| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-20 11:46 -0500 (Mon, 20 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" | 4777 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4502 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4461 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4416 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4403 |
| 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 978/2286 | 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: 2025-01-20 08:10:13 -0000 (Mon, 20 Jan 2025) |
| EndedAt: 2025-01-20 08:25:11 -0000 (Mon, 20 Jan 2025) |
| EllapsedTime: 897.9 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/Rtmp9YiOCn/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
2025-01-20 08:17:32.536731 INFO::preprocessReads.R/preprocessReads: starting...
2025-01-20 08:17:32.546819 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
2025-01-20 08:17:32.552921 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
2025-01-20 08:17:32.555966 DEBUG::tools.R/processChunks: starting...
2025-01-20 08:17:35.992116 DEBUG::tools.R/processChunks: waiting for chunkid=[ ] ...
2025-01-20 08:17:35.994249 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp9YiOCn/test.alignReads.2ec92225730876/chunks/chunk_000001/logs/progress.log
2025-01-20 08:17:38.903772 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.048 minutes
2025-01-20 08:17:38.905847 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/Rtmp9YiOCn/test.alignReads.2ec92225730876/chunks/chunk_000002/logs/progress.log
2025-01-20 08:17:41.825402 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.049 minutes
2025-01-20 08:17:41.827414 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/Rtmp9YiOCn/test.alignReads.2ec92225730876/chunks/chunk_000003/logs/progress.log
2025-01-20 08:17:44.708483 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.048 minutes
2025-01-20 08:17:44.75211 DEBUG::tools.R/processChunks: done
2025-01-20 08:17:44.757915 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-01-20 08:17:44.761348 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.alignReads.2ec92225730876/results/test_pe.adapter_contaminated_1.RData
2025-01-20 08:17:44.765475 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-01-20 08:17:44.768169 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.alignReads.2ec92225730876/results/test_pe.adapter_contaminated_2.RData
2025-01-20 08:17:44.781671 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
2025-01-20 08:17:44.785053 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.alignReads.2ec92225730876/results/test_pe.summary_preprocess.tab
2025-01-20 08:17:44.78983 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp9YiOCn/test.alignReads.2ec92225730876/bams/processed.aligner_input_1.fastq ...
2025-01-20 08:17:44.796647 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp9YiOCn/test.alignReads.2ec92225730876/bams/processed.aligner_input_2.fastq ...
2025-01-20 08:17:44.802432 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp9YiOCn/test.alignReads.2ec92225730876/reports/shortReadReport_1 ...
2025-01-20 08:17:46.794658 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp9YiOCn/test.alignReads.2ec92225730876/reports/shortReadReport_2 ...
2025-01-20 08:17:50.239115 INFO::preprocessReads.R/preprocessReads: done
2025-01-20 08:17:50.304019 INFO::alignReads.R/alignReads: starting alignment...
2025-01-20 08:17:50.310927 DEBUG::tools.R/processChunks: starting...
2025-01-20 08:17:53.748649 DEBUG::tools.R/processChunks: waiting for chunkid=[ ] ...
2025-01-20 08:17:53.750753 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp9YiOCn/test.alignReads.2ec92225730876/chunks/chunk_000001/logs/progress.log
2025-01-20 08:17:56.912665 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.053 minutes
2025-01-20 08:17:56.914857 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/Rtmp9YiOCn/test.alignReads.2ec92225730876/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.
2025-01-20 08:17:59.649327 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.046 minutes
2025-01-20 08:17:59.651774 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/Rtmp9YiOCn/test.alignReads.2ec92225730876/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.
2025-01-20 08:18:02.418129 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.046 minutes
2025-01-20 08:18:02.421998 DEBUG::tools.R/processChunks: done
2025-01-20 08:18:02.423994 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.
2025-01-20 08:18:02.778795 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-01-20 08:18:02.795567 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.alignReads.2ec92225730876/results/test_pe.summary_alignment.tab
2025-01-20 08:18:02.806913 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.alignReads.2ec92225730876/results/test_pe.summary_analyzed_bamstats.tab
2025-01-20 08:18:02.809517 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-01-20 08:18:03.106137 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.alignReads.2ec92225730876/results/test_pe.summary_target_lengths.tab
2025-01-20 08:18:03.169482 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-01-20 08:18:03.170822 INFO::alignReads.R/alignReads: done
done successfully.
Executing test function test.alignReads.sparsechunks ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp9YiOCn/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
2025-01-20 08:18:03.481227 INFO::preprocessReads.R/preprocessReads: starting...
2025-01-20 08:18:03.484669 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
2025-01-20 08:18:03.56608 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 2 , totnbreads= 26 )
2025-01-20 08:18:03.572559 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
2025-01-20 08:18:03.576852 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
2025-01-20 08:18:03.57946 DEBUG::tools.R/processChunks: starting...
2025-01-20 08:18:07.010683 DEBUG::tools.R/processChunks: waiting for chunkid=[ ] ...
2025-01-20 08:18:07.01279 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp9YiOCn/test.alignReads.sparsechunks.2ec922152e9dcb/chunks/chunk_000001/logs/progress.log
2025-01-20 08:18:09.871616 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.048 minutes
2025-01-20 08:18:09.873581 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/Rtmp9YiOCn/test.alignReads.sparsechunks.2ec922152e9dcb/chunks/chunk_000002/logs/progress.log
2025-01-20 08:18:12.700537 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.047 minutes
2025-01-20 08:18:12.702579 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/Rtmp9YiOCn/test.alignReads.sparsechunks.2ec922152e9dcb/chunks/chunk_000003/logs/progress.log
2025-01-20 08:18:15.664621 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.049 minutes
2025-01-20 08:18:15.666675 DEBUG::tools.R/processChunks: starting chunkid= 4 ; see logfile= /home/biocbuild/tmp/Rtmp9YiOCn/test.alignReads.sparsechunks.2ec922152e9dcb/chunks/chunk_000004/logs/progress.log
2025-01-20 08:18:18.468618 DEBUG::tools.R/processChunks: done with chunkid= 4 ; elapsed.time= 0.047 minutes
2025-01-20 08:18:18.511043 DEBUG::tools.R/processChunks: done
2025-01-20 08:18:18.515533 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-01-20 08:18:18.518765 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.alignReads.sparsechunks.2ec922152e9dcb/results/test_pe.adapter_contaminated_1.RData
2025-01-20 08:18:18.523823 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-01-20 08:18:18.526427 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.alignReads.sparsechunks.2ec922152e9dcb/results/test_pe.adapter_contaminated_2.RData
2025-01-20 08:18:18.540793 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
2025-01-20 08:18:18.543994 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.alignReads.sparsechunks.2ec922152e9dcb/results/test_pe.summary_preprocess.tab
2025-01-20 08:18:18.549133 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp9YiOCn/test.alignReads.sparsechunks.2ec922152e9dcb/bams/processed.aligner_input_1.fastq ...
