-14 07:51:50.280078 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/Rtmp9exJFi/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt
2025-01-14 07:51:50.609759 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-01-14 07:51:50.61201 INFO::analyzeVariants.R/buildTallyParam: restricting variant calls using 'which'
2025-01-14 07:51:54.29452 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-01-14 07:51:54.415056 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-01-14 07:51:54.441159 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-01-14 07:51:54.443185 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.wrap.callVariants.which.2d418739fe662d/results/test_pe.raw_variants.RData
2025-01-14 07:51:54.445685 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.wrap.callVariants.which.2d418739fe662d/results/test_pe.filtered_variants.RData
2025-01-14 07:51:54.447574 INFO::analyzeVariants.R/wrap.callVariants: ...done
done successfully.
Executing test function test.writeVCF.NULL ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp9exJFi/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt
2025-01-14 07:51:54.648294 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-01-14 07:51:54.650296 INFO::analyzeVariants.R/writeVCF: ...done
done successfully.
Executing test function test.writeVCF.vcfStat ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp9exJFi/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt
2025-01-14 07:51:54.897085 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-01-14 07:51:55.223651 INFO::analyzeVariants.R/writeVCF: ...done
done successfully.
Executing test function test.isFirstFragment ... done successfully.
Executing test function test.buildCountsGRangesList ... 403 genes were dropped because they have exons located on both strands of the
same reference sequence or on more than one reference sequence, so cannot be
represented by a single genomic range.
Use 'single.strand.genes.only=FALSE' to get all the genes in a GRangesList
object, or use suppressMessages() to suppress this message.
done successfully.
Executing test function test.generateSingleGeneDERs ... done successfully.
Executing test function test.computeCoverage ... done successfully.
Executing test function test.isSparse ... done successfully.
Executing test function test.mergeCoverage ... 2025-01-14 07:53:13.748355 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/kdfgwplb/merged/results/bla.coverage.RData
2025-01-14 07:53:13.751717 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/Rtmp9exJFi/kdfgwplb/merged/results/bla.coverage.bw
2025-01-14 07:53:13.872073 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/kdfgwplb/merged/results/bla.summary_coverage.tab
done successfully.
Executing test function test.mergeCoverage.sparse ... 2025-01-14 07:53:15.286577 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/oeudwkry/merged/results/bla.coverage.RData
2025-01-14 07:53:15.288561 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/Rtmp9exJFi/oeudwkry/merged/results/bla.coverage.bw
2025-01-14 07:53:15.30428 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/oeudwkry/merged/results/bla.summary_coverage.tab
done successfully.
Executing test function test.checkConfig.analyzeVariants ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp9exJFi/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/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/Rtmp9exJFi/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp9exJFi/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp9exJFi/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp9exJFi/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/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/Rtmp9exJFi/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp9exJFi/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp9exJFi/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp9exJFi/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/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/Rtmp9exJFi/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt
2025-01-14 07:53:17.003817 INFO::detectRRNA.R/detectRRNA: searching for rRNA contamination...
2025-01-14 07:53:17.005392 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/tmp/Rtmp9exJFi/test.detectRRNA.2d41877b856c/bams/rRNA_contam/input1.fastq
2025-01-14 07:53:17.0102 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/Rtmp9exJFi/test.detectRRNA.2d41877b856c/bams/rRNA_contam/test_se /home/biocbuild/tmp/Rtmp9exJFi/test.detectRRNA.2d41877b856c/bams/rRNA_contam/input1.fastq 2>&1
2025-01-14 07:53:17.124823 INFO::detectRRNA.R/detectRRNA: contaminated fraction= 1
2025-01-14 07:53:17.126263 INFO::detectRRNA.R/detectRRNA: done
done successfully.
Executing test function test.detectRRNA.paired_end ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp9exJFi/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt
2025-01-14 07:53:17.326062 INFO::detectRRNA.R/detectRRNA: searching for rRNA contamination...
2025-01-14 07:53:17.327517 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/tmp/Rtmp9exJFi/test.detectRRNA.paired_end.2d41872ccce146/bams/rRNA_contam/input1.fastq
2025-01-14 07:53:17.329837 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/tmp/Rtmp9exJFi/test.detectRRNA.paired_end.2d41872ccce146/bams/rRNA_contam/input2.fastq
2025-01-14 07:53:17.333284 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/Rtmp9exJFi/test.detectRRNA.paired_end.2d41872ccce146/bams/rRNA_contam/test_pe /home/biocbuild/tmp/Rtmp9exJFi/test.detectRRNA.paired_end.2d41872ccce146/bams/rRNA_contam/input1.fastq -a paired /home/biocbuild/tmp/Rtmp9exJFi/test.detectRRNA.paired_end.2d41872ccce146/bams/rRNA_contam/input2.fastq 2>&1
2025-01-14 07:53:17.618557 INFO::detectRRNA.R/detectRRNA: contaminated fraction= 1
2025-01-14 07:53:17.620075 INFO::detectRRNA.R/detectRRNA: done
done successfully.
Executing test function test.getRRNAIds ... 2025-01-14 07:53:17.652148 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/Rtmp9exJFi/test_get_rRNA_idsuptbsdoe/test_pe /home/biocbuild/tmp/Rtmp9exJFi/test_get_rRNA_idsuptbsdoe/1.fastq -a paired /home/biocbuild/tmp/Rtmp9exJFi/test_get_rRNA_idsuptbsdoe/2.fastq 2>&1
done successfully.
