__STDOUT LOG__
Job runs on fgcz-h-901
at /scratch/samtoolsmpileup_multi_2024-11-01--13-05-39_temp2311800
Starting EzAppMpileup Mpileup_Variants samtoolsmpileup_multi_2024-11-01--13-05-39_temp2311800 2024-11-01 13:05:51
found parameter in name: minReadDepth = 5
cp /srv/GT/analysis/course_sushi/public/gstore/projects/p1003/Bowtie2_myPre_WES_all_2024-11-01--10-56-48/NA12878_chr10.bam local.bam
cp /srv/GT/analysis/course_sushi/public/gstore/projects/p1003/Bowtie2_myPre_WES_all_2024-11-01--10-56-48/NA12889_chr10.bam local.bam
cp /srv/GT/analysis/course_sushi/public/gstore/projects/p1003/Bowtie2_myPre_WES_all_2024-11-01--10-56-48/NA12890_chr10.bam local.bam
cp /srv/GT/analysis/course_sushi/public/gstore/projects/p1003/Bowtie2_myPre_WES_all_2024-11-01--10-56-48/NA12891_chr10.bam local.bam
cp /srv/GT/analysis/course_sushi/public/gstore/projects/p1003/Bowtie2_myPre_WES_all_2024-11-01--10-56-48/NA12890_chr10.bam.bai local.bam.bai
java -Djava.io.tmpdir=. -Xmx7g -jar /usr/local/ngseq/packages/Tools/Picard/3.2.0/picard.jar AddOrReplaceReadGroups TMP_DIR=. MAX_RECORDS_IN_RAM=2000000 I=local.bam O=withRg.bam SORT_ORDER=coordinate RGID=RGID_NA12890_chr10 RGPL=illumina RGSM=NA12890_chr10 RGLB=RGLB_NA12890_chr10 RGPU=RGPU_NA12890_chr10 VERBOSITY=WARNING > addreplace.stdout 2> addreplace.stderr
cp /srv/GT/analysis/course_sushi/public/gstore/projects/p1003/Bowtie2_myPre_WES_all_2024-11-01--10-56-48/NA12889_chr10.bam.bai local.bam.bai
java -Djava.io.tmpdir=. -Xmx7g -jar /usr/local/ngseq/packages/Tools/Picard/3.2.0/picard.jar AddOrReplaceReadGroups TMP_DIR=. MAX_RECORDS_IN_RAM=2000000 I=local.bam O=withRg.bam SORT_ORDER=coordinate RGID=RGID_NA12889_chr10 RGPL=illumina RGSM=NA12889_chr10 RGLB=RGLB_NA12889_chr10 RGPU=RGPU_NA12889_chr10 VERBOSITY=WARNING > addreplace.stdout 2> addreplace.stderr
cp /srv/GT/analysis/course_sushi/public/gstore/projects/p1003/Bowtie2_myPre_WES_all_2024-11-01--10-56-48/NA12878_chr10.bam.bai local.bam.bai
java -Djava.io.tmpdir=. -Xmx7g -jar /usr/local/ngseq/packages/Tools/Picard/3.2.0/picard.jar AddOrReplaceReadGroups TMP_DIR=. MAX_RECORDS_IN_RAM=2000000 I=local.bam O=withRg.bam SORT_ORDER=coordinate RGID=RGID_NA12878_chr10 RGPL=illumina RGSM=NA12878_chr10 RGLB=RGLB_NA12878_chr10 RGPU=RGPU_NA12878_chr10 VERBOSITY=WARNING > addreplace.stdout 2> addreplace.stderr
cp /srv/GT/analysis/course_sushi/public/gstore/projects/p1003/Bowtie2_myPre_WES_all_2024-11-01--10-56-48/NA12891_chr10.bam.bai local.bam.bai
java -Djava.io.tmpdir=. -Xmx7g -jar /usr/local/ngseq/packages/Tools/Picard/3.2.0/picard.jar AddOrReplaceReadGroups TMP_DIR=. MAX_RECORDS_IN_RAM=2000000 I=local.bam O=withRg.bam SORT_ORDER=coordinate RGID=RGID_NA12891_chr10 RGPL=illumina RGSM=NA12891_chr10 RGLB=RGLB_NA12891_chr10 RGPU=RGPU_NA12891_chr10 VERBOSITY=WARNING > addreplace.stdout 2> addreplace.stderr
java -Djava.io.tmpdir=. -Xmx7g -jar /usr/local/ngseq/packages/Tools/Picard/3.2.0/picard.jar MarkDuplicates TMP_DIR=. MAX_RECORDS_IN_RAM=2000000 I=withRg.bam O=dedup.bam REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT METRICS_FILE=dupmetrics.txt VERBOSITY=WARNING >markdup.stdout 2> markdup.stderr
