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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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error, output file is empty data/ep.gff #861

Open gladjabo opened 2 days ago

gladjabo commented 2 days ago

Dear

I met with such error: [Fri Sep 20 17:27:52 2024] Enqueueing pair 2238009/2240249 (99.9%). Est. time left: 00:00:34 (hh:mm:ss) [Fri Sep 20 17:28:47 2024] 2240249/2240249 (100%) pairs aligned [Fri Sep 20 17:28:47 2024] Alignment of pairs finished [Fri Sep 20 17:28:47 2024] Translating coordinates from local pair level to contig level [Fri Sep 20 17:29:59 2024] Finished spliced alignment [Fri Sep 20 17:30:03 2024] Flagging top chains [Fri Sep 20 17:31:13 2024] Processing the output [Fri Sep 20 17:36:16 2024] Output processed [Fri Sep 20 17:36:16 2024] ProtHint finished. sort: cannot create temporary file in '/scratch/364418.1.all.q': No such file or directory ERROR in file /opt/BRAKER/scripts/braker.pl at line 5417 Failed to execute: /usr/bin/perl /opt/ETP/bin/gmes/gmes_petap.pl --verbose --seq /isilon/projects/J-001961_4DWheat/Genome_assembly/Genome/Carberry/braker/genome.fa --EP /isilon/projects/J-001961_4DWheat/Genome_assembly/Genome/Carberry/braker/genemark_hintsfile.gff --cores=48 --gc_donor 0.001 --evidence /isilon/projects/J-001961_4DWheat/Genome_assembly/Genome/Carberry/braker/genemark_evidence.gff --soft_mask auto 1>/isilon/projects/J-001961_4DWheat/Genome_assembly/Genome/Carberry/braker/GeneMark-EP.stdout 2>/isilon/projects/J-001961_4DWheat/Genome_assembly/Genome/Carberry/braker/errors/GeneMark-EP.stderr Failed to execute: /usr/bin/perl /opt/ETP/bin/gmes/gmes_petap.pl --verbose --seq /isilon/projects/J-001961_4DWheat/Genome_assembly/Genome/Carberry/braker/genome.fa --EP /isilon/projects/J-001961_4DWheat/Genome_assembly/Genome/Carberry/braker/genemark_hintsfile.gff --cores=48 --gc_donor 0.001 --evidence /isilon/projects/J-001961_4DWheat/Genome_assembly/Genome/Carberry/braker/genemark_evidence.gff --soft_mask auto 1>/isilon/projects/J-001961_4DWheat/Genome_assembly/Genome/Carberry/braker/GeneMark-EP.stdout 2>/isilon/projects/J-001961_4DWheat/Genome_assembly/Genome/Carberry/braker/errors/GeneMark-EP.stderr ! INFO: Cleaning up image...

and GeneMAark-EP stdout shows:

check before the run

hard_mask is in the 'auto' mode. hard_mask was set to: 100

creat directories

commit input data

error, output file is empty data/ep.gff error on call: /opt/ETP/bin/gmes/reformat_gff.pl --out data/ep.gff --trace info/dna.trace --in /isilon/projects/J-001961_4DWheat/Genome_assembly/Genome/Carberry/braker/genemark_hintsfile.gff --quiet

Could you please help me with this? thanks

Best Bosen

gladjabo commented 2 days ago

However when I separated my wheat genome into chromosomes, brakers3 run successfully. Could this error that be caused by memory size?