Executing test function test.getRRNAIds_random ... 2025-01-14 07:53:17.962461 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/Rtmp9exJFi/test_get_rRNAIds_randomgraloxzv/test_pe /home/biocbuild/tmp/Rtmp9exJFi/test_get_rRNAIds_randomgraloxzv/1.fastq 2>&1
done successfully.
Executing test function test.filterByLength ... 2025-01-14 07:53:18.14347 INFO::filterQuality.R/filterQuality: filterByLength...
2025-01-14 07:53:18.145558 INFO::filterQuality.R/filterByLength: fraction of filtered short reads= 0.5
2025-01-14 07:53:18.146929 INFO::filterQuality.R/filterByLength: done
2025-01-14 07:53:18.220141 INFO::filterQuality.R/filterQuality: filterByLength...
2025-01-14 07:53:18.221495 INFO::filterQuality.R/filterByLength: fraction of filtered short reads= 1
2025-01-14 07:53:18.222794 INFO::filterQuality.R/filterByLength: done
done successfully.
Executing test function test.isAboveQualityThresh ... done successfully.
Executing test function test.trimTailsByQuality ... 2025-01-14 07:53:18.30216 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-01-14 07:53:18.31576 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-01-14 07:53:18.317387 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-01-14 07:53:18.324278 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-01-14 07:53:18.325868 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-01-14 07:53:18.332773 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-01-14 07:53:18.334358 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-01-14 07:53:18.341267 INFO::preprocessReads.R/preprocessReadsChunk: done
done successfully.
Executing test function test.callVariantsGATK ... Timing stopped at: 0 0 0.001
Error in DEACTIVATED("callVariantsGATK() tests need gatk.path option set") :
callVariantsGATK() tests need gatk.path option set
In addition: There were 50 or more warnings (use warnings() to see the first 50)
done successfully.
Executing test function test.callVariantsGATK.withFiltering ... Timing stopped at: 0 0 0.001
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/Rtmp9exJFi/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt
2025-01-14 07:53:18.762247 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-14 07:53:18.765961 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/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/Rtmp9exJFi/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt
2025-01-14 07:53:19.011578 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-14 07:53:19.141768 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-01-14 07:53:19.145839 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-14 07:53:19.149345 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/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/Rtmp9exJFi/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt
2025-01-14 07:53:19.450989 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/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/Rtmp9exJFi/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt
2025-01-14 07:53:19.642396 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/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/Rtmp9exJFi/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt
2025-01-14 07:53:19.854579 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-14 07:53:19.947116 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-01-14 07:53:19.950771 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-14 07:53:19.954284 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp9exJFi/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt
2025-01-14 07:53:20.235597 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-14 07:53:20.296353 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-01-14 07:53:20.300348 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-14 07:53:20.304148 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/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/Rtmp9exJFi/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt
done successfully.
Executing test function test.mergeLanes ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp9exJFi/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt
2025-01-14 07:53:21.238712 INFO::preprocessReads.R/preprocessReads: starting...
2025-01-14 07:53:21.245715 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-14 07:53:21.250686 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-01-14 07:53:21.253655 DEBUG::tools.R/processChunks: starting...
2025-01-14 07:53:24.711788 DEBUG::tools.R/processChunks: waiting for chunkid=[ ] ...
2025-01-14 07:53:24.713876 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/chunks/chunk_000001/logs/progress.log
2025-01-14 07:53:27.483041 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.046 minutes
2025-01-14 07:53:27.484926 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/chunks/chunk_000002/logs/progress.log
2025-01-14 07:53:30.250237 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.046 minutes
2025-01-14 07:53:30.252309 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/chunks/chunk_000003/logs/progress.log
2025-01-14 07:53:33.030071 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.046 minutes
2025-01-14 07:53:33.091703 DEBUG::tools.R/processChunks: done
2025-01-14 07:53:33.095673 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-01-14 07:53:33.09829 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/results/test_pe.adapter_contaminated_1.RData
2025-01-14 07:53:33.101623 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-01-14 07:53:33.104143 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/results/test_pe.adapter_contaminated_2.RData
2025-01-14 07:53:33.116201 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=26 highqual_reads=25 adapter_contam=1 read_length=75 rRNA_contam_reads=0 processed_reads=25 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-01-14 07:53:33.118968 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/results/test_pe.summary_preprocess.tab
2025-01-14 07:53:33.122648 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/bams/processed.aligner_input_1.fastq ...
2025-01-14 07:53:33.129569 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/bams/processed.aligner_input_2.fastq ...
2025-01-14 07:53:33.135647 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/reports/shortReadReport_1 ...
2025-01-14 07:53:35.070073 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/reports/shortReadReport_2 ...
2025-01-14 07:53:36.77027 INFO::preprocessReads.R/preprocessReads: done
2025-01-14 07:53:36.846734 INFO::alignReads.R/alignReads: starting alignment...
2025-01-14 07:53:36.851765 DEBUG::tools.R/processChunks: starting...
2025-01-14 07:53:40.408901 DEBUG::tools.R/processChunks: waiting for chunkid=[ ] ...