2025-01-20 08:18:18.55627 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp9YiOCn/test.alignReads.sparsechunks.2ec922152e9dcb/bams/processed.aligner_input_2.fastq ...
2025-01-20 08:18:18.561916 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp9YiOCn/test.alignReads.sparsechunks.2ec922152e9dcb/reports/shortReadReport_1 ...
2025-01-20 08:18:20.512298 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp9YiOCn/test.alignReads.sparsechunks.2ec922152e9dcb/reports/shortReadReport_2 ...
2025-01-20 08:18:24.450698 INFO::preprocessReads.R/preprocessReads: done
done successfully.
Executing test function test.alignReadsOneSingleEnd ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp9YiOCn/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
2025-01-20 08:18:24.655683 INFO::alignReads.R/alignReadsChunk: running gsnap...
2025-01-20 08:18:24.662096 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/Rtmp9YiOCn/test.alignReadsOneSingleEnd.2ec92263d79a99/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
2025-01-20 08:18:24.81214 INFO::alignReads.R/createSummaryAlignment: counting unique bam reads...
2025-01-20 08:18:24.948253 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.alignReadsOneSingleEnd.2ec92263d79a99/results/test.alignReads.summary_alignment.tab
2025-01-20 08:18:24.999546 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.alignReadsOneSingleEnd.2ec92263d79a99/results/test.alignReads.summary_analyzed_bamstats.tab
2025-01-20 08:18:25.00176 INFO::alignReads.R/alignReadsChunk: done
done successfully.
Executing test function test.annotateVariants ... Timing stopped at: 0.005 0 0.003
Error in DEACTIVATED("Skipped annotateVariants() test") :
Skipped annotateVariants() test
In addition: There were 11 warnings (use warnings() to see them)
done successfully.
Executing test function test.callVariantsVariantTools.genotype ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp9YiOCn/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
2025-01-20 08:18:25.402052 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.genotype.2ec922cf85c06/results/test_pe.coverage.RData
2025-01-20 08:18:25.404481 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.genotype.2ec922cf85c06/results/test_pe.coverage.bw
2025-01-20 08:18:25.589496 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.genotype.2ec922cf85c06/results/test_pe.summary_coverage.tab
2025-01-20 08:18:25.591821 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-01-20 08:18:38.633894 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-01-20 08:18:38.753952 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-01-20 08:18:38.777783 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-01-20 08:18:38.779775 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.genotype.2ec922cf85c06/results/test_pe.raw_variants.RData
2025-01-20 08:18:38.782799 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.genotype.2ec922cf85c06/results/test_pe.filtered_variants.RData
2025-01-20 08:18:38.784594 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-01-20 08:18:38.786192 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-01-20 08:18:39.324423 INFO::analyzeVariants.R/writeVCF: ...done
2025-01-20 08:18:39.325994 INFO::analyzeVariants.R/.callGenotypes: calling genotypes...
2025-01-20 08:20:11.554252 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-01-20 08:20:12.208879 INFO::analyzeVariants.R/writeVCF: ...done
2025-01-20 08:20:12.210385 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/Rtmp9YiOCn/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
2025-01-20 08:20:12.845906 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-01-20 08:20:25.930178 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-01-20 08:20:26.079095 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-01-20 08:20:26.112074 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-01-20 08:20:26.114697 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.wrap.callVariants.2ec9227389f3da/results/test_pe.raw_variants.RData
2025-01-20 08:20:26.11869 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.wrap.callVariants.2ec9227389f3da/results/test_pe.filtered_variants.RData
2025-01-20 08:20:26.121168 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/Rtmp9YiOCn/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
2025-01-20 08:20:26.394421 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-01-20 08:20:39.224136 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-01-20 08:20:39.324934 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-01-20 08:20:39.351652 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-01-20 08:20:39.353785 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.wrap.callVariants.filters.2ec922436f1c68/results/test_pe.raw_variants.RData
2025-01-20 08:20:39.357401 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.wrap.callVariants.filters.2ec922436f1c68/results/test_pe.filtered_variants.RData
2025-01-20 08:20:39.359772 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-01-20 08:20:39.362427 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-01-20 08:20:53.256671 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-01-20 08:20:53.318701 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-01-20 08:20:53.344947 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-01-20 08:20:53.346959 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.wrap.callVariants.filters.2ec922436f1c68/results/test_pe.raw_variants.RData
2025-01-20 08:20:53.350321 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.wrap.callVariants.filters.2ec922436f1c68/results/test_pe.filtered_variants.RData
2025-01-20 08:20:53.352988 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/Rtmp9YiOCn/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
2025-01-20 08:20:53.714882 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-01-20 08:20:53.717016 INFO::analyzeVariants.R/buildTallyParam: restricting variant calls using 'which'
2025-01-20 08:20:57.622191 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-01-20 08:20:57.739702 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-01-20 08:20:57.765759 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-01-20 08:20:57.767766 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.wrap.callVariants.which.2ec9227c771428/results/test_pe.raw_variants.RData
2025-01-20 08:20:57.770192 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.wrap.callVariants.which.2ec9227c771428/results/test_pe.filtered_variants.RData
2025-01-20 08:20:57.772019 INFO::analyzeVariants.R/wrap.callVariants: ...done
done successfully.
