__STDOUT LOG__ Job runs on fgcz-h-906 at /scratch/Bowtie2_2024-11-01--10-45-40_NA12890_chr10_temp2262746 Starting EzAppBowtie2 Bowtie2_2024-11-01--10-45-40_NA12890_chr10_temp2262746 2024-11-01 10:46:29 fastp --in1 /srv/GT/analysis/course_sushi/public/gstore/projects/p1000/chr10_WES_reads_subSampled/NA12890_chr10_R1.fastq.gz --in2 /srv/GT/analysis/course_sushi/public/gstore/projects/p1000/chr10_WES_reads_subSampled/NA12890_chr10_R2.fastq.gz --out1 trimmed_R1.fastq.gz --out2 trimmed_R2.fastq.gz --thread 8 --trim_front1 0 --trim_tail1 0 --cut_front --cut_front_window_size 4 --cut_front_mean_quality 20 --cut_right --cut_right_window_size 4 --cut_right_mean_quality 20 --cut_tail --cut_tail_window_size 4 --cut_tail_mean_quality 20 --average_qual 20 --adapter_fasta adapters.fa --max_len1 0 --max_len2 0 --trim_poly_x --poly_x_min_len 10 --length_required 18 --compression 9 2> NA12890_chr10_preprocessing.log cat fastp.json >> NA12890_chr10_preprocessing.log bowtie2 --no-mixed --no-discordant --very-sensitive -X 1000 -p 8 --rg-id NA12890_chr10 --rg SM:NA12890_chr10 --rg LB:RGLB_NA12890_chr10 --rg PL:illumina --rg PU:RGPU_NA12890_chr10 -x /srv/GT/reference/Homo_sapiens/Ensembl/GRCh37.p13/Sequence/BOWTIE2Index/genome -1 /scratch/Bowtie2_2024-11-01--10-45-40_NA12890_chr10_temp2262746/NA12890_chr10-trimmed_R1.fastq.gz -2 /scratch/Bowtie2_2024-11-01--10-45-40_NA12890_chr10_temp2262746/NA12890_chr10-trimmed_R2.fastq.gz 2> NA12890_chr10_bowtie2.log | samtools view -S -b - > bowtie.bam samtools sort -l 9 -m 2625M -@ 8 bowtie.bam -o sorted.bam samtools index sorted.bam java -Djava.io.tmpdir=. -Xmx30g -jar /usr/local/ngseq/packages/Tools/Picard/3.2.0/picard.jar MarkDuplicates I=sorted.bam O=NA12890_chr10.bam M=/tmp/RtmpzyVePs/file2286e94e48f3e5 REMOVE_DUPLICATES=false > /dev/null 2>&1 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] stats4 stats graphics grDevices utils datasets methods [8] base other attached packages: [1] withr_3.0.0 ezRun_3.19.1 lubridate_1.9.3 [4] forcats_1.0.0 stringr_1.5.1 dplyr_1.1.4 [7] purrr_1.0.2 readr_2.1.5 tidyr_1.3.1 [10] tibble_3.2.1 ggplot2_3.5.1 tidyverse_2.0.0 [13] GenomicRanges_1.56.1 Biostrings_2.72.1 GenomeInfoDb_1.40.1 [16] XVector_0.44.0 IRanges_2.38.0 S4Vectors_0.42.0 [19] BiocGenerics_0.50.0 data.table_1.15.4 loaded via a namespace (and not attached): [1] gtable_0.3.5 jsonlite_1.8.8 compiler_4.4.0 [4] crayon_1.5.2 tidyselect_1.2.1 bitops_1.0-7 [7] Rsamtools_2.20.0 parallel_4.4.0 scales_1.3.0 [10] BiocParallel_1.38.0 R6_2.5.1 generics_0.1.3 [13] munsell_0.5.1 GenomeInfoDbData_1.2.12 tzdb_0.4.0 [16] pillar_1.9.0 rlang_1.1.4 utf8_1.2.4 [19] stringi_1.8.4 timechange_0.3.0 cli_3.6.2 [22] magrittr_2.0.3 zlibbioc_1.50.0 grid_4.4.0 [25] hms_1.1.3 lifecycle_1.0.4 vctrs_0.6.5 [28] glue_1.7.0 codetools_0.2-20 fansi_1.0.6 [31] colorspace_2.1-1 httr_1.4.7 tools_4.4.0 [34] pkgconfig_2.0.3 UCSC.utils_1.0.0 Finished EzAppBowtie2 Bowtie2_2024-11-01--10-45-40_NA12890_chr10_temp2262746 2024-11-01 10:47:05 [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 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 1.0.0 ✔ 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: 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: sushi_app unknown param: isLastJob Loading required package: withr [bam_sort_core] merging from 0 files and 8 in-memory blocks...