[BUG]: fcs-gx Error: Process failed with retcode -13 and 1 #101
Description
fcs-gx does not run regularly giving process failed with retcode -13. This error will be given for some samples in a batch and then run on those that errored when submitted again. It may not work on anything for a whole day of testing and then work on everything the next day. eg. on Friday I could not get it working with a script that has worked before on multiple samples, tried a lot of things and nothing worked, then 2 samples in a batch worked. Today I re run it and everything worked. But then this afternoon it is not working again.
To Reproduce
Copy the full run_fcsadaptor.sh/run_gx.py command used.
python3 /app/bin/run_gx \
--fasta ${assembly} \
--tax-id $taxid \
--out-dir ./NCBI \
--gx-db /tmp/gxdb \
--debug
If you are having trouble with your genome, please ensure that you can run the pipeline with one of our test genomes first. If your installation works fine with the sample input, please tell us if you are willing and able to share your genome with us, if asked.
Software versions (please complete the following information):
- OS [e.g. CentOS 7, macOS , etc.].
- Cloud Platform VM [e.g. AWS , GCP], if applicable.
- Singularity version [`singularity-ce version 4.1.0].
- Singularity FCS image version [
https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/releases/0.5.4/fcs-gx.sif]. - Python version if using FCS-GX [`Python 3.11.6].
- Nextflow/24.04.3
Log Files
log_1.txt
Warning: missing header '##[["GX hits",2,1]]'
####### Cleaning up process ['cat', 'OG2.ilmn.240716.v129mh.fasta']
Error: Process failed with retcode -13: ['cat', 'OG2.ilmn.240716.v129mh.fasta'])
####### Cleaning up process ['tee', '/dev/fd/6']
Error: Process failed with retcode -13: ['tee', '/dev/fd/6'])
####### Cleaning up process ['/app/bin/gx', 'split-fasta']
Error: Process failed with retcode -13: ['/app/bin/gx', 'split-fasta'])
####### Cleaning up process ['pv', '-Wbratpe', '--interval=0.5', '--size=4979093308', '--buffer-size=104857600']
####### Cleaning up process ['/busybox/time', '-v', 'nice', '-n19', '/app/bin/gx', 'align', '--gx-db=/tmp/gxdb/all.gxi', '--repeats-basis-fa=/dev/fd/3']
Error: Process failed with retcode 1: ['/busybox/time', '-v', 'nice', '-n19', '/app/bin/gx', 'align', '--gx-db=/tmp/gxdb/all.gxi', '--repeats-basis-fa=/dev/fd/3'])
####### Cleaning up process ['pv', '--quiet', '--buffer-size=104857600']
####### Cleaning up process ['/app/bin/gx', 'taxify', '--gx-db=/tmp/gxdb/all.gxi', '--output=./NCBI/OG2.ilmn.240716.v129mh.396785.taxonomy.rpt.tmp', '--asserted-div=anml:fishes', '--db-exclude-locs=/app/bin/db_exclude.locs.tsv']
####### Cleaning up process ['/app/bin/gx', 'get-fasta-stats']
####### Cleaning up process ['cat', 'OG2.ilmn.240716.v129mh.fasta']
Additional context
This is being run as part of a nextflow.
The fasta file i am using is zipped (I am using zipped because last time i was getting errors i zipped it and it worked, however it has not been working this time, zipped or unzipped)
This is also the same issue that Lauren Huet (my colleague) was reporting on behalf of both of us in this closed thread #80