Executing test function test.writeVCF.NULL ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp9YiOCn/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
2025-01-20 08:20:57.975293 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-01-20 08:20:57.977098 INFO::analyzeVariants.R/writeVCF: ...done
done successfully.
Executing test function test.writeVCF.vcfStat ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp9YiOCn/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
2025-01-20 08:20:58.216237 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-01-20 08:20:58.53762 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 ... 2025-01-20 08:22:11.854873 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/xligaueo/merged/results/bla.coverage.RData
2025-01-20 08:22:11.858434 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/xligaueo/merged/results/bla.coverage.bw
2025-01-20 08:22:11.975159 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/xligaueo/merged/results/bla.summary_coverage.tab
done successfully.
Executing test function test.mergeCoverage.sparse ... 2025-01-20 08:22:13.332028 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/czexoiqy/merged/results/bla.coverage.RData
2025-01-20 08:22:13.334207 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/czexoiqy/merged/results/bla.coverage.bw
2025-01-20 08:22:13.349562 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/czexoiqy/merged/results/bla.summary_coverage.tab
done successfully.
Executing test function test.checkConfig.analyzeVariants ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp9YiOCn/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/Rtmp9YiOCn/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/Rtmp9YiOCn/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/Rtmp9YiOCn/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/Rtmp9YiOCn/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/Rtmp9YiOCn/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/Rtmp9YiOCn/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/Rtmp9YiOCn/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/Rtmp9YiOCn/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/Rtmp9YiOCn/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
2025-01-20 08:22:14.999865 INFO::detectRRNA.R/detectRRNA: searching for rRNA contamination...
2025-01-20 08:22:15.001523 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/tmp/Rtmp9YiOCn/test.detectRRNA.2ec92268ffdb0d/bams/rRNA_contam/input1.fastq
2025-01-20 08:22:15.006611 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/Rtmp9YiOCn/test.detectRRNA.2ec92268ffdb0d/bams/rRNA_contam/test_se /home/biocbuild/tmp/Rtmp9YiOCn/test.detectRRNA.2ec92268ffdb0d/bams/rRNA_contam/input1.fastq 2>&1
2025-01-20 08:22:15.119456 INFO::detectRRNA.R/detectRRNA: contaminated fraction= 1
2025-01-20 08:22:15.120942 INFO::detectRRNA.R/detectRRNA: done
done successfully.
Executing test function test.detectRRNA.paired_end ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp9YiOCn/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
2025-01-20 08:22:15.319992 INFO::detectRRNA.R/detectRRNA: searching for rRNA contamination...
2025-01-20 08:22:15.321427 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/tmp/Rtmp9YiOCn/test.detectRRNA.paired_end.2ec9227648399b/bams/rRNA_contam/input1.fastq
2025-01-20 08:22:15.323641 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/tmp/Rtmp9YiOCn/test.detectRRNA.paired_end.2ec9227648399b/bams/rRNA_contam/input2.fastq
2025-01-20 08:22:15.327007 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/Rtmp9YiOCn/test.detectRRNA.paired_end.2ec9227648399b/bams/rRNA_contam/test_pe /home/biocbuild/tmp/Rtmp9YiOCn/test.detectRRNA.paired_end.2ec9227648399b/bams/rRNA_contam/input1.fastq -a paired /home/biocbuild/tmp/Rtmp9YiOCn/test.detectRRNA.paired_end.2ec9227648399b/bams/rRNA_contam/input2.fastq 2>&1
2025-01-20 08:22:15.584046 INFO::detectRRNA.R/detectRRNA: contaminated fraction= 1
2025-01-20 08:22:15.585456 INFO::detectRRNA.R/detectRRNA: done
done successfully.
Executing test function test.getRRNAIds ... 2025-01-20 08:22:15.61414 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/Rtmp9YiOCn/test_get_rRNA_idsijsgrxfp/test_pe /home/biocbuild/tmp/Rtmp9YiOCn/test_get_rRNA_idsijsgrxfp/1.fastq -a paired /home/biocbuild/tmp/Rtmp9YiOCn/test_get_rRNA_idsijsgrxfp/2.fastq 2>&1
done successfully.
Executing test function test.getRRNAIds_random ... 2025-01-20 08:22:15.89267 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/Rtmp9YiOCn/test_get_rRNAIds_randomgdseyibx/test_pe /home/biocbuild/tmp/Rtmp9YiOCn/test_get_rRNAIds_randomgdseyibx/1.fastq 2>&1
done successfully.
Executing test function test.filterByLength ... 2025-01-20 08:22:16.055427 INFO::filterQuality.R/filterQuality: filterByLength...
2025-01-20 08:22:16.057335 INFO::filterQuality.R/filterByLength: fraction of filtered short reads= 0.5
2025-01-20 08:22:16.058593 INFO::filterQuality.R/filterByLength: done
2025-01-20 08:22:16.124987 INFO::filterQuality.R/filterQuality: filterByLength...
2025-01-20 08:22:16.126243 INFO::filterQuality.R/filterByLength: fraction of filtered short reads= 1
2025-01-20 08:22:16.127439 INFO::filterQuality.R/filterByLength: done
done successfully.
Executing test function test.isAboveQualityThresh ... done successfully.
Executing test function test.trimTailsByQuality ... 2025-01-20 08:22:16.201126 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-01-20 08:22:16.213979 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-01-20 08:22:16.215568 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-01-20 08:22:16.222275 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-01-20 08:22:16.223795 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-01-20 08:22:16.230492 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-01-20 08:22:16.231964 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-01-20 08:22:16.238619 INFO::preprocessReads.R/preprocessReadsChunk: done
done successfully.
