__STDOUT LOG__ Job runs on fgcz-h-901 at /scratch/Kraken_2024-12-13--09-46-13_sample1_temp2616016 Starting EzAppKraken Kraken_2024-12-13--09-46-13_sample1_temp2616016 2024-12-13 09:46:22 fastp --in1 /srv/GT/analysis/course_sushi/public/gstore/projects/p6000/MetaAtlas_data/sample1_R1.fastq.gz --out1 trimmed_R1.fastq.gz --thread 4 --trim_front1 0 --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> sample1_preprocessing.log cat fastp.json >> sample1_preprocessing.log kraken2 -db /srv/GT/databases/kraken2/bacteria --confidence 0 --minimum-base-quality 0 --output sample1.txt --report sample1.report.txt --threads 4 /scratch/Kraken_2024-12-13--09-46-13_sample1_temp2616016/sample1-trimmed_R1.fastq.gz 1> sample1.log ezRun tag: 81a203b2a83152a315eaa7463292c4b4d9afaa20 ezRun github link: https://github.com/uzh/ezRun/tree/81a203b2a83152a315eaa7463292c4b4d9afaa20 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 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 magrittr_2.0.3 [19] zlibbioc_1.50.0 grid_4.4.0 hms_1.1.3 [22] lifecycle_1.0.4 vctrs_0.6.5 glue_1.7.0 [25] fansi_1.0.6 colorspace_2.1-1 httr_1.4.7 [28] tools_4.4.0 pkgconfig_2.0.3 UCSC.utils_1.0.0 Finished EzAppKraken Kraken_2024-12-13--09-46-13_sample1_temp2616016 2024-12-13 09:46:35 __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: 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 Loading database information...Failed attempt to allocate 33482573528bytes; you may not have enough free memory to load this database. If your computer has enough RAM, perhaps reducing memory usage from other programs could help you load this database? classify: unable to allocate hash table memory Error in ezSystem(cmd) : kraken2 -db /srv/GT/databases/kraken2/bacteria --confidence 0 --minimum-base-quality 0 --output sample1.txt --report sample1.report.txt --threads 4 /scratch/Kraken_2024-12-13--09-46-13_sample1_temp2616016/sample1-trimmed_R1.fastq.gz 1> sample1.log failed Calls: -> withCallingHandlers -> runMethod -> ezSystem error exists: gxtx_data_mngt@fgcz.system mail sent to: gxtx_data_mngt@fgcz.system Execution halted