2025-01-14 07:53:40.411116 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/chunks/chunk_000001/logs/progress.log
2025-01-14 07:53:43.026058 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.044 minutes
2025-01-14 07:53:43.028253 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/chunks/chunk_000002/logs/progress.log
[bam_translate] PG tag "A" on read "highqualPEsInManyTxsOfMultiTxGene:1:1:1:16#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1MicrobialPE2MultimappingIntergenic:1:1:1:19#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInOneTxOfMultiTxGene:1:1:1:15#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1UniqueUtrPE2MultimappingIntergenic:1:1:1:18#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-01-14 07:53:45.686921 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.044 minutes
2025-01-14 07:53:45.689138 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/chunks/chunk_000003/logs/progress.log
[bam_translate] PG tag "A" on read "highqualPE1GeneFusionMidExonDiffChrPE2MultimappingIntergenic:1:1:1:25#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-01-14 07:53:48.344719 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.044 minutes
2025-01-14 07:53:48.348067 DEBUG::tools.R/processChunks: done
2025-01-14 07:53:48.350066 INFO::alignReads.R/mergeBAMsAcrossDirs: starting...
[bam_translate] PG tag "A" on read "highqualAdapterContamIn3PrimeEnd:1:1:1:7#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInManyTxsOfMultiTxGene:1:1:1:16#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1MicrobialPE2MultimappingIntergenic:1:1:1:19#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1GeneFusionMidExonDiffChrPE2MultimappingIntergenic:1:1:1:25#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1UniqueUtrPE2MultimappingIntergenic:1:1:1:18#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInOneTxOfMultiTxGene:1:1:1:15#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-01-14 07:53:48.665697 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-01-14 07:53:48.676354 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/results/test_pe.summary_alignment.tab
2025-01-14 07:53:48.686694 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/results/test_pe.summary_analyzed_bamstats.tab
2025-01-14 07:53:48.68937 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-01-14 07:53:48.95056 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/results/test_pe.summary_target_lengths.tab
2025-01-14 07:53:49.01446 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-01-14 07:53:49.015896 INFO::alignReads.R/alignReads: done
2025-01-14 07:53:49.090056 INFO::countGenomicFeatures.R/countGenomicFeatures: starting...
2025-01-14 07:53:49.110942 DEBUG::tools.R/processChunks: starting...
2025-01-14 07:53:52.610946 DEBUG::tools.R/processChunks: waiting for chunkid=[ ] ...
2025-01-14 07:53:52.613126 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/chunks/chunk_000001/logs/progress.log
2025-01-14 07:53:55.192194 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.043 minutes
2025-01-14 07:53:55.194499 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/chunks/chunk_000002/logs/progress.log
2025-01-14 07:53:57.789306 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.043 minutes
2025-01-14 07:53:57.791531 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/chunks/chunk_000003/logs/progress.log
2025-01-14 07:54:00.389385 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.043 minutes
2025-01-14 07:54:00.392934 DEBUG::tools.R/processChunks: done
2025-01-14 07:54:00.395171 INFO::countGenomicFeatures.R/mergeCounts: starting...
2025-01-14 07:54:00.412544 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/results/test_pe.counts_exon.tab
2025-01-14 07:54:00.426544 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/results/test_pe.counts_exon_disjoint.tab
2025-01-14 07:54:00.435829 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/results/test_pe.counts_gene.tab
2025-01-14 07:54:00.443263 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/results/test_pe.counts_gene_coding.tab
2025-01-14 07:54:00.450787 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/results/test_pe.counts_gene_exonic.tab
2025-01-14 07:54:00.458587 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/results/test_pe.counts_intergenic.tab
2025-01-14 07:54:00.471031 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/results/test_pe.counts_intron.tab
2025-01-14 07:54:00.475 INFO::countGenomicFeatures.R/mergeCounts: done
2025-01-14 07:54:00.483267 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/results/test_pe.summary_counts.tab
2025-01-14 07:54:00.485811 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2025-01-14 07:54:00.855872 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2025-01-14 07:54:00.857179 INFO::countGenomicFeatures.R/countGenomicFeatures: done...
2025-01-14 07:54:00.966943 INFO::coverage.R/calculateCoverage: starting...
2025-01-14 07:54:00.971664 DEBUG::tools.R/processChunks: starting...
2025-01-14 07:54:04.547019 DEBUG::tools.R/processChunks: waiting for chunkid=[ ] ...
2025-01-14 07:54:04.549409 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/chunks/chunk_000001/logs/progress.log
2025-01-14 07:54:06.765244 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.037 minutes
2025-01-14 07:54:06.76754 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/chunks/chunk_000002/logs/progress.log
2025-01-14 07:54:08.989319 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.037 minutes
2025-01-14 07:54:08.99153 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/chunks/chunk_000003/logs/progress.log
2025-01-14 07:54:11.208056 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.037 minutes
2025-01-14 07:54:11.211376 DEBUG::tools.R/processChunks: done
2025-01-14 07:54:12.952553 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/results/test_pe.coverage.RData
2025-01-14 07:54:12.954408 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/results/test_pe.coverage.bw
2025-01-14 07:54:12.969595 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/results/test_pe.summary_coverage.tab
2025-01-14 07:54:12.971378 INFO::coverage.R/calculateCoverage: done
2025-01-14 07:54:12.974141 INFO::analyzeVariants/analyzeVariants: starting ...