Executing test function test.callVariantsGATK ... Timing stopped at: 0.001 0 0.001
Error in DEACTIVATED("callVariantsGATK() tests need gatk.path option set") :
callVariantsGATK() tests need gatk.path option set
In addition: There were 50 or more warnings (use warnings() to see the first 50)
done successfully.
Executing test function test.callVariantsGATK.withFiltering ... Timing stopped at: 0 0 0
Error in DEACTIVATED("callVariantsGATK() tests need gatk.path option set") :
callVariantsGATK() tests need gatk.path option set
done successfully.
Executing test function test.checkGATKJar ... Timing stopped at: 0 0 0
Error in DEACTIVATED("checkGATKJar() test needs gatk.path option set") :
checkGATKJar() test needs gatk.path option set
done successfully.
Executing test function test.excludeVariantsByRegion ... done successfully.
Executing test function test.gatk ... Timing stopped at: 0 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: 0.001 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/Rtmp9YiOCn/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
2025-01-20 08:22:16.634854 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
2025-01-20 08:22:16.638148 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/Rtmp9YiOCn/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
2025-01-20 08:22:16.865621 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
2025-01-20 08:22:16.994195 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-01-20 08:22:16.998133 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
2025-01-20 08:22:17.001365 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/Rtmp9YiOCn/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
2025-01-20 08:22:17.289749 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/Rtmp9YiOCn/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
2025-01-20 08:22:17.470112 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/Rtmp9YiOCn/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
2025-01-20 08:22:17.672678 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
2025-01-20 08:22:17.758155 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-01-20 08:22:17.76172 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
2025-01-20 08:22:17.765158 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/Rtmp9YiOCn/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
2025-01-20 08:22:18.027816 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
2025-01-20 08:22:18.082447 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-01-20 08:22:18.085979 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
2025-01-20 08:22:18.089345 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/Rtmp9YiOCn/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/Rtmp9YiOCn/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
2025-01-20 08:22:19.000195 INFO::preprocessReads.R/preprocessReads: starting...
2025-01-20 08:22:19.007166 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
2025-01-20 08:22:19.012096 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
2025-01-20 08:22:19.015001 DEBUG::tools.R/processChunks: starting...
2025-01-20 08:22:22.341188 DEBUG::tools.R/processChunks: waiting for chunkid=[ ] ...
2025-01-20 08:22:22.343191 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/chunks/chunk_000001/logs/progress.log
2025-01-20 08:22:25.137757 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.047 minutes
2025-01-20 08:22:25.139788 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/chunks/chunk_000002/logs/progress.log
2025-01-20 08:22:27.922082 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.046 minutes
2025-01-20 08:22:27.924168 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/chunks/chunk_000003/logs/progress.log
2025-01-20 08:22:30.707784 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.046 minutes
2025-01-20 08:22:30.762017 DEBUG::tools.R/processChunks: done
2025-01-20 08:22:30.766071 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-01-20 08:22:30.768737 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/results/test_pe.adapter_contaminated_1.RData
2025-01-20 08:22:30.772025 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-01-20 08:22:30.774542 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/results/test_pe.adapter_contaminated_2.RData
2025-01-20 08:22:30.786859 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
2025-01-20 08:22:30.78961 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/results/test_pe.summary_preprocess.tab
2025-01-20 08:22:30.793281 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/bams/processed.aligner_input_1.fastq ...
2025-01-20 08:22:30.799913 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/bams/processed.aligner_input_2.fastq ...
2025-01-20 08:22:30.805056 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/reports/shortReadReport_1 ...
2025-01-20 08:22:32.629288 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/reports/shortReadReport_2 ...
2025-01-20 08:22:34.311758 INFO::preprocessReads.R/preprocessReads: done
2025-01-20 08:22:34.388372 INFO::alignReads.R/alignReads: starting alignment...
2025-01-20 08:22:34.393065 DEBUG::tools.R/processChunks: starting...
2025-01-20 08:22:37.747726 DEBUG::tools.R/processChunks: waiting for chunkid=[ ] ...
2025-01-20 08:22:37.749827 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/chunks/chunk_000001/logs/progress.log
2025-01-20 08:22:40.408971 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.044 minutes
2025-01-20 08:22:40.411209 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/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.
2025-01-20 08:22:43.062426 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.044 minutes
2025-01-20 08:22:43.068841 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/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.
2025-01-20 08:22:45.678659 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.043 minutes
2025-01-20 08:22:45.681993 DEBUG::tools.R/processChunks: done
2025-01-20 08:22:45.68385 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.
2025-01-20 08:22:45.967493 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-01-20 08:22:45.977631 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/results/test_pe.summary_alignment.tab
2025-01-20 08:22:45.98744 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/results/test_pe.summary_analyzed_bamstats.tab
2025-01-20 08:22:45.989927 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-01-20 08:22:46.24759 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/results/test_pe.summary_target_lengths.tab
2025-01-20 08:22:46.309517 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-01-20 08:22:46.310827 INFO::alignReads.R/alignReads: done
2025-01-20 08:22:46.390923 INFO::countGenomicFeatures.R/countGenomicFeatures: starting...
2025-01-20 08:22:46.412907 DEBUG::tools.R/processChunks: starting...
2025-01-20 08:22:49.9474 DEBUG::tools.R/processChunks: waiting for chunkid=[ ] ...
2025-01-20 08:22:49.949631 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/chunks/chunk_000001/logs/progress.log
2025-01-20 08:22:52.544936 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.043 minutes
2025-01-20 08:22:52.547221 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/chunks/chunk_000002/logs/progress.log
2025-01-20 08:22:55.123628 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.043 minutes
2025-01-20 08:22:55.125843 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/chunks/chunk_000003/logs/progress.log
2025-01-20 08:22:57.694247 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.043 minutes
2025-01-20 08:22:57.701771 DEBUG::tools.R/processChunks: done
2025-01-20 08:22:57.70406 INFO::countGenomicFeatures.R/mergeCounts: starting...
