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Gaius-Augustus / BRAKER

BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes
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fix_in_frame_stop_codon_genes.py crashes on line 701 #873

Open rainmanv84 opened 1 month ago

rainmanv84 commented 1 month ago

Running BRAKER 3.0.8 on Ubuntu-20.04 (WSL2) in Singularity-CE-4.2.1

On some genomes the pipeline crashes:

braker.log: /opt/conda/bin/python3 /opt/Augustus/scripts/fix_in_frame_stop_codon_genes.py -g /home/rainman/Work/Gene_annotation/wd/GCA_001051215.1_ASM105121v1_genomic.fna/genome.fa -t /home/rainman/Work/Gene_annotation/wd/GCA_001051215.1_ASM105121v1_genomic.fna/augustus.hints.gtf -b /home/rainman/Work/Gene_annotation/wd/GCA_001051215.1_ASM105121v1_genomic.fna/bad_genes.lst -o augustus.hints_fix_ifs_ -s GCA_001051215.1_ASM105121v1_genomic.fna -m on --UTR off --print_utr off -a /home/rainman/Work/Gene_annotation/wd/GCA_001051215.1_ASM105121v1_genomic.fna/config -C /opt/cdbfasta -A /opt/Augustus/bin/ -S /opt/Augustus/scripts/ -H /home/rainman/Work/Gene_annotation/wd/GCA_001051215.1_ASM105121v1_genomic.fna/hintsfile.gff -e /opt/BRAKER/scripts/cfg/ep.cfg > /home/rainman/Work/Gene_annotation/wd/GCA_001051215.1_ASM105121v1_genomic.fna/fix_in_frame_stop_codon_genes_augustus.hints.log 2> /home/rainman/Work/Gene_annotation/wd/GCA_001051215.1_ASM105121v1_genomic.fna/errors/fix_in_frame_stop_codon_genes_augustus.hints.err

fix_IFSlog: no errors

fix_in_frame_stop_codon_genes_augustus.hints.err: Traceback (most recent call last): File "/opt/Augustus/scripts/fix_in_frame_stop_codon_genes.py", line 701, in <module> with multiprocessing.Pool(processes = args.cores) as pool: File "/opt/conda/lib/python3.10/multiprocessing/context.py", line 119, in Pool return Pool(processes, initializer, initargs, maxtasksperchild, File "/opt/conda/lib/python3.10/multiprocessing/pool.py", line 191, in __init__ self._setup_queues() File "/opt/conda/lib/python3.10/multiprocessing/pool.py", line 346, in _setup_queues self._inqueue = self._ctx.SimpleQueue() File "/opt/conda/lib/python3.10/multiprocessing/context.py", line 113, in SimpleQueue return SimpleQueue(ctx=self.get_context()) File "/opt/conda/lib/python3.10/multiprocessing/queues.py", line 341, in __init__ self._rlock = ctx.Lock() File "/opt/conda/lib/python3.10/multiprocessing/context.py", line 68, in Lock return Lock(ctx=self.get_context()) File "/opt/conda/lib/python3.10/multiprocessing/synchronize.py", line 162, in __init__ SemLock.__init__(self, SEMAPHORE, 1, 1, ctx=ctx) File "/opt/conda/lib/python3.10/multiprocessing/synchronize.py", line 57, in __init__ sl = self._semlock = _multiprocessing.SemLock( FileNotFoundError: [Errno 2] No such file or directory

Solution (at least for me): export TMPPATH=/tmp/

rainmanv84 commented 1 month ago

Oops, the above mentioned solution did not resolve the situation completely. Crashes got somewhat more rare, but still present at the same place