2025-01-14 07:54:13.091021 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-01-14 07:54:17.615299 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-01-14 07:54:17.733987 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-01-14 07:54:17.759402 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-01-14 07:54:17.761365 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/results/test_pe.raw_variants.RData
2025-01-14 07:54:17.763669 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/results/test_pe.filtered_variants.RData
2025-01-14 07:54:17.765526 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-01-14 07:54:17.766951 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-01-14 07:54:18.099285 INFO::analyzeVariants.R/writeVCF: ...done
2025-01-14 07:54:18.248816 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/results/test_pe.summary_variants.tab
2025-01-14 07:54:18.251611 INFO::analyzeVariants/analyzeVariants: done
2025-01-14 07:54:18.255508 INFO::Pipeline run successful.
2025-01-14 07:54:18.485408 INFO::mergeLanes.R/doMergeLanes: starting...
2025-01-14 07:54:18.490948 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-01-14 07:54:18.49415 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/merged/results/merged.adapter_contaminated_1.RData
2025-01-14 07:54:18.498193 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-01-14 07:54:18.501079 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/merged/results/merged.adapter_contaminated_2.RData
2025-01-14 07:54:18.517712 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=26 highqual_reads=25 adapter_contam=1 read_length=75 rRNA_contam_reads=0 processed_reads=25 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-01-14 07:54:18.521162 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/merged/results/merged.summary_preprocess.tab
2025-01-14 07:54:18.524472 INFO::alignReads.R/mergeBAMsAcrossDirs: starting...
[bam_translate] PG tag "A" on read "highqualAdapterContamIn3PrimeEnd:1:1:1:7#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInManyTxsOfMultiTxGene:1:1:1:16#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1MicrobialPE2MultimappingIntergenic:1:1:1:19#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1GeneFusionMidExonDiffChrPE2MultimappingIntergenic:1:1:1:25#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1UniqueUtrPE2MultimappingIntergenic:1:1:1:18#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInOneTxOfMultiTxGene:1:1:1:15#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-01-14 07:54:18.883577 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-01-14 07:54:18.893895 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/merged/results/merged.summary_alignment.tab
2025-01-14 07:54:18.905514 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/merged/results/merged.summary_analyzed_bamstats.tab
2025-01-14 07:54:18.908492 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-01-14 07:54:19.192707 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/merged/results/merged.summary_target_lengths.tab
2025-01-14 07:54:19.260566 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-01-14 07:54:19.303084 INFO::countGenomicFeatures.R/mergeCounts: starting...
2025-01-14 07:54:19.326775 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/merged/results/merged.counts_exon.tab
2025-01-14 07:54:19.341851 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/merged/results/merged.counts_exon_disjoint.tab
2025-01-14 07:54:19.351351 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/merged/results/merged.counts_gene.tab
2025-01-14 07:54:19.359416 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/merged/results/merged.counts_gene_coding.tab
2025-01-14 07:54:19.367421 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/merged/results/merged.counts_gene_exonic.tab
2025-01-14 07:54:19.375553 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/merged/results/merged.counts_intergenic.tab
2025-01-14 07:54:19.38969 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/merged/results/merged.counts_intron.tab
2025-01-14 07:54:19.393689 INFO::countGenomicFeatures.R/mergeCounts: done
2025-01-14 07:54:19.401863 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/merged/results/merged.summary_counts.tab
2025-01-14 07:54:19.404376 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2025-01-14 07:54:19.69889 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2025-01-14 07:54:21.972776 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/merged/results/merged.coverage.RData
2025-01-14 07:54:21.975603 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/merged/results/merged.coverage.bw
2025-01-14 07:54:21.990721 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/merged/results/merged.summary_coverage.tab
2025-01-14 07:54:22.029938 INFO::analyzeVariants/analyzeVariants: starting ...
2025-01-14 07:54:22.113204 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-01-14 07:54:26.269077 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-01-14 07:54:26.382151 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-01-14 07:54:26.406617 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-01-14 07:54:26.4086 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/merged/results/merged.raw_variants.RData
2025-01-14 07:54:26.41092 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/merged/results/merged.filtered_variants.RData
2025-01-14 07:54:26.412746 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-01-14 07:54:26.41421 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-01-14 07:54:26.734932 INFO::analyzeVariants.R/writeVCF: ...done
2025-01-14 07:54:26.87895 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.mergeLanes.2d418731998940/merged/results/merged.summary_variants.tab
2025-01-14 07:54:26.881722 INFO::analyzeVariants/analyzeVariants: done
2025-01-14 07:54:26.88882 INFO::mergeLanes.R/doMergeLanes: merge lanes successful.
done successfully.
Executing test function test.markDuplicates ... Timing stopped at: 0 0 0
Error in DEACTIVATED("Skipped markDuplicates() test") :
Skipped markDuplicates() test
In addition: There were 28 warnings (use warnings() to see them)
done successfully.
Executing test function test.markDuplicates_w_outfile ... Timing stopped at: 0 0 0
Error in DEACTIVATED("Skipped markDuplicates() test") :
Skipped markDuplicates() test
done successfully.
