MikeWLloyd
commented
1 month ago Exit status 143 typically occurs either when the memory request, or the wallclock request has been exceeded.
Can you provide the number of reads in S3_R1_001.fastq.gz?
The second thing to check would be to look in the directory that should be printed to the end of the Nextflow log:
For example:
Command executed:
Rscript my_script.R
Command exit status:
143
Command output:
...text....
Command error:
...text...
Work dir:
/scratch/$USER/workdir/eb/33d560d5f3e2ee78d5db43ba072228
In this example, you would navigate to: /scratch/$USER/workdir/eb/33d560d5f3e2ee78d5db43ba072228 and look at the .command.log file. What (if anything) is appended to the end of that log file? E.g., if you are on slurm you would likely see some epilogue information (memory usage, wall clock usage, etc.). Does that log report memory usage that exceeds the request (200GB).
This step GBRS_BAM2EMASE is known to be memory intensive. To fix this issue, increase the memory allocation in the modules/gbrs/gbrs_bam2emase.nf file beyond 200GB.
lawtyunc
Hi Jackson Lab, I was running your cs-nf-GBRS pipeline and was were able to have it work over one sample but when we tried to run this over multiple samples, we run into this error.
Caused by: Process
GBRS:RUN_EMASE:GBRS_BAM2EMASE (S3)terminated with an error exit status (143)Command executed:
gbrs bam2emase -i S3_mapped_R2.bam -m /path/to/output/emase.fullTranscripts.info -h A,B,C,D,E,F,G,H -o S3_mapped_R2.emase.h5
Command exit status: 143 We have also been seeing this error as well with exit status 143
Command executed:
set -o pipefail
zcat S3_R1_001.fastq.gz \ | bowtie -p 8 -q -a --best --strata --sam -v 3 -x /path/to/output/bowtie.transcripts - 2> S3.bowtie_R1.log \ | samtools view -bS - > S3_mapped_R1.bam
Command exit status: 143
Do you know what may be causing this issue?