__STDOUT LOG__ Job runs on fgcz-c-045 at /scratch/test_masa1_2024-11-15--10-21-41_temp2976705 Starting EzAppFastqc FastQC test_masa1_2024-11-15--10-21-41_temp2976705 2024-11-15 10:23:01 fastqc --extract -o . -t 1 -a /srv/GT/databases/adapter/adapter_list.txt --kmers 7 --dir . -q /srv/GT/analysis/course_sushi/public/gstore/projects/p1001/ventricles_100k/MutantSample_1_R1.fastq.gz /srv/GT/analysis/course_sushi/public/gstore/projects/p1001/ventricles_100k/MutantSample_1_R2.fastq.gz /srv/GT/analysis/course_sushi/public/gstore/projects/p1001/ventricles_100k/MutantSample_2_R1.fastq.gz /srv/GT/analysis/course_sushi/public/gstore/projects/p1001/ventricles_100k/MutantSample_2_R2.fastq.gz > fastqc.out 2> fastqc.err multiqc --outdir ../multi_FastQC . ezRun tag: 12c261c2ce8151e53ef4c76eaf246835848d0b8b ezRun github link: https://github.com/uzh/ezRun/tree/12c261c2ce8151e53ef4c76eaf246835848d0b8b 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] ezRun_3.19.1 lubridate_1.9.3 forcats_1.0.0 [4] stringr_1.5.1 dplyr_1.1.4 purrr_1.0.2 [7] readr_2.1.5 tidyr_1.3.1 tibble_3.2.1 [10] ggplot2_3.5.1 tidyverse_2.0.0 GenomicRanges_1.56.1 [13] Biostrings_2.72.1 GenomeInfoDb_1.40.1 XVector_0.44.0 [16] IRanges_2.38.0 S4Vectors_0.42.0 BiocGenerics_0.50.0 [19] 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 scales_1.3.0 [7] R6_2.5.1 generics_0.1.3 munsell_0.5.1 [10] GenomeInfoDbData_1.2.12 tzdb_0.4.0 pillar_1.9.0 [13] rlang_1.1.4 utf8_1.2.4 stringi_1.8.4 [16] timechange_0.3.0 cli_3.6.2 withr_3.0.0 [19] magrittr_2.0.3 zlibbioc_1.50.0 grid_4.4.0 [22] hms_1.1.3 lifecycle_1.0.4 vctrs_0.6.5 [25] glue_1.7.0 fansi_1.0.6 colorspace_2.1-1 [28] httr_1.4.7 tools_4.4.0 pkgconfig_2.0.3 [31] UCSC.utils_1.0.0 Finished EzAppFastqc FastQC test_masa1_2024-11-15--10-21-41_temp2976705 2024-11-15 10:23:28 [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: sushi_app unknown param: isLastJob /// MultiQC 🔍 v1.24 version_check | MultiQC Version v1.25.1 now available! file_search | Search path: /scratch/test_masa1_2024-11-15--10-21-41_temp2976705/FastQC fastqc | Found 4 reports write_results | Data : /scratch/test_masa1_2024-11-15--10-21-41_temp2976705/multi_FastQC/multiqc_data write_results | Report : /scratch/test_masa1_2024-11-15--10-21-41_temp2976705/multi_FastQC/multiqc_report.html multiqc | MultiQC complete