Executing test function test.preprocessReads ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp9exJFi/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt
2025-01-14 07:54:27.251807 INFO::preprocessReads.R/preprocessReads: starting...
2025-01-14 07:54:27.275982 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-14 07:54:27.298185 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-01-14 07:54:27.301402 DEBUG::tools.R/processChunks: starting...
2025-01-14 07:54:30.84619 DEBUG::tools.R/processChunks: waiting for chunkid=[ ] ...
2025-01-14 07:54:30.848322 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp9exJFi/test.preprocessReads.2d41872198f60/chunks/chunk_000001/logs/progress.log
2025-01-14 07:54:33.613947 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.046 minutes
2025-01-14 07:54:33.663741 DEBUG::tools.R/processChunks: done
2025-01-14 07:54:33.66702 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-01-14 07:54:33.669519 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.preprocessReads.2d41872198f60/results/test_pe.adapter_contaminated_1.RData
2025-01-14 07:54:33.672161 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-01-14 07:54:33.674483 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.preprocessReads.2d41872198f60/results/test_pe.adapter_contaminated_2.RData
2025-01-14 07:54:33.683541 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=26 highqual_reads=25 adapter_contam=1 read_length=75 rRNA_contam_reads=0 processed_reads=25 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-01-14 07:54:33.68632 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.preprocessReads.2d41872198f60/results/test_pe.summary_preprocess.tab
2025-01-14 07:54:33.68929 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp9exJFi/test.preprocessReads.2d41872198f60/bams/processed.aligner_input_1.fastq ...
2025-01-14 07:54:33.696997 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp9exJFi/test.preprocessReads.2d41872198f60/bams/processed.aligner_input_2.fastq ...
2025-01-14 07:54:33.703136 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp9exJFi/test.preprocessReads.2d41872198f60/reports/shortReadReport_1 ...
2025-01-14 07:54:35.571031 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp9exJFi/test.preprocessReads.2d41872198f60/reports/shortReadReport_2 ...
2025-01-14 07:54:37.239449 INFO::preprocessReads.R/preprocessReads: done
done successfully.
Executing test function test.preprocessReads.minichunks ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp9exJFi/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt
2025-01-14 07:54:37.54622 INFO::preprocessReads.R/preprocessReads: starting...
2025-01-14 07:54:37.553611 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-14 07:54:37.558769 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-01-14 07:54:37.561868 DEBUG::tools.R/processChunks: starting...
2025-01-14 07:54:41.076496 DEBUG::tools.R/processChunks: waiting for chunkid=[ ] ...
2025-01-14 07:54:41.078775 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp9exJFi/test.preprocessReads.minichunks.2d418743e5546f/chunks/chunk_000001/logs/progress.log
2025-01-14 07:54:43.855196 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.046 minutes
2025-01-14 07:54:43.85716 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/Rtmp9exJFi/test.preprocessReads.minichunks.2d418743e5546f/chunks/chunk_000002/logs/progress.log
2025-01-14 07:54:46.636775 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.046 minutes
2025-01-14 07:54:46.63889 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/Rtmp9exJFi/test.preprocessReads.minichunks.2d418743e5546f/chunks/chunk_000003/logs/progress.log
2025-01-14 07:54:49.406864 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.046 minutes
2025-01-14 07:54:49.454561 DEBUG::tools.R/processChunks: done
2025-01-14 07:54:49.458333 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-01-14 07:54:49.460953 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.preprocessReads.minichunks.2d418743e5546f/results/test_pe.adapter_contaminated_1.RData
2025-01-14 07:54:49.464294 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-01-14 07:54:49.467174 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.preprocessReads.minichunks.2d418743e5546f/results/test_pe.adapter_contaminated_2.RData
2025-01-14 07:54:49.479576 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=26 highqual_reads=25 adapter_contam=1 read_length=75 rRNA_contam_reads=0 processed_reads=25 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-01-14 07:54:49.482564 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.preprocessReads.minichunks.2d418743e5546f/results/test_pe.summary_preprocess.tab
2025-01-14 07:54:49.486458 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp9exJFi/test.preprocessReads.minichunks.2d418743e5546f/bams/processed.aligner_input_1.fastq ...
2025-01-14 07:54:49.49314 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp9exJFi/test.preprocessReads.minichunks.2d418743e5546f/bams/processed.aligner_input_2.fastq ...
2025-01-14 07:54:49.49887 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp9exJFi/test.preprocessReads.minichunks.2d418743e5546f/reports/shortReadReport_1 ...
2025-01-14 07:54:51.382968 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp9exJFi/test.preprocessReads.minichunks.2d418743e5546f/reports/shortReadReport_2 ...
2025-01-14 07:54:52.98651 INFO::preprocessReads.R/preprocessReads: done
done successfully.
Executing test function test.preprocessReads_single_end ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp9exJFi/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt
2025-01-14 07:54:53.29182 INFO::preprocessReads.R/preprocessReads: starting...
2025-01-14 07:54:53.316039 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-14 07:54:53.319512 DEBUG::tools.R/processChunks: starting...
2025-01-14 07:54:57.058073 DEBUG::tools.R/processChunks: waiting for chunkid=[ ] ...