java -Djava.io.tmpdir=. -Xmx7g -jar /usr/local/ngseq/packages/Tools/Picard/3.2.0/picard.jar MarkDuplicates TMP_DIR=. MAX_RECORDS_IN_RAM=2000000 I=withRg.bam O=dedup.bam REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT METRICS_FILE=dupmetrics.txt VERBOSITY=WARNING >markdup.stdout 2> markdup.stderr
java -Djava.io.tmpdir=. -Xmx7g -jar /usr/local/ngseq/packages/Tools/Picard/3.2.0/picard.jar MarkDuplicates TMP_DIR=. MAX_RECORDS_IN_RAM=2000000 I=withRg.bam O=dedup.bam REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT METRICS_FILE=dupmetrics.txt VERBOSITY=WARNING >markdup.stdout 2> markdup.stderr
java -Djava.io.tmpdir=. -Xmx7g -jar /usr/local/ngseq/packages/Tools/Picard/3.2.0/picard.jar MarkDuplicates TMP_DIR=. MAX_RECORDS_IN_RAM=2000000 I=withRg.bam O=dedup.bam REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT METRICS_FILE=dupmetrics.txt VERBOSITY=WARNING >markdup.stdout 2> markdup.stderr
mv dedup.bam /scratch/samtoolsmpileup_multi_2024-11-01--13-05-39_temp2311800/NA12890_chr10-proc/NA12890_chr10.bam
samtools index /scratch/samtoolsmpileup_multi_2024-11-01--13-05-39_temp2311800/NA12890_chr10-proc/NA12890_chr10.bam
mv dedup.bam /scratch/samtoolsmpileup_multi_2024-11-01--13-05-39_temp2311800/NA12889_chr10-proc/NA12889_chr10.bam
samtools index /scratch/samtoolsmpileup_multi_2024-11-01--13-05-39_temp2311800/NA12889_chr10-proc/NA12889_chr10.bam
cp /srv/GT/analysis/course_sushi/public/gstore/projects/p1003/Bowtie2_myPre_WES_all_2024-11-01--10-56-48/NA12892_chr10.bam local.bam
mv dedup.bam /scratch/samtoolsmpileup_multi_2024-11-01--13-05-39_temp2311800/NA12878_chr10-proc/NA12878_chr10.bam
samtools index /scratch/samtoolsmpileup_multi_2024-11-01--13-05-39_temp2311800/NA12878_chr10-proc/NA12878_chr10.bam
cp /srv/GT/analysis/course_sushi/public/gstore/projects/p1003/Bowtie2_myPre_WES_all_2024-11-01--10-56-48/NA12892_chr10.bam.bai local.bam.bai
java -Djava.io.tmpdir=. -Xmx7g -jar /usr/local/ngseq/packages/Tools/Picard/3.2.0/picard.jar AddOrReplaceReadGroups TMP_DIR=. MAX_RECORDS_IN_RAM=2000000 I=local.bam O=withRg.bam SORT_ORDER=coordinate RGID=RGID_NA12892_chr10 RGPL=illumina RGSM=NA12892_chr10 RGLB=RGLB_NA12892_chr10 RGPU=RGPU_NA12892_chr10 VERBOSITY=WARNING > addreplace.stdout 2> addreplace.stderr
mv dedup.bam /scratch/samtoolsmpileup_multi_2024-11-01--13-05-39_temp2311800/NA12891_chr10-proc/NA12891_chr10.bam
samtools index /scratch/samtoolsmpileup_multi_2024-11-01--13-05-39_temp2311800/NA12891_chr10-proc/NA12891_chr10.bam
java -Djava.io.tmpdir=. -Xmx7g -jar /usr/local/ngseq/packages/Tools/Picard/3.2.0/picard.jar MarkDuplicates TMP_DIR=. MAX_RECORDS_IN_RAM=2000000 I=withRg.bam O=dedup.bam REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT METRICS_FILE=dupmetrics.txt VERBOSITY=WARNING >markdup.stdout 2> markdup.stderr
mv dedup.bam /scratch/samtoolsmpileup_multi_2024-11-01--13-05-39_temp2311800/NA12892_chr10-proc/NA12892_chr10.bam
samtools index /scratch/samtoolsmpileup_multi_2024-11-01--13-05-39_temp2311800/NA12892_chr10-proc/NA12892_chr10.bam