2025-01-20 08:22:57.720555 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/results/test_pe.counts_exon.tab
2025-01-20 08:22:57.734174 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/results/test_pe.counts_exon_disjoint.tab
2025-01-20 08:22:57.743099 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/results/test_pe.counts_gene.tab
2025-01-20 08:22:57.750081 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/results/test_pe.counts_gene_coding.tab
2025-01-20 08:22:57.757217 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/results/test_pe.counts_gene_exonic.tab
2025-01-20 08:22:57.764449 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/results/test_pe.counts_intergenic.tab
2025-01-20 08:22:57.776102 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/results/test_pe.counts_intron.tab
2025-01-20 08:22:57.779764 INFO::countGenomicFeatures.R/mergeCounts: done
2025-01-20 08:22:57.787444 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/results/test_pe.summary_counts.tab
2025-01-20 08:22:57.789819 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2025-01-20 08:22:58.158731 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2025-01-20 08:22:58.160025 INFO::countGenomicFeatures.R/countGenomicFeatures: done...
2025-01-20 08:22:58.233871 INFO::coverage.R/calculateCoverage: starting...
2025-01-20 08:22:58.238253 DEBUG::tools.R/processChunks: starting...
2025-01-20 08:23:01.62688 DEBUG::tools.R/processChunks: waiting for chunkid=[ ] ...
2025-01-20 08:23:01.628995 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/chunks/chunk_000001/logs/progress.log
2025-01-20 08:23:03.826876 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.037 minutes
2025-01-20 08:23:03.829195 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/chunks/chunk_000002/logs/progress.log
2025-01-20 08:23:06.019508 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.036 minutes
2025-01-20 08:23:06.021737 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/chunks/chunk_000003/logs/progress.log
2025-01-20 08:23:08.244334 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.037 minutes
2025-01-20 08:23:08.248279 DEBUG::tools.R/processChunks: done
2025-01-20 08:23:10.832751 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/results/test_pe.coverage.RData
2025-01-20 08:23:10.834667 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/results/test_pe.coverage.bw
2025-01-20 08:23:10.850061 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/results/test_pe.summary_coverage.tab
2025-01-20 08:23:10.851853 INFO::coverage.R/calculateCoverage: done
2025-01-20 08:23:10.854045 INFO::analyzeVariants/analyzeVariants: starting ...
2025-01-20 08:23:10.9331 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-01-20 08:23:14.592216 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-01-20 08:23:14.703254 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-01-20 08:23:14.727679 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-01-20 08:23:14.729513 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/results/test_pe.raw_variants.RData
2025-01-20 08:23:14.731722 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/results/test_pe.filtered_variants.RData
2025-01-20 08:23:14.733511 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-01-20 08:23:14.734903 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-01-20 08:23:15.060061 INFO::analyzeVariants.R/writeVCF: ...done
2025-01-20 08:23:15.207775 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/results/test_pe.summary_variants.tab
2025-01-20 08:23:15.210625 INFO::analyzeVariants/analyzeVariants: done
2025-01-20 08:23:15.214757 INFO::Pipeline run successful.
2025-01-20 08:23:15.389045 INFO::mergeLanes.R/doMergeLanes: starting...
2025-01-20 08:23:15.394358 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-01-20 08:23:15.39744 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/merged/results/merged.adapter_contaminated_1.RData
2025-01-20 08:23:15.401363 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-01-20 08:23:15.404126 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/merged/results/merged.adapter_contaminated_2.RData
2025-01-20 08:23:15.418808 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
2025-01-20 08:23:15.422101 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/merged/results/merged.summary_preprocess.tab
2025-01-20 08:23:15.425172 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.
2025-01-20 08:23:15.770068 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-01-20 08:23:15.781213 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/merged/results/merged.summary_alignment.tab
2025-01-20 08:23:15.79378 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/merged/results/merged.summary_analyzed_bamstats.tab
2025-01-20 08:23:15.796898 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-01-20 08:23:16.072683 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/merged/results/merged.summary_target_lengths.tab
2025-01-20 08:23:16.140236 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-01-20 08:23:16.177311 INFO::countGenomicFeatures.R/mergeCounts: starting...
2025-01-20 08:23:16.202132 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/merged/results/merged.counts_exon.tab
2025-01-20 08:23:16.217973 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/merged/results/merged.counts_exon_disjoint.tab
2025-01-20 08:23:16.227431 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/merged/results/merged.counts_gene.tab
2025-01-20 08:23:16.235142 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/merged/results/merged.counts_gene_coding.tab
2025-01-20 08:23:16.243014 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/merged/results/merged.counts_gene_exonic.tab
2025-01-20 08:23:16.251526 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/merged/results/merged.counts_intergenic.tab
2025-01-20 08:23:16.266194 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/merged/results/merged.counts_intron.tab
2025-01-20 08:23:16.270111 INFO::countGenomicFeatures.R/mergeCounts: done
2025-01-20 08:23:16.278871 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/merged/results/merged.summary_counts.tab
2025-01-20 08:23:16.281425 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2025-01-20 08:23:16.583548 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2025-01-20 08:23:19.128054 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/merged/results/merged.coverage.RData
2025-01-20 08:23:19.130955 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/merged/results/merged.coverage.bw
2025-01-20 08:23:19.146539 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/merged/results/merged.summary_coverage.tab
2025-01-20 08:23:19.190971 INFO::analyzeVariants/analyzeVariants: starting ...
2025-01-20 08:23:19.266768 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-01-20 08:23:23.092876 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-01-20 08:23:23.208945 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-01-20 08:23:23.234772 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-01-20 08:23:23.236797 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/merged/results/merged.raw_variants.RData
2025-01-20 08:23:23.23911 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/merged/results/merged.filtered_variants.RData
2025-01-20 08:23:23.241006 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-01-20 08:23:23.242488 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-01-20 08:23:23.5731 INFO::analyzeVariants.R/writeVCF: ...done
2025-01-20 08:23:23.714131 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.mergeLanes.2ec9223eb3ccb6/merged/results/merged.summary_variants.tab
2025-01-20 08:23:23.7168 INFO::analyzeVariants/analyzeVariants: done
2025-01-20 08:23:23.719872 INFO::mergeLanes.R/doMergeLanes: merge lanes successful.
done successfully.