2025-01-14 07:54:57.060249 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp9exJFi/test.preprocessReads_single_end.2d41874dcda76d/chunks/chunk_000001/logs/progress.log
2025-01-14 07:54:59.53871 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.041 minutes
2025-01-14 07:54:59.552174 DEBUG::tools.R/processChunks: done
2025-01-14 07:54:59.55539 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-01-14 07:54:59.557801 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.preprocessReads_single_end.2d41874dcda76d/results/test_se.adapter_contaminated_1.RData
2025-01-14 07:54:59.566988 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=26 highqual_reads=25 adapter_contam=1 read_length=75 rRNA_contam_reads=0 processed_reads=25 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-01-14 07:54:59.569698 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.preprocessReads_single_end.2d41874dcda76d/results/test_se.summary_preprocess.tab
2025-01-14 07:54:59.572459 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp9exJFi/test.preprocessReads_single_end.2d41874dcda76d/bams/processed.aligner_input_1.fastq ...
2025-01-14 07:54:59.578346 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp9exJFi/test.preprocessReads_single_end.2d41874dcda76d/reports/shortReadReport_1 ...
2025-01-14 07:55:01.489102 INFO::preprocessReads.R/preprocessReads: done
done successfully.
Executing test function test.readRNASeqEnds ... done successfully.
Executing test function test.readRNASeqEnds.dupmark ... done successfully.
Executing test function test.how_many ... done successfully.
Executing test function test.plotDF ... done successfully.
Executing test function test.relativeBarPlot ... done successfully.
Executing test function test.runPipeline ... checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt
2025-01-14 07:55:02.242707 INFO::preprocessReads.R/preprocessReads: starting...
2025-01-14 07:55:02.266378 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/extdata/H1993_TP53_subset2500_1.fastq.gz
2025-01-14 07:55:02.288724 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/extdata/H1993_TP53_subset2500_2.fastq.gz
2025-01-14 07:55:02.291784 DEBUG::tools.R/processChunks: starting...
2025-01-14 07:55:05.904024 DEBUG::tools.R/processChunks: waiting for chunkid=[ ] ...
2025-01-14 07:55:05.906135 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= test/chunks/chunk_000001/logs/progress.log
2025-01-14 07:55:08.875595 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.049 minutes
2025-01-14 07:55:08.931242 DEBUG::tools.R/processChunks: done
2025-01-14 07:55:08.934604 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-01-14 07:55:08.937091 INFO::io.R/saveWithID: saving file= test/results/test.adapter_contaminated_1.RData
2025-01-14 07:55:08.939791 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-01-14 07:55:08.942155 INFO::io.R/saveWithID: saving file= test/results/test.adapter_contaminated_2.RData
2025-01-14 07:55:08.951646 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=2500 highqual_reads=2500 adapter_contam=0 read_length=100 rRNA_contam_reads=0 processed_reads=2500 input_min_read_length=100 input_max_read_length=100 processed_min_read_length=71 processed_max_read_length=100
2025-01-14 07:55:08.954571 INFO::io.R/saveWithID: saving file= test/results/test.summary_preprocess.tab
2025-01-14 07:55:08.957619 INFO::preprocessReads.R/mergePreprocessedReads: merging file= test/bams/processed.aligner_input_1.fastq ...
2025-01-14 07:55:08.964239 INFO::preprocessReads.R/mergePreprocessedReads: merging file= test/bams/processed.aligner_input_2.fastq ...
2025-01-14 07:55:08.970497 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= test/reports/shortReadReport_1 ...
2025-01-14 07:55:11.158578 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= test/reports/shortReadReport_2 ...
2025-01-14 07:55:13.169016 INFO::preprocessReads.R/preprocessReads: done
2025-01-14 07:55:13.244986 INFO::alignReads.R/alignReads: starting alignment...
2025-01-14 07:55:13.249814 DEBUG::tools.R/processChunks: starting...
2025-01-14 07:55:17.853274 DEBUG::tools.R/processChunks: waiting for chunkid=[ ] ...
2025-01-14 07:55:17.855668 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.
2025-01-14 07:55:23.883702 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.1 minutes
2025-01-14 07:55:23.886966 DEBUG::tools.R/processChunks: done
2025-01-14 07:55:23.888787 INFO::alignReads.R/mergeBAMsAcrossDirs: starting...
2025-01-14 07:55:23.922719 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-01-14 07:55:23.930666 INFO::io.R/saveWithID: saving file= test/results/test.summary_alignment.tab
2025-01-14 07:55:23.938088 INFO::io.R/saveWithID: saving file= test/results/test.summary_analyzed_bamstats.tab
2025-01-14 07:55:23.940788 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-01-14 07:55:24.134712 INFO::io.R/saveWithID: saving file= test/results/test.summary_target_lengths.tab
2025-01-14 07:55:24.195186 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-01-14 07:55:24.196478 INFO::alignReads.R/alignReads: done
2025-01-14 07:55:24.281056 INFO::countGenomicFeatures.R/countGenomicFeatures: starting...
2025-01-14 07:55:24.299527 DEBUG::tools.R/processChunks: starting...
2025-01-14 07:55:27.712126 DEBUG::tools.R/processChunks: waiting for chunkid=[ ] ...
