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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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braker3 failed when running with --prot_seq #703

Closed woodoo46 closed 12 months ago

woodoo46 commented 12 months ago

Hi, there,

I am running braker3 with --prot_seq option. Any idea of what is going?

[Tue Nov 14 00:31:01 2023] 96827/96827 (100%) pairs aligned [Tue Nov 14 00:31:01 2023] Alignment of pairs finished [Tue Nov 14 00:31:01 2023] Translating coordinates from local pair level to contig level [Tue Nov 14 00:31:07 2023] Finished spliced alignment [Tue Nov 14 00:31:07 2023] Flagging top chains [Tue Nov 14 00:31:13 2023] Processing the output [Tue Nov 14 00:31:34 2023] Output processed [Tue Nov 14 00:31:34 2023] ProtHint finished. sort: cannot create temporary file in '/localhd/6566873': No such file or directory ERROR in file /opt/BRAKER/scripts/braker.pl at line 5302 Failed to execute: /usr/bin/perl /opt/ETP/bin/gmes/gmes_petap.pl --verbose --seq

KatharinaHoff commented 12 months ago

sort will attempt to create temporary files when sth is too large to sort in memory. I assume that this is the cause of the problem, here. Not really sure why sort would not be able to create that file, though. Are you using a container?

On Tue, Nov 14, 2023 at 4:26 PM woodoo46 @.***> wrote:

Hi, there,

I am running braker3 with --prot_seq option. Any idea of what is going?

[Tue Nov 14 00:31:01 2023] 96827/96827 (100%) pairs aligned [Tue Nov 14 00:31:01 2023] Alignment of pairs finished [Tue Nov 14 00:31:01 2023] Translating coordinates from local pair level to contig level [Tue Nov 14 00:31:07 2023] Finished spliced alignment [Tue Nov 14 00:31:07 2023] Flagging top chains [Tue Nov 14 00:31:13 2023] Processing the output [Tue Nov 14 00:31:34 2023] Output processed [Tue Nov 14 00:31:34 2023] ProtHint finished. sort: cannot create temporary file in '/localhd/6566873': No such file or directory ERROR in file /opt/BRAKER/scripts/braker.pl at line 5302 Failed to execute: /usr/bin/perl /opt/ETP/bin/gmes/gmes_petap.pl --verbose --seq

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woodoo46 commented 12 months ago

Yes. I am using a container, I did not bind /localhd.

dmacguigan commented 11 months ago

I am having this same exact issue. Also running BRAKER 3.0.6 as a Singularity image. I call BRAKER with singularity run -H ${PWD} ${BRAKER_SIF} braker.pl, where BRAKER_SIF is the path to my BRAKER .sif file. @woodoo46, what was your solution?

[Thu Dec 14 20:40:04 2023] ProtHint finished.
sort: cannot create temporary file in '/scratch/14487641': No such file or directory
ERROR in file /opt/BRAKER/scripts/braker.pl at line 5302
Failed to execute: /usr/bin/perl /opt/ETP/bin/gmes/gmes_petap.pl --verbose --seq /projects/academic/tkrabben/MacGuigan/genome_annotations/Mmel_annotation/Mmel_BRAKER/genome.fa --EP /projects/academic/tkrabben/MacGuigan/genome_annotations/Mmel_annotation/Mmel_BRAKER/genemark_hintsfile.gff --cores=20  --gc_donor 0.001 --evidence /projects/academic/tkrabben/MacGuigan/genome_annotations/Mmel_annotation/Mmel_BRAKER/genemark_evidence.gff  --soft_mask auto 1>/projects/academic/tkrabben/MacGuigan/genome_annotations/Mmel_annotation/Mmel_BRAKER/GeneMark-EP.stdout 2>/projects/academic/tkrabben/MacGuigan/genome_annotations/Mmel_annotation/Mmel_BRAKER/errors/GeneMark-EP.stderr
Failed to execute: /usr/bin/perl /opt/ETP/bin/gmes/gmes_petap.pl --verbose --seq /projects/academic/tkrabben/MacGuigan/genome_annotations/Mmel_annotation/Mmel_BRAKER/genome.fa --EP /projects/academic/tkrabben/MacGuigan/genome_annotations/Mmel_annotation/Mmel_BRAKER/genemark_hintsfile.gff --cores=20  --gc_donor 0.001 --evidence /projects/academic/tkrabben/MacGuigan/genome_annotations/Mmel_annotation/Mmel_BRAKER/genemark_evidence.gff  --soft_mask auto 1>/projects/academic/tkrabben/MacGuigan/genome_annotations/Mmel_annotation/Mmel_BRAKER/GeneMark-EP.stdout 2>/projects/academic/tkrabben/MacGuigan/genome_annotations/Mmel_annotation/Mmel_BRAKER/errors/GeneMark-EP.stderr !
woodoo46 commented 11 months ago

If you are using singularity, you need to bind the proper directory through -B option. I forgot that last time. Hopefully, this helps.

dmacguigan commented 11 months ago

Would you mind providing an example? I'm a bit confused because /scratch/14487641 does not exist on my system.

woodoo46 commented 11 months ago

singularity exec -B /data -B /localhd ${container} braker.pl --gff3 --genome=${genome} --species ${species} --threads ${threads} --workingdir=${workdir} ${other}

here, $other is other parameters can be passed to braker3. If you do not have "/scratch/14487641", you may need to create by yourself. On our older system, we need to create it by ourself.