__STDOUT LOG__
Job runs on fgcz-h-166
at /scratch/Kraken_2024-12-13--09-46-11_sample1_temp2129510
Starting EzAppKraken Kraken_2024-12-13--09-46-11_sample1_temp2129510 2024-12-13 09:46:18
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--09-46-11_sample1_temp2129510/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--09-46-11_sample1_temp2129510 2024-12-13 09:47:51
__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...Killed
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--09-46-11_sample1_temp2129510/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
slurmstepd-fgcz-h-166: error: Detected 1 oom-kill event(s) in StepId=13132.batch. Some of your processes may have been killed by the cgroup out-of-memory handler.