2025-01-14 07:55:27.714213 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= test/chunks/chunk_000001/logs/progress.log
2025-01-14 07:55:30.326465 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.044 minutes
2025-01-14 07:55:30.329756 DEBUG::tools.R/processChunks: done
2025-01-14 07:55:30.33185 INFO::countGenomicFeatures.R/mergeCounts: starting...
2025-01-14 07:55:30.343194 INFO::io.R/saveWithID: saving file= test/results/test.counts_exon.tab
2025-01-14 07:55:30.353018 INFO::io.R/saveWithID: saving file= test/results/test.counts_exon_disjoint.tab
2025-01-14 07:55:30.360271 INFO::io.R/saveWithID: saving file= test/results/test.counts_gene.tab
2025-01-14 07:55:30.365479 INFO::io.R/saveWithID: saving file= test/results/test.counts_gene_coding.tab
2025-01-14 07:55:30.370644 INFO::io.R/saveWithID: saving file= test/results/test.counts_gene_exonic.tab
2025-01-14 07:55:30.375703 INFO::io.R/saveWithID: saving file= test/results/test.counts_intergenic.tab
2025-01-14 07:55:30.383224 INFO::io.R/saveWithID: saving file= test/results/test.counts_intron.tab
2025-01-14 07:55:30.387141 INFO::countGenomicFeatures.R/mergeCounts: done
2025-01-14 07:55:30.391863 INFO::io.R/saveWithID: saving file= test/results/test.summary_counts.tab
2025-01-14 07:55:30.39418 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2025-01-14 07:55:30.676765 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2025-01-14 07:55:30.67807 INFO::countGenomicFeatures.R/countGenomicFeatures: done...
2025-01-14 07:55:30.774342 INFO::coverage.R/calculateCoverage: starting...
2025-01-14 07:55:30.778842 DEBUG::tools.R/processChunks: starting...
2025-01-14 07:55:34.25123 DEBUG::tools.R/processChunks: waiting for chunkid=[ ] ...
2025-01-14 07:55:34.253426 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= test/chunks/chunk_000001/logs/progress.log
2025-01-14 07:55:36.630906 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.04 minutes
2025-01-14 07:55:36.634281 DEBUG::tools.R/processChunks: done
2025-01-14 07:55:39.987309 INFO::io.R/saveWithID: saving file= test/results/test.coverage.RData
2025-01-14 07:55:39.989494 INFO::coverage.R/saveCoverage: saving file= test/results/test.coverage.bw
2025-01-14 07:55:40.09672 INFO::io.R/saveWithID: saving file= test/results/test.summary_coverage.tab
2025-01-14 07:55:40.098525 INFO::coverage.R/calculateCoverage: done
2025-01-14 07:55:40.100241 INFO::analyzeVariants/analyzeVariants: starting ...
2025-01-14 07:55:40.185914 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-01-14 07:55:53.629122 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-01-14 07:55:53.744581 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-01-14 07:55:53.769902 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-01-14 07:55:53.77185 INFO::io.R/saveWithID: saving file= test/results/test.raw_variants.RData
2025-01-14 07:55:53.77511 INFO::io.R/saveWithID: saving file= test/results/test.filtered_variants.RData
2025-01-14 07:55:53.777058 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-01-14 07:55:53.778563 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-01-14 07:55:54.114851 INFO::analyzeVariants.R/writeVCF: ...done
2025-01-14 07:55:54.262856 INFO::io.R/saveWithID: saving file= test/results/test.summary_variants.tab
2025-01-14 07:55:54.265662 INFO::analyzeVariants/analyzeVariants: done
2025-01-14 07:55:54.271599 INFO::Pipeline run successful.
done successfully.
Executing test function test.calculateTargetLength ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp9exJFi/tp53-config.txt
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt
2025-01-14 07:55:54.567798 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9exJFi/test.calcTargetLengths.2d4187295a2d87/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 -- Tue Jan 14 07:56:09 2025
***********************************************
Number of test functions: 61
Number of deactivated test functions: 10
Number of errors: 0
Number of failures: 0
1 Test Suite :
HTSeqGenie unit testing - 61 test functions, 0 errors, 0 failures
Details
***************************
Test Suite: HTSeqGenie unit testing
Test function regexp: ^test.+
Test file regexp: ^runit.+\.[rR]$
Involved directory:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests
---------------------------
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.alignReads.R
test.alignReads: (2 checks) ... OK (31.42 seconds)
test.alignReads.sparsechunks: (2 checks) ... OK (20.43 seconds)
test.alignReadsOneSingleEnd: (2 checks) ... OK (0.57 seconds)
---------------------------
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.analyzeVariants.R
test.annotateVariants : DEACTIVATED, Skipped annotateVariants() test
test.callVariantsVariantTools.genotype: (2 checks) ... OK (106.66 seconds)
test.wrap.callVariants: (4 checks) ... OK (13.7 seconds)
test.wrap.callVariants.filters: (2 checks) ... OK (28.34 seconds)
test.wrap.callVariants.which: (1 checks) ... OK (4.17 seconds)
test.writeVCF.NULL: (1 checks) ... OK (0.2 seconds)
test.writeVCF.vcfStat: (4 checks) ... OK (0.72 seconds)
---------------------------
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.bamUtils.R
test.isFirstFragment: (5 checks) ... OK (0 seconds)
