__STDOUT LOG__
Job runs on fgcz-h-901
at /scratch/Kraken_2024-12-13--09-46-13_sample2_temp2616015
Starting EzAppKraken Kraken_2024-12-13--09-46-13_sample2_temp2616015 2024-12-13 09:46:22
fastp --in1 /srv/GT/analysis/course_sushi/public/gstore/projects/p6000/MetaAtlas_data/sample2_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> sample2_preprocessing.log
cat fastp.json >> sample2_preprocessing.log
kraken2 -db /srv/GT/databases/kraken2/bacteria --confidence 0 --minimum-base-quality 0 --output sample2.txt --report sample2.report.txt --threads 4 /scratch/Kraken_2024-12-13--09-46-13_sample2_temp2616015/sample2-trimmed_R1.fastq.gz 1> sample2.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_sample2_temp2616015 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 sample2.txt --report sample2.report.txt --threads 4 /scratch/Kraken_2024-12-13--09-46-13_sample2_temp2616015/sample2-trimmed_R1.fastq.gz 1> sample2.log
failed
Calls: -> withCallingHandlers -> runMethod -> ezSystem
error exists: gxtx_data_mngt@fgcz.system
mail sent to: gxtx_data_mngt@fgcz.system
Execution halted