Error while running hmmscan with autoTrinotate.pl

[pbluescript]

Hello everyone

While running autoTrinotate.pl I got this error after 2 days of hmmscan run:

* Running CMD: hmmscan --cpu 22 --domtblout TrinotatePFAM.out /mnt/beegfs/manoud/aa_assembly_run4/annotation/Pfam-A.hmm /mnt/beegfs/manoud/aa_assembly_run4/trinity/Trinity.fasta.transdecoder.pep > pfam.log
sh: line 1: 78343 Aborted                  hmmscan --cpu 22 --domtblout TrinotatePFAM.out /mnt/beegfs/manoud/aa_assembly_run4/annotation/Pfam-A.hmm /mnt/beegfs/manoud/aa_assembly_run4/trinity/Trinity.fasta.transdecoder.pep > pfam.log 2> tmp.9400.stderr
Fast filter only works for local alignment
Error, cmd: hmmscan --cpu 22 --domtblout TrinotatePFAM.out /mnt/beegfs/manoud/aa_assembly_run4/annotation/Pfam-A.hmm /mnt/beegfs/manoud/aa_assembly_run4/trinity/Trinity.fasta.transdecoder.pep > pfam.log 2>tmp.9400.stderr died with ret 34304 at /mnt/beegfs/manoud/aa_assembly_run4/annotation/trinotate/Trinotate-Trinotate-v3.2.1/auto/../PerlLib/Pipeliner.pm line 102.
    Pipeliner::run(Pipeliner=HASH(0x55555578a920)) called at /mnt/beegfs/manoud/aa_assembly_run4/annotation/trinotate/Trinotate-Trinotate-v3.2.1/auto/autoTrinotate.pl line 109

It generated TrinotatePFAM.out and pfam.log files, so it looks like the hmmscan worked but not completely (Cf. screen capture)

I didn't find any relevant information about this issue on the web. Could you please, bring me some help on this case?

Thanks a lot !

[brianjohnhaas]

hi,

If hmmscan is causing trouble, you can comment out that step (and the downstream loading step for it) and revisit it later. This way it won't hold you back from getting an almost complete Trinotate report.

best,

~b

On Mon, Mar 29, 2021 at 5:08 AM pbluescript @.***> wrote:

Hello everyone

While running autoTrinotate.pl I got this error after 2 days of hmmscan run:

• Running CMD: hmmscan --cpu 22 --domtblout TrinotatePFAM.out /mnt/beegfs/manoud/aa_assembly_run4/annotation/Pfam-A.hmm /mnt/beegfs/manoud/aa_assembly_run4/trinity/Trinity.fasta.transdecoder.pep > pfam.log sh: line 1: 78343 Aborted hmmscan --cpu 22 --domtblout TrinotatePFAM.out /mnt/beegfs/manoud/aa_assembly_run4/annotation/Pfam-A.hmm /mnt/beegfs/manoud/aa_assembly_run4/trinity/Trinity.fasta.transdecoder.pep > pfam.log 2> tmp.9400.stderr Fast filter only works for local alignment Error, cmd: hmmscan --cpu 22 --domtblout TrinotatePFAM.out /mnt/beegfs/manoud/aa_assembly_run4/annotation/Pfam-A.hmm /mnt/beegfs/manoud/aa_assembly_run4/trinity/Trinity.fasta.transdecoder.pep > pfam.log 2>tmp.9400.stderr died with ret 34304 at /mnt/beegfs/manoud/aa_assembly_run4/annotation/trinotate/Trinotate-Trinotate-v3.2.1/auto/../PerlLib/Pipeliner.pm line 102. Pipeliner::run(Pipeliner=HASH(0x55555578a920)) called at /mnt/beegfs/manoud/aa_assembly_run4/annotation/trinotate/Trinotate-Trinotate-v3.2.1/auto/autoTrinotate.pl line 109

It generated TrinotatePFAM.out and pfam.log files, so it looks like the hmmscan worked but not completely (Cf. screen capture)

I didn't find any relevant information about this issue on the web. Could you please, bring me some help on this case?

Thanks a lot !

[image: image] https://user-images.githubusercontent.com/77439355/112813235-456d4480-907e-11eb-9f31-c6c6965e1322.png

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Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas

[pbluescript]

Thank you for the answer, this is what I've finally done.