---------------------------
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.buildGenomicFeatures.R
test.buildCountsGRangesList: (3 checks) ... OK (41.71 seconds)
test.generateSingleGeneDERs: (4 checks) ... OK (34.03 seconds)
---------------------------
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.calculateCoverage.R
test.computeCoverage: (9 checks) ... OK (0.98 seconds)
test.isSparse: (5 checks) ... OK (0.13 seconds)
test.mergeCoverage: (1 checks) ... OK (1.65 seconds)
test.mergeCoverage.sparse: (2 checks) ... OK (1.46 seconds)
---------------------------
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.checkConfig.R
test.checkConfig.analyzeVariants: (5 checks) ... OK (0.21 seconds)
test.findTemplate: (5 checks) ... OK (0.01 seconds)
---------------------------
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.config.R
test.checkConfig: (5 checks) ... OK (0.43 seconds)
test.checkConfig.alignReads: (5 checks) ... OK (0.48 seconds)
test.getConfig: (14 checks) ... OK (0 seconds)
test.loadConfig: (2 checks) ... OK (0 seconds)
test.parseDCF: (7 checks) ... OK (0 seconds)
test.updateConfig: (1 checks) ... OK (0 seconds)
---------------------------
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/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 (0.11 seconds)
---------------------------
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.detectRRNA.R
test.detectRRNA: (1 checks) ... OK (0.32 seconds)
test.detectRRNA.paired_end: (1 checks) ... OK (0.49 seconds)
test.getRRNAIds: (1 checks) ... OK (0.31 seconds)
test.getRRNAIds_random: (1 checks) ... OK (0.2 seconds)
---------------------------
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.filterQuality.R
test.filterByLength: (2 checks) ... OK (0.09 seconds)
test.isAboveQualityThresh: (3 checks) ... OK (0.07 seconds)
test.trimTailsByQuality: (4 checks) ... OK (0.05 seconds)
---------------------------
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/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 (0.23 seconds)
test.gatk : DEACTIVATED, gatk() tests need gatk.path option set
test.realignIndels : DEACTIVATED, test.realignIndels() tests need gatk.path option set
test.realignIndelsGATK : DEACTIVATED, realignIndelsGATK() tests need gatk.path option set
test.realignIndelsGATK.parallel : DEACTIVATED, realignIndelsGATK() tests need gatk.path option set
test_zipUp: (3 checks) ... OK (0 seconds)
---------------------------
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.io.R
test.FastQStreamer.getReads.pefq: (1 checks) ... OK (0.24 seconds)
test.FastQStreamer.getReads.pefq.subsample: (1 checks) ... OK (0.43 seconds)
test.FastQStreamer.getReads.segz: (1 checks) ... OK (0.2 seconds)
test.FastQStreamer.getReads.truncated: (1 checks) ... OK (0.22 seconds)
test.FastQStreamer.subsampler.isdeterministic: (3 checks) ... OK (0.73 seconds)
test.createTmpDir: (4 checks) ... OK (0 seconds)
test.detectQualityInFASTQFile: (3 checks) ... OK (0.18 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-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.mergeLanes.R
test.mergeLanes: (6 checks) ... OK (66.11 seconds)
---------------------------
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.picard.R
test.markDuplicates : DEACTIVATED, Skipped markDuplicates() test
test.markDuplicates_w_outfile : DEACTIVATED, Skipped markDuplicates() test
---------------------------
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.preprocessReads.R
test.preprocessReads: (5 checks) ... OK (10.29 seconds)
test.preprocessReads.minichunks: (5 checks) ... OK (15.75 seconds)
test.preprocessReads_single_end: (5 checks) ... OK (8.5 seconds)
---------------------------
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.readRNASeqEnds.R
test.readRNASeqEnds: (6 checks) ... OK (0.13 seconds)
test.readRNASeqEnds.dupmark: (2 checks) ... OK (0.13 seconds)
---------------------------
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.reportPipelineQA.R
test.how_many: (3 checks) ... OK (0 seconds)
test.plotDF: (3 checks) ... OK (0.15 seconds)
test.relativeBarPlot: (2 checks) ... OK (0.05 seconds)
---------------------------
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.runPipeline.R
test.runPipeline: (1 checks) ... OK (52.32 seconds)
---------------------------
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.targetLengths.R
test.calculateTargetLength: (4 checks) ... OK (0.3 seconds)
---------------------------
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.tools.R
test.sclapply: (10 checks) ... OK (14.56 seconds)
test.tryKeepTraceback: (3 checks) ... OK (0.01 seconds)
---------------------------
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.trimReads.R
test.truncateReads: (7 checks) ... OK (0.09 seconds)
test.truncateReads.trim5: (15 checks) ... OK (0.27 seconds)
runTests.R: OK !
There were 50 or more warnings (use warnings() to see the first 50)
>
> proc.time()
user system elapsed
329.026 104.618 481.826
HTSeqGenie.Rcheck/HTSeqGenie-Ex.timings
| name | user | system | elapsed | |
| HTSeqGenie | 0 | 0 | 0 | |
| buildGenomicFeaturesFromTxDb | 0.001 | 0.000 | 0.000 | |
| runPipeline | 0 | 0 | 0 | |