issue with autotrinotate.pl

Question

[hydra_questions]

Hi!

I keep getting the error below while trying to run the autoTrinotate.pl script for my Trinity-assembled transcriptome (fasta file).

Any advice on where the issue may lie would be greatly appreciated! Thanks

/home/russod/Trinotate/auto/autoTrinotate.pl --Trinotate_sqlite /home/russod/Trinotate.sqlite --transcripts /home/russod/Trinity.fasta --gene_to_trans_map /home/russod/fastp-denovo/Trinity.fasta.gene_trans_map --conf /home/russod/Trinotate/auto/conf.txt --CPU 8

..

Running CMD: /home/russod/tmhmm-2.0c/bin/tmhmm --short < /home/russod/Trinity.fasta.transdecoder.pep > tmhmm.out Error, cmd: /home/russod/tmhmm-2.0c/bin/tmhmm --short < /home/russod/Trinity.fasta.transdecoder.pep > tmhmm.out 2>tmp.7530.stderr died with ret 36096 at /home/russod/Trinotate/auto/../PerlLib/Pipeliner.pm line 102. Pipeliner::run(Pipeliner=HASH(0x7fffdf450fe0)) called at /home/russod/Trinotate/auto/autoTrinotate.pl line 109

[Dunois]

You should try raising this issue over at the trinityrnaseq-users Google Groups forum. The Trinotate maintainers are active there, and they'd be able to assist you better.