bcftools mpileup -Ou -f /srv/GT/reference/Homo_sapiens/Ensembl/GRCh37.p13/Sequence/WholeGenomeFasta/genome.fa --skip-indels --annotate AD,INFO/AD,ADF,ADR,SP /scratch/samtoolsmpileup_multi_2024-11-01--13-05-39_temp2311800/NA12878_chr10-proc/NA12878_chr10.bam /scratch/samtoolsmpileup_multi_2024-11-01--13-05-39_temp2311800/NA12889_chr10-proc/NA12889_chr10.bam /scratch/samtoolsmpileup_multi_2024-11-01--13-05-39_temp2311800/NA12890_chr10-proc/NA12890_chr10.bam /scratch/samtoolsmpileup_multi_2024-11-01--13-05-39_temp2311800/NA12891_chr10-proc/NA12891_chr10.bam /scratch/samtoolsmpileup_multi_2024-11-01--13-05-39_temp2311800/NA12892_chr10-proc/NA12892_chr10.bam | bcftools call -Ou --multiallelic-caller --keep-alts --variants-only - | bcftools filter --output-type z --output Mpileup_Variants.vcf.gz --include "MIN(DP)>5" -
ezRun tag: 82f28d6295b8f19d29b1e7e1ea9f2b825daabddf
ezRun github link: https://github.com/uzh/ezRun/tree/82f28d6295b8f19d29b1e7e1ea9f2b825daabddf
R version 4.4.0 (2024-04-24)
Platform: x86_64-pc-linux-gnu
Running under: Debian GNU/Linux 12 (bookworm)
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.11.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: Europe/Zurich
tzcode source: system (glibc)
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] htmltools_0.5.8.1 DT_0.33
[3] RColorBrewer_1.1-3 readxl_1.4.3
[5] htmlwidgets_1.6.4 webshot_0.5.5
[7] plotly_4.10.4 kableExtra_1.4.0
[9] knitr_1.47 VariantAnnotation_1.50.0
[11] Rsamtools_2.20.0 SummarizedExperiment_1.34.0
[13] Biobase_2.64.0 MatrixGenerics_1.16.0
[15] matrixStats_1.3.0 ezRun_3.19.1
[17] lubridate_1.9.3 forcats_1.0.0
[19] stringr_1.5.1 dplyr_1.1.4
[21] purrr_1.0.2 readr_2.1.5
[23] tidyr_1.3.1 tibble_3.2.1
[25] ggplot2_3.5.1 tidyverse_2.0.0
[27] GenomicRanges_1.56.1 Biostrings_2.72.1
[29] GenomeInfoDb_1.40.1 XVector_0.44.0
[31] IRanges_2.38.0 S4Vectors_0.42.0
[33] BiocGenerics_0.50.0 data.table_1.15.4
loaded via a namespace (and not attached):
[1] DBI_1.2.3 bitops_1.0-7 rlang_1.1.4
[4] magrittr_2.0.3 compiler_4.4.0 RSQLite_2.3.7
[7] GenomicFeatures_1.56.0 png_0.1-8 systemfonts_1.1.0
[10] vctrs_0.6.5 pkgconfig_2.0.3 crayon_1.5.2
[13] fastmap_1.2.0 utf8_1.2.4 rmarkdown_2.27
[16] tzdb_0.4.0 UCSC.utils_1.0.0 bit_4.0.5
[19] xfun_0.45 zlibbioc_1.50.0 cachem_1.1.0
[22] jsonlite_1.8.8 blob_1.2.4 highr_0.11
[25] DelayedArray_0.30.1 BiocParallel_1.38.0 R6_2.5.1
[28] bslib_0.7.0 stringi_1.8.4 rtracklayer_1.64.0
[31] cellranger_1.1.0 jquerylib_0.1.4 Matrix_1.7-0
[34] timechange_0.3.0 tidyselect_1.2.1 rstudioapi_0.16.0
[37] abind_1.4-5 yaml_2.3.8 codetools_0.2-20
[40] curl_5.2.1 lattice_0.22-6 withr_3.0.0
[43] KEGGREST_1.44.0 evaluate_0.24.0 xml2_1.3.6
[46] pillar_1.9.0 generics_0.1.3 RCurl_1.98-1.14
[49] hms_1.1.3 munsell_0.5.1 scales_1.3.0
[52] glue_1.7.0 lazyeval_0.2.2 tools_4.4.0
[55] BiocIO_1.14.0 BSgenome_1.72.0 GenomicAlignments_1.40.0
[58] XML_3.99-0.16.1 grid_4.4.0 crosstalk_1.2.1
[61] AnnotationDbi_1.66.0 colorspace_2.1-1 GenomeInfoDbData_1.2.12
[64] restfulr_0.0.15 cli_3.6.2 fansi_1.0.6
[67] S4Arrays_1.4.1 viridisLite_0.4.2 svglite_2.1.3
[70] gtable_0.3.5 sass_0.4.9 digest_0.6.35
[73] SparseArray_1.4.8 rjson_0.2.21 memoise_2.0.1
[76] lifecycle_1.0.4 httr_1.4.7 bit64_4.0.5
Finished EzAppMpileup Mpileup_Variants samtoolsmpileup_multi_2024-11-01--13-05-39_temp2311800 2024-11-01 13:08:09
[1] "Success"
__SCRIPT END__
__STDERR LOG__
Loading required package: data.table
Loading required package: Biostrings
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, aperm, append, as.data.frame, basename, cbind,
colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: ‘S4Vectors’
The following objects are masked from ‘package:data.table’:
first, second
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findMatches
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expand.grid, I, unname
Loading required package: IRanges
Attaching package: ‘IRanges’
The following object is masked from ‘package:data.table’:
shift
Loading required package: XVector
Loading required package: GenomeInfoDb
Attaching package: ‘Biostrings’
The following object is masked from ‘package:base’:
strsplit
Loading required package: GenomicRanges
Loading required package: tidyverse
── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
✔ dplyr 1.1.4 ✔ readr 2.1.5
✔ forcats 1.0.0 ✔ stringr 1.5.1
✔ ggplot2 3.5.1 ✔ tibble 3.2.1
✔ lubridate 1.9.3 ✔ tidyr 1.3.1
✔ purrr 1.0.2
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ lubridate::%within%() masks IRanges::%within%()
✖ dplyr::between() masks data.table::between()
✖ dplyr::collapse() masks Biostrings::collapse(), IRanges::collapse()
✖ dplyr::combine() masks BiocGenerics::combine()
✖ purrr::compact() masks XVector::compact()
✖ dplyr::desc() masks IRanges::desc()
✖ tidyr::expand() masks S4Vectors::expand()
✖ dplyr::filter() masks stats::filter()
✖ dplyr::first() masks S4Vectors::first(), data.table::first()
✖ lubridate::hour() masks data.table::hour()
✖ lubridate::isoweek() masks data.table::isoweek()
✖ dplyr::lag() masks stats::lag()
✖ dplyr::last() masks data.table::last()
✖ lubridate::mday() masks data.table::mday()
✖ lubridate::minute() masks data.table::minute()
✖ lubridate::month() masks data.table::month()
✖ ggplot2::Position() masks BiocGenerics::Position(), base::Position()
✖ lubridate::quarter() masks data.table::quarter()
✖ purrr::reduce() masks GenomicRanges::reduce(), IRanges::reduce()
✖ dplyr::rename() masks S4Vectors::rename()
✖ lubridate::second() masks S4Vectors::second(), data.table::second()
✖ lubridate::second<-() masks S4Vectors::second<-()
✖ dplyr::slice() masks XVector::slice(), IRanges::slice()
✖ purrr::transpose() masks data.table::transpose()
✖ lubridate::wday() masks data.table::wday()
✖ lubridate::week() masks data.table::week()
✖ lubridate::yday() masks data.table::yday()
✖ lubridate::year() masks data.table::year()
ℹ Use the conflicted package () to force all conflicts to become errors
unknown param: partition
unknown param: sushi_app
unknown param: isLastJob
Loading required package: VariantAnnotation
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: ‘matrixStats’
The following object is masked from ‘package:dplyr’:
count
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: SummarizedExperiment
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
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anyMissing, rowMedians
Loading required package: Rsamtools
Attaching package: ‘VariantAnnotation’
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fixed
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tabulate
Loading required package: parallel
Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid
[mpileup] 5 samples in 5 input files
[mpileup] maximum number of reads per input file set to -d 250
[WARNING] This document format requires a nonempty element.
Defaulting to 'Mpileup.knit' as the title.
To specify a title, use 'title' in metadata or --metadata title="...".