/srv/GT/analysis/course_sushi/public/gstore/projects/p1001/STAR_2025-11-25--15-44-24/scripts/Map_S2_undiff_NextSeq500_20190507_NS278_o5638_subSampled_2185.sh_sushiID2447_2025-11-25--15-44-47_o.log -------------------------------------------------- Job runs on fgcz-h-902 at /scratch/STAR_2025-11-25--15-44-24_S2_undiff_temp293902 Starting EzAppSTAR STAR_2025-11-25--15-44-24_S2_undiff_temp293902 2025-11-25 15:44:56 EXECUTED CMD: fastp --in1 /srv/GT/analysis/course_sushi/public/gstore/projects/p1000/NextSeq500_20190507_NS278_o5638_subSampled/20190507.A-S2_undiff_R1-subsample.fastq.gz --out1 trimmed_R1.fastq.gz --thread 8 --trim_front1 4 --trim_tail1 0 --average_qual 0 --adapter_fasta adapters.fa --max_len1 0 --max_len2 0 --trim_poly_x --poly_x_min_len 10 --length_required 18 --compression 4 2> S2_undiff_preprocessing.log EXECUTED CMD: cat fastp.json >> S2_undiff_preprocessing.log EXECUTED CMD: STAR --genomeDir /srv/GT/reference/Homo_sapiens/GENCODE/GRCh38.p14/Annotation/Release_48-2025-07-03/Genes/genes_STARIndex --readFilesIn /scratch/STAR_2025-11-25--15-44-24_S2_undiff_temp293902/S2_undiff-trimmed_R1.fastq.gz --twopassMode None --runThreadN 8 --sjdbOverhang 150 --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --outMultimapperOrder Random --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 100000 --alignMatesGapMax 100000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif --alignEndsProtrude 10 ConcordantPair --outSAMmultNmax 4 --outSAMattributes All --outStd BAM_Unsorted --outSAMtype BAM Unsorted --outSAMattrRGline ID:S2_undiff SM:S2_undiff --readFilesCommand zcat > Aligned.out.bam EXECUTED CMD: samtools sort -l 9 -m 2625M -@ 8 Aligned.out.bam -o S2_undiff.bam EXECUTED CMD: samtools index S2_undiff.bam EXECUTED CMD: infer_experiment.py -r /srv/GT/reference/Homo_sapiens/GENCODE/GRCh38.p14/Annotation/Release_48-2025-07-03/Genes/genes.bed -i S2_undiff.bam -s 1000000 This is SingleEnd Data Fraction of reads failed to determine: 0.0437 Fraction of reads explained by "++,--": 0.0050 Fraction of reads explained by "+-,-+": 0.9514 ezRun tag: 28496712ee737d3a120e054f95c1bc9b6b30a722 ezRun github link: https://github.com/uzh/ezRun/tree/28496712ee737d3a120e054f95c1bc9b6b30a722 R version 4.5.0 (2025-04-11) 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 LAPACK version 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] stats4 stats graphics grDevices utils datasets methods [8] base other attached packages: [1] GenomicFeatures_1.60.0 AnnotationDbi_1.70.0 Biobase_2.68.0 [4] withr_3.0.2 ezRun_3.21.1 lubridate_1.9.4 [7] forcats_1.0.1 stringr_1.5.2 dplyr_1.1.4 [10] purrr_1.1.0 readr_2.1.5 tidyr_1.3.1 [13] tibble_3.3.0 ggplot2_4.0.0 tidyverse_2.0.0 [16] GenomicRanges_1.60.0 Biostrings_2.76.0 GenomeInfoDb_1.44.3 [19] XVector_0.48.0 IRanges_2.42.0 S4Vectors_0.46.0 [22] BiocGenerics_0.54.1 generics_0.1.4 data.table_1.17.8 loaded via a namespace (and not attached): [1] SummarizedExperiment_1.38.1 KEGGREST_1.48.0 [3] gtable_0.3.6 rjson_0.2.23 [5] lattice_0.22-7 tzdb_0.5.0 [7] bitops_1.0-9 vctrs_0.6.5 [9] tools_4.5.0 parallel_4.5.0 [11] curl_6.2.3 RSQLite_2.3.11 [13] blob_1.2.4 pkgconfig_2.0.3 [15] Matrix_1.7-3 RColorBrewer_1.1-3 [17] S7_0.2.0 lifecycle_1.0.4 [19] GenomeInfoDbData_1.2.14 compiler_4.5.0 [21] farver_2.1.2 Rsamtools_2.24.0 [23] codetools_0.2-20 yaml_2.3.10 [25] RCurl_1.98-1.17 pillar_1.11.1 [27] crayon_1.5.3 BiocParallel_1.42.2 [29] DelayedArray_0.34.1 cachem_1.1.0 [31] abind_1.4-8 tidyselect_1.2.1 [33] stringi_1.8.7 restfulr_0.0.15 [35] fastmap_1.2.0 grid_4.5.0 [37] SparseArray_1.8.1 cli_3.6.5 [39] magrittr_2.0.4 S4Arrays_1.8.1 [41] dichromat_2.0-0.1 XML_3.99-0.18 [43] scales_1.4.0 UCSC.utils_1.4.0 [45] bit64_4.6.0-1 timechange_0.3.0 [47] httr_1.4.7 matrixStats_1.5.0 [49] bit_4.6.0 png_0.1-8 [51] hms_1.1.3 memoise_2.0.1 [53] BiocIO_1.18.0 rtracklayer_1.68.0 [55] rlang_1.1.6 glue_1.8.0 [57] DBI_1.2.3 jsonlite_2.0.0 [59] R6_2.6.1 MatrixGenerics_1.20.0 [61] GenomicAlignments_1.44.0 Finished EzAppSTAR STAR_2025-11-25--15-44-24_S2_undiff_temp293902 2025-11-25 15:47:00 [1] "Success" ___STDOUT_END___ /srv/GT/analysis/course_sushi/public/gstore/projects/p1001/STAR_2025-11-25--15-44-24/scripts/Map_S2_undiff_NextSeq500_20190507_NS278_o5638_subSampled_2185.sh_sushiID2447_2025-11-25--15-44-47_e.log -------------------------------------------------- + set -o pipefail + umask 0002 + SCRATCH_DIR=/scratch/STAR_2025-11-25--15-44-24_S2_undiff_temp293902 + GSTORE_DIR=/srv/GT/analysis/course_sushi/public/gstore/projects + INPUT_DATASET=/srv/GT/analysis/course_sushi/public/gstore/projects/p1001/STAR_2025-11-25--15-44-24/input_dataset.tsv + LAST_JOB=FALSE ++ hostname + echo 'Job runs on fgcz-h-902' + echo 'at /scratch/STAR_2025-11-25--15-44-24_S2_undiff_temp293902' + mkdir /scratch/STAR_2025-11-25--15-44-24_S2_undiff_temp293902 + cd /scratch/STAR_2025-11-25--15-44-24_S2_undiff_temp293902 + source /usr/local/ngseq/etc/lmod_profile +++ eval 'echo /usr/local/ngseq/etc/modules:/etc/fgcz-envmods/lmod:/etc/lmod/modules:/usr/share/lmod/lmod/modulefiles' ++++ echo /usr/local/ngseq/etc/modules:/etc/fgcz-envmods/lmod:/etc/lmod/modules:/usr/share/lmod/lmod/modulefiles ++ export MODULEPATH=/usr/local/ngseq/etc/modules:/usr/local/ngseq/etc/modules:/etc/fgcz-envmods/lmod:/etc/lmod/modules:/usr/share/lmod/lmod/modulefiles ++ MODULEPATH=/usr/local/ngseq/etc/modules:/usr/local/ngseq/etc/modules:/etc/fgcz-envmods/lmod:/etc/lmod/modules:/usr/share/lmod/lmod/modulefiles ++ source /usr/share/lmod/lmod/init/profile +++ '[' -z '' ']' +++ LMOD_ALLOW_ROOT_USE=yes +++ '[' -n '' ']' +++ '[' yes '!=' yes ']' +++ '[' -z /usr/share/modulefiles ']' +++ findExec READLINK_CMD /bin/readlink readlink +++ Nm=READLINK_CMD +++ confPath=/bin/readlink +++ execNm=readlink +++ eval READLINK_CMD=/bin/readlink ++++ READLINK_CMD=/bin/readlink +++ '[' '!' -x /bin/readlink ']' +++ unset Nm confPath execNm +++ findExec PS_CMD /bin/ps ps +++ Nm=PS_CMD +++ confPath=/bin/ps +++ execNm=ps +++ eval PS_CMD=/bin/ps ++++ PS_CMD=/bin/ps +++ '[' '!' -x /bin/ps ']' +++ unset Nm confPath execNm +++ findExec EXPR_CMD /usr/bin/expr expr +++ Nm=EXPR_CMD +++ confPath=/usr/bin/expr +++ execNm=expr +++ eval EXPR_CMD=/usr/bin/expr ++++ EXPR_CMD=/usr/bin/expr +++ '[' '!' -x /usr/bin/expr ']' +++ unset Nm confPath execNm +++ findExec BASENAME_CMD /usr/bin/basename basename +++ Nm=BASENAME_CMD +++ confPath=/usr/bin/basename +++ execNm=basename +++ eval BASENAME_CMD=/usr/bin/basename ++++ BASENAME_CMD=/usr/bin/basename +++ '[' '!' -x /usr/bin/basename ']' +++ unset Nm confPath execNm +++ unset -f findExec +++ '[' -f /proc/293902/exe ']' ++++ /bin/readlink /proc/293902/exe +++ my_shell=/usr/bin/bash ++++ /usr/bin/expr /usr/bin/bash : '-*\(.