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Gaius-Augustus / GALBA

GALBA is a pipeline for fully automated prediction of protein coding gene structures with AUGUSTUS in novel eukaryotic genomes for the scenario where high quality proteins from one or several closely related species are available.
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Error regarding pygustus in singularity run: "No space left on device" #50

Closed maxnest closed 3 months ago

maxnest commented 4 months ago

Dear colleagues, Thank you for developing an extremely useful pipeline! Unfortunately, I encountered some difficulties. On a local computer, the pipeline performed well when working with one of the genomes. However, when running the pipeline on a remote server, after 3 hours of analysis, the pipeline send the following error (GALBA.log):

"... Thu Apr 11 16:14:34 2024: RUNNING AUGUSTUS Thu Apr 11 16:14:34 2024: AUGUSTUS with hints Thu Apr 11 16:14:34 2024: copy extrinsic file /opt/GALBA/scripts/cfg/galba.cfg to working directory cp /opt/GALBA/scripts/cfg/galba.cfg /scratch/project_2000784/GALBA_test/New_test/species/Lolivaceus_container_2/ex1.cfg /opt/conda/bin/python3 /scratch/project_2000784/GALBA_test/New _test/pygustus_hints.py 1> /scratch/project_2000784/GALBA_test/New_test/pygustus_hints.out 2>/scratch/project_2000784/GALBA_test/New_test/errors/pygustus_hints.err"

The last ten lines of the pygustus_hints.err: "... util.execute_bin_parallel( File "/opt/conda/lib/python3.10/site-packages/pygustus/util.py", line 32, in execute_bin_parallel run_information = fm.split( File "/opt/conda/lib/python3.10/site-packages/pygustus/fasta_methods.py", line 97, in split write_file([seq_record], inputfile, outputdir, fileidx) File "/opt/conda/lib/python3.10/site-packages/pygustus/fasta_methods.py", line 156, in write_file SeqIO.write(records_to_write, splitpath, 'fasta') File "/opt/conda/lib/python3.10/site-packages/Bio/SeqIO/init.py", line 524, in write fp.write(format_function(record)) OSError: [Errno 28] No space left on device"

At the same time, the server has slightly less than 1 TB of free space available for storing files. I run GALBA through a container and tried to specify different directories for writing files:

_nohup apptainer exec -H $WORKDIR:/home/mnestere -B $WORKDIR:$WORKDIR $GALBA galba.pl --species=${SPECIES} --gff3 --threads $THREADS --workingdir=${WORKDIR} --genome=${FASTA} --protseq=${REFPROTEINS}

I would be grateful for any help! Maksim

KatharinaHoff commented 4 months ago

Pygustus tries to write in /tmp on the machine.

KatharinaHoff commented 3 months ago

I will close this issue because it's not really a software issue.