Executing test function test.markDuplicates ... Timing stopped at: 0 0 0.001
Error in DEACTIVATED("Skipped markDuplicates() test") :
Skipped markDuplicates() test
In addition: There were 28 warnings (use warnings() to see them)
done successfully.
Executing test function test.markDuplicates_w_outfile ... Timing stopped at: 0 0 0
Error in DEACTIVATED("Skipped markDuplicates() test") :
Skipped markDuplicates() test
done successfully.
Executing test function test.preprocessReads ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp9YiOCn/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
2025-01-20 08:23:24.051378 INFO::preprocessReads.R/preprocessReads: starting...
2025-01-20 08:23:24.074398 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
2025-01-20 08:23:24.082331 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
2025-01-20 08:23:24.085365 DEBUG::tools.R/processChunks: starting...
2025-01-20 08:23:27.506459 DEBUG::tools.R/processChunks: waiting for chunkid=[ ] ...
2025-01-20 08:23:27.508479 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp9YiOCn/test.preprocessReads.2ec92273a3d774/chunks/chunk_000001/logs/progress.log
2025-01-20 08:23:30.253513 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.046 minutes
2025-01-20 08:23:30.301838 DEBUG::tools.R/processChunks: done
2025-01-20 08:23:30.304877 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-01-20 08:23:30.307168 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.preprocessReads.2ec92273a3d774/results/test_pe.adapter_contaminated_1.RData
2025-01-20 08:23:30.309702 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-01-20 08:23:30.311882 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.preprocessReads.2ec92273a3d774/results/test_pe.adapter_contaminated_2.RData
2025-01-20 08:23:30.320721 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
2025-01-20 08:23:30.323405 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.preprocessReads.2ec92273a3d774/results/test_pe.summary_preprocess.tab
2025-01-20 08:23:30.329537 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp9YiOCn/test.preprocessReads.2ec92273a3d774/bams/processed.aligner_input_1.fastq ...
2025-01-20 08:23:30.335205 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp9YiOCn/test.preprocessReads.2ec92273a3d774/bams/processed.aligner_input_2.fastq ...
2025-01-20 08:23:30.340455 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp9YiOCn/test.preprocessReads.2ec92273a3d774/reports/shortReadReport_1 ...
2025-01-20 08:23:32.198932 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp9YiOCn/test.preprocessReads.2ec92273a3d774/reports/shortReadReport_2 ...
2025-01-20 08:23:33.824082 INFO::preprocessReads.R/preprocessReads: done
done successfully.
Executing test function test.preprocessReads.minichunks ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp9YiOCn/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
2025-01-20 08:23:34.121799 INFO::preprocessReads.R/preprocessReads: starting...
2025-01-20 08:23:34.128623 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
2025-01-20 08:23:34.133468 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
2025-01-20 08:23:34.136453 DEBUG::tools.R/processChunks: starting...
2025-01-20 08:23:37.591328 DEBUG::tools.R/processChunks: waiting for chunkid=[ ] ...
2025-01-20 08:23:37.593375 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp9YiOCn/test.preprocessReads.minichunks.2ec92228e5e7ae/chunks/chunk_000001/logs/progress.log
2025-01-20 08:23:40.340137 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.046 minutes
2025-01-20 08:23:40.342064 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/Rtmp9YiOCn/test.preprocessReads.minichunks.2ec92228e5e7ae/chunks/chunk_000002/logs/progress.log
2025-01-20 08:23:43.117841 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.046 minutes
2025-01-20 08:23:43.119793 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/Rtmp9YiOCn/test.preprocessReads.minichunks.2ec92228e5e7ae/chunks/chunk_000003/logs/progress.log
2025-01-20 08:23:45.866198 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.046 minutes
2025-01-20 08:23:45.914355 DEBUG::tools.R/processChunks: done
2025-01-20 08:23:45.918098 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-01-20 08:23:45.92062 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.preprocessReads.minichunks.2ec92228e5e7ae/results/test_pe.adapter_contaminated_1.RData
2025-01-20 08:23:45.923753 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-01-20 08:23:45.926129 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.preprocessReads.minichunks.2ec92228e5e7ae/results/test_pe.adapter_contaminated_2.RData
2025-01-20 08:23:45.93748 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
2025-01-20 08:23:45.940032 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.preprocessReads.minichunks.2ec92228e5e7ae/results/test_pe.summary_preprocess.tab
2025-01-20 08:23:45.943575 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp9YiOCn/test.preprocessReads.minichunks.2ec92228e5e7ae/bams/processed.aligner_input_1.fastq ...
2025-01-20 08:23:45.950134 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp9YiOCn/test.preprocessReads.minichunks.2ec92228e5e7ae/bams/processed.aligner_input_2.fastq ...
2025-01-20 08:23:45.955766 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp9YiOCn/test.preprocessReads.minichunks.2ec92228e5e7ae/reports/shortReadReport_1 ...
2025-01-20 08:23:47.828838 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp9YiOCn/test.preprocessReads.minichunks.2ec92228e5e7ae/reports/shortReadReport_2 ...
2025-01-20 08:23:49.502825 INFO::preprocessReads.R/preprocessReads: done
done successfully.
Executing test function test.preprocessReads_single_end ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp9YiOCn/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
2025-01-20 08:23:49.801371 INFO::preprocessReads.R/preprocessReads: starting...
2025-01-20 08:23:49.824487 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
2025-01-20 08:23:49.827606 DEBUG::tools.R/processChunks: starting...
2025-01-20 08:23:53.238036 DEBUG::tools.R/processChunks: waiting for chunkid=[ ] ...