*\)' +++ my_shell=/usr/bin/bash ++++ /usr/bin/basename /usr/bin/bash +++ my_shell=bash +++ case ${my_shell} in +++ '[' -f /usr/share/lmod/lmod/init/bash ']' +++ . /usr/share/lmod/lmod/init/bash ++++ '[' -z '' ']' ++++ case "$-" in ++++ __lmod_vx=x ++++ '[' -n x ']' ++++ set +x Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for this output (/usr/share/lmod/lmod/init/bash) Shell debugging restarted ++++ unset __lmod_vx +++ unset my_shell PS_CMD EXPR_CMD BASENAME_CMD MODULEPATH_INIT LMOD_ALLOW_ROOT_USE READLINK_CMD ++ export NGSEQ=/usr/local/ngseq ++ NGSEQ=/usr/local/ngseq ++ export ngsrc=/usr/local/ngseq/srcm ++ ngsrc=/usr/local/ngseq/srcm ++ export ngpkg=/usr/local/ngseq/packages ++ ngpkg=/usr/local/ngseq/packages ++ export ngmdf=/usr/local/ngseq/etc/modules ++ ngmdf=/usr/local/ngseq/etc/modules ++ '[' -d /usr/local/ngseq/. ']' ++ PATH=/usr/local/ngseq/bin:/home/trxcopy/.conda/envs/gi_sushi_jobmanager_2024/bin:/misc/ngseq12/miniforge3/condabin:/usr/local/ngseq/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games ++ export PATH ++ LD_LIBRARY_PATH=/usr/local/ngseq/lib:/usr/local/ngseq/lib ++ export LD_LIBRARY_PATH ++ alias 'lmodInit=. /usr/local/ngseq/etc/lmod_profile' + module add Aligner/STAR/2.7.11b Tools/samtools/1.20 Dev/jdk/21 Dev/R/4.5.0 Dev/Python/3.12.8 Tools/Picard/3.2.0 QC/fastp/0.23.4 + local __lmod_my_status + local __lmod_sh_dbg + '[' -z '' ']' + case "$-" in + __lmod_sh_dbg=x + '[' -n x ']' + set +x Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output Shell debugging restarted + return 0 + R --vanilla --slave Loading required package: data.table Loading required package: Biostrings 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’: anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, saveRDS, table, tapply, 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 The following object is masked from ‘package:utils’: findMatches The following objects are masked from ‘package:base’: 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 1.0.1 ✔ stringr 1.5.2 ✔ ggplot2 4.0.0 ✔ tibble 3.3.0 ✔ lubridate 1.9.4 ✔ tidyr 1.3.1 ✔ purrr 1.1.0 ── 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: secondRef unknown param: trim_front1 unknown param: trim_tail1 unknown param: cut_front_window_size unknown param: cut_front_mean_quality unknown param: cut_tail_window_size unknown param: cut_tail_mean_quality unknown param: cut_right_window_size unknown param: cut_right_mean_quality unknown param: average_qual unknown param: poly_x_min_len unknown param: length_required unknown param: cmdOptionsFastp unknown param: barcodePattern unknown param: sushi_app unknown param: isLastJob Loading required package: withr [bam_sort_core] merging from 0 files and 8 in-memory blocks... Loading required package: GenomicFeatures Loading required package: AnnotationDbi 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: ‘AnnotationDbi’ The following object is masked from ‘package:dplyr’: select Reading reference gene model /srv/GT/reference/Homo_sapiens/GENCODE/GRCh38.p14/Annotation/Release_48-2025-07-03/Genes/genes.bed ... Done Loading SAM/BAM file ... Finished Total 69521 usable reads were sampled + rsync -r S2_undiff.bam /srv/GT/analysis/course_sushi/public/gstore/projects/p1001/STAR_2025-11-25--15-44-24/ + rsync -r S2_undiff.bam.bai /srv/GT/analysis/course_sushi/public/gstore/projects/p1001/STAR_2025-11-25--15-44-24/ + rsync -r S2_undiff-igv.html /srv/GT/analysis/course_sushi/public/gstore/projects/p1001/STAR_2025-11-25--15-44-24/ + rsync -r S2_undiff_preprocessing.log /srv/GT/analysis/course_sushi/public/gstore/projects/p1001/STAR_2025-11-25--15-44-24/ + rsync -r S2_undiff_STAR.log /srv/GT/analysis/course_sushi/public/gstore/projects/p1001/STAR_2025-11-25--15-44-24/ + cd /scratch + rm -rf /scratch/STAR_2025-11-25--15-44-24_S2_undiff_temp293902 ___STDERR_END___