/srv/GT/analysis/course_sushi/public/gstore/projects/p1001/o35755_Canu_2025-05-21--12-02-35/scripts/Assemble_mut22_ventricles_100k_1.sh_sushiID1017_2025-05-21--12-03-01_o.log
--------------------------------------------------
Job runs on fgcz-h-124
at /scratch/o35755_Canu_2025-05-21--12-02-35_mut22_temp2378578
Starting EzAppCanu o35755_Canu_2025-05-21--12-02-35_mut22_temp2378578 2025-05-21 12:03:07
cp -r /srv/GT/analysis/course_sushi/public/gstore/projects/p1001/ventricles_100k/MutantSample_2_R1.fastq.gz .
mkdir smrt_input
tar -zxf MutantSample_2_R1.fastq.gz --strip-components=4 -C smrt_input
ezRun tag: 0614a98fa9e9b0925054bc558d4fc2a15c71559f
ezRun github link: https://github.com/uzh/ezRun/tree/0614a98fa9e9b0925054bc558d4fc2a15c71559f
R version 4.4.2 (2024-10-31)
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=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.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_3.20.1 lubridate_1.9.4 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_1.58.0
[13] Biostrings_2.74.0 GenomeInfoDb_1.42.1 XVector_0.46.0
[16] IRanges_2.40.1 S4Vectors_0.44.0 BiocGenerics_0.52.0
[19] data.table_1.16.4
loaded via a namespace (and not attached):
[1] gtable_0.3.6 jsonlite_1.8.9 compiler_4.4.2
[4] crayon_1.5.3 tidyselect_1.2.1 scales_1.3.0
[7] R6_2.5.1 generics_0.1.3 munsell_0.5.1
[10] GenomeInfoDbData_1.2.13 pillar_1.10.0 tzdb_0.4.0
[13] rlang_1.1.4 stringi_1.8.4 timechange_0.3.0
[16] cli_3.6.3 withr_3.0.2 magrittr_2.0.3
[19] zlibbioc_1.52.0 grid_4.4.2 hms_1.1.3
[22] lifecycle_1.0.4 vctrs_0.6.5 glue_1.8.0
[25] colorspace_2.1-1 httr_1.4.7 tools_4.4.2
[28] pkgconfig_2.0.3 UCSC.utils_1.2.0
Finished EzAppCanu o35755_Canu_2025-05-21--12-02-35_mut22_temp2378578 2025-05-21 12:03:07
___STDOUT_END___
/srv/GT/analysis/course_sushi/public/gstore/projects/p1001/o35755_Canu_2025-05-21--12-02-35/scripts/Assemble_mut22_ventricles_100k_1.sh_sushiID1017_2025-05-21--12-03-01_e.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, saveRDS, 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 1.9.4 ✔ 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: inputType
unknown param: sushi_app
unknown param: isLastJob
tar: This does not look like a tar archive
tar: Skipping to next header
tar: Exiting with failure status due to previous errors
Error in ezSystem(paste("tar -zxf", SMRT_File, "--strip-components=4 -C smrt_input")) :
tar -zxf MutantSample_2_R1.fastq.gz --strip-components=4 -C smrt_input
failed
Calls: -> withCallingHandlers -> runMethod -> ezSystem
error exists: gxtx_data_mngt@fgcz.system
mail sent to: gxtx_data_mngt@fgcz.system
Execution halted
___STDERR_END___