2025-01-20 08:23:53.240167 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp9YiOCn/test.preprocessReads_single_end.2ec922f08837a/chunks/chunk_000001/logs/progress.log
2025-01-20 08:23:55.694679 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.041 minutes
2025-01-20 08:23:55.7082 DEBUG::tools.R/processChunks: done
2025-01-20 08:23:55.71135 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-01-20 08:23:55.713746 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.preprocessReads_single_end.2ec922f08837a/results/test_se.adapter_contaminated_1.RData
2025-01-20 08:23:55.723103 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
2025-01-20 08:23:55.7259 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.preprocessReads_single_end.2ec922f08837a/results/test_se.summary_preprocess.tab
2025-01-20 08:23:55.728833 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp9YiOCn/test.preprocessReads_single_end.2ec922f08837a/bams/processed.aligner_input_1.fastq ...
2025-01-20 08:23:55.734351 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp9YiOCn/test.preprocessReads_single_end.2ec922f08837a/reports/shortReadReport_1 ...
2025-01-20 08:23:57.519509 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
2025-01-20 08:23:58.252291 INFO::preprocessReads.R/preprocessReads: starting...
2025-01-20 08:23:58.276654 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
2025-01-20 08:23:58.283009 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
2025-01-20 08:23:58.286119 DEBUG::tools.R/processChunks: starting...
2025-01-20 08:24:02.359011 DEBUG::tools.R/processChunks: waiting for chunkid=[ ] ...
2025-01-20 08:24:02.361052 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= test/chunks/chunk_000001/logs/progress.log
2025-01-20 08:24:05.313991 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.049 minutes
2025-01-20 08:24:05.37399 DEBUG::tools.R/processChunks: done
2025-01-20 08:24:05.377145 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-01-20 08:24:05.379405 INFO::io.R/saveWithID: saving file= test/results/test.adapter_contaminated_1.RData
2025-01-20 08:24:05.381893 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-01-20 08:24:05.384021 INFO::io.R/saveWithID: saving file= test/results/test.adapter_contaminated_2.RData
2025-01-20 08:24:05.39247 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
2025-01-20 08:24:05.395079 INFO::io.R/saveWithID: saving file= test/results/test.summary_preprocess.tab
2025-01-20 08:24:05.397777 INFO::preprocessReads.R/mergePreprocessedReads: merging file= test/bams/processed.aligner_input_1.fastq ...
2025-01-20 08:24:05.403888 INFO::preprocessReads.R/mergePreprocessedReads: merging file= test/bams/processed.aligner_input_2.fastq ...
2025-01-20 08:24:05.410223 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= test/reports/shortReadReport_1 ...
2025-01-20 08:24:07.46782 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= test/reports/shortReadReport_2 ...
2025-01-20 08:24:09.283716 INFO::preprocessReads.R/preprocessReads: done
2025-01-20 08:24:09.365419 INFO::alignReads.R/alignReads: starting alignment...
2025-01-20 08:24:09.370114 DEBUG::tools.R/processChunks: starting...
2025-01-20 08:24:12.833889 DEBUG::tools.R/processChunks: waiting for chunkid=[ ] ...
2025-01-20 08:24:12.835991 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.
2025-01-20 08:24:18.866721 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.1 minutes
2025-01-20 08:24:18.874227 DEBUG::tools.R/processChunks: done
2025-01-20 08:24:18.876162 INFO::alignReads.R/mergeBAMsAcrossDirs: starting...
2025-01-20 08:24:18.910985 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-01-20 08:24:18.919231 INFO::io.R/saveWithID: saving file= test/results/test.summary_alignment.tab
2025-01-20 08:24:18.926841 INFO::io.R/saveWithID: saving file= test/results/test.summary_analyzed_bamstats.tab
2025-01-20 08:24:18.929583 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-01-20 08:24:19.128288 INFO::io.R/saveWithID: saving file= test/results/test.summary_target_lengths.tab
2025-01-20 08:24:19.190314 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-01-20 08:24:19.191617 INFO::alignReads.R/alignReads: done
2025-01-20 08:24:19.294973 INFO::countGenomicFeatures.R/countGenomicFeatures: starting...
2025-01-20 08:24:19.312933 DEBUG::tools.R/processChunks: starting...
2025-01-20 08:24:23.275132 DEBUG::tools.R/processChunks: waiting for chunkid=[ ] ...
2025-01-20 08:24:23.27792 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= test/chunks/chunk_000001/logs/progress.log
2025-01-20 08:24:25.899259 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.044 minutes
2025-01-20 08:24:25.90284 DEBUG::tools.R/processChunks: done
2025-01-20 08:24:25.905123 INFO::countGenomicFeatures.R/mergeCounts: starting...
2025-01-20 08:24:25.917404 INFO::io.R/saveWithID: saving file= test/results/test.counts_exon.tab
2025-01-20 08:24:25.927521 INFO::io.R/saveWithID: saving file= test/results/test.counts_exon_disjoint.tab
2025-01-20 08:24:25.934936 INFO::io.R/saveWithID: saving file= test/results/test.counts_gene.tab
2025-01-20 08:24:25.940129 INFO::io.R/saveWithID: saving file= test/results/test.counts_gene_coding.tab
2025-01-20 08:24:25.945342 INFO::io.R/saveWithID: saving file= test/results/test.counts_gene_exonic.tab
2025-01-20 08:24:25.950487 INFO::io.R/saveWithID: saving file= test/results/test.counts_intergenic.tab
2025-01-20 08:24:25.957991 INFO::io.R/saveWithID: saving file= test/results/test.counts_intron.tab
2025-01-20 08:24:25.961879 INFO::countGenomicFeatures.R/mergeCounts: done
2025-01-20 08:24:25.966805 INFO::io.R/saveWithID: saving file= test/results/test.summary_counts.tab
2025-01-20 08:24:25.969146 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2025-01-20 08:24:26.252986 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2025-01-20 08:24:26.254269 INFO::countGenomicFeatures.R/countGenomicFeatures: done...
2025-01-20 08:24:26.331709 INFO::coverage.R/calculateCoverage: starting...
2025-01-20 08:24:26.336616 DEBUG::tools.R/processChunks: starting...
2025-01-20 08:24:29.943651 DEBUG::tools.R/processChunks: waiting for chunkid=[ ] ...
2025-01-20 08:24:29.945969 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= test/chunks/chunk_000001/logs/progress.log
2025-01-20 08:24:32.326228 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.04 minutes
2025-01-20 08:24:32.329706 DEBUG::tools.R/processChunks: done
2025-01-20 08:24:34.479641 INFO::io.R/saveWithID: saving file= test/results/test.coverage.RData
2025-01-20 08:24:34.481987 INFO::coverage.R/saveCoverage: saving file= test/results/test.coverage.bw
2025-01-20 08:24:34.59765 INFO::io.R/saveWithID: saving file= test/results/test.summary_coverage.tab
2025-01-20 08:24:34.599502 INFO::coverage.R/calculateCoverage: done
2025-01-20 08:24:34.601245 INFO::analyzeVariants/analyzeVariants: starting ...
2025-01-20 08:24:34.687484 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-01-20 08:24:48.004609 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-01-20 08:24:48.114381 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-01-20 08:24:48.138144 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-01-20 08:24:48.139982 INFO::io.R/saveWithID: saving file= test/results/test.raw_variants.RData
2025-01-20 08:24:48.143069 INFO::io.R/saveWithID: saving file= test/results/test.filtered_variants.RData
2025-01-20 08:24:48.144863 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-01-20 08:24:48.146284 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-01-20 08:24:48.463214 INFO::analyzeVariants.R/writeVCF: ...done
2025-01-20 08:24:48.611593 INFO::io.R/saveWithID: saving file= test/results/test.summary_variants.tab
2025-01-20 08:24:48.614356 INFO::analyzeVariants/analyzeVariants: done
2025-01-20 08:24:48.619664 INFO::Pipeline run successful.
done successfully.
Executing test function test.calculateTargetLength ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp9YiOCn/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
2025-01-20 08:24:48.923074 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp9YiOCn/test.calcTargetLengths.2ec92278ce7f7c/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 -- Mon Jan 20 08:25:04 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 (32.33 seconds)
test.alignReads.sparsechunks: (2 checks) ... OK (21.27 seconds)
test.alignReadsOneSingleEnd: (2 checks) ... OK (0.55 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 (107.64 seconds)
test.wrap.callVariants: (4 checks) ... OK (13.47 seconds)
test.wrap.callVariants.filters: (2 checks) ... OK (27.23 seconds)
test.wrap.callVariants.which: (1 checks) ... OK (4.42 seconds)
test.writeVCF.NULL: (1 checks) ... OK (0.2 seconds)
test.writeVCF.vcfStat: (4 checks) ... OK (0.7 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 (37.89 seconds)
test.generateSingleGeneDERs: (4 checks) ... OK (32.69 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 (1.61 seconds)
test.mergeCoverage.sparse: (2 checks) ... OK (1.4 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 (0.2 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 (0.41 seconds)
test.checkConfig.alignReads: (5 checks) ... OK (0.46 seconds)
test.getConfig: (14 checks) ... OK (0 seconds)
test.loadConfig: (2 checks) ... OK (0 seconds)
test.parseDCF: (7 checks) ... OK (0 seconds)
test.updateConfig: (1 checks) ... OK (0 seconds)
---------------------------
Test file: /home/biocbuild/R/R-4.5.0-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 (0.12 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 (0.31 seconds)
test.detectRRNA.paired_end: (1 checks) ... OK (0.46 seconds)
test.getRRNAIds: (1 checks) ... OK (0.28 seconds)
test.getRRNAIds_random: (1 checks) ... OK (0.18 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 (0.08 seconds)
test.isAboveQualityThresh: (3 checks) ... OK (0.06 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 (0.21 seconds)
test.gatk : DEACTIVATED, gatk() tests need gatk.path option set
test.realignIndels : DEACTIVATED, test.realignIndels() tests need gatk.path option set
test.realignIndelsGATK : DEACTIVATED, realignIndelsGATK() tests need gatk.path option set
test.realignIndelsGATK.parallel : DEACTIVATED, realignIndelsGATK() tests need gatk.path option set
test_zipUp: (3 checks) ... OK (0 seconds)
---------------------------
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.io.R
test.FastQStreamer.getReads.pefq: (1 checks) ... OK (0.23 seconds)
test.FastQStreamer.getReads.pefq.subsample: (1 checks) ... OK (0.42 seconds)
test.FastQStreamer.getReads.segz: (1 checks) ... OK (0.19 seconds)
test.FastQStreamer.getReads.truncated: (1 checks) ... OK (0.2 seconds)
test.FastQStreamer.subsampler.isdeterministic: (3 checks) ... OK (0.68 seconds)
test.createTmpDir: (4 checks) ... OK (0 seconds)
test.detectQualityInFASTQFile: (3 checks) ... OK (0.17 seconds)
test.getObjectFilename: (4 checks) ... OK (0.01 seconds)
test.safeUnlink: (2 checks) ... OK (0.01 seconds)
test.writeAudit: (0 checks) ... OK (0.21 seconds)
---------------------------
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.mergeLanes.R
test.mergeLanes: (6 checks) ... OK (65.15 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 (10.07 seconds)
test.preprocessReads.minichunks: (5 checks) ... OK (15.68 seconds)
test.preprocessReads_single_end: (5 checks) ... OK (8.02 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 (0.12 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 (0.14 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 (50.65 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 (0.29 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 (15.23 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 (0.26 seconds)
runTests.R: OK !
There were 50 or more warnings (use warnings() to see the first 50)
>
> proc.time()
user system elapsed
323.295 102.518 474.385
HTSeqGenie.Rcheck/HTSeqGenie-Ex.timings
| name | user | system | elapsed | |
| HTSeqGenie | 0.001 | 0.000 | 0.000 | |
| buildGenomicFeaturesFromTxDb | 0 | 0 | 0 | |
| runPipeline | 0.000 | 0.000 | 0.001 | |