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I first ran TransDecoder.LongOrfs and then Predict and I got that error message:
Selecting best orfsError, cannot find file blastp.outfmt6 at /usr/local/packages/transdecoder-5.7.1/util/select_best_ORFs_per_transcript.pl line 315.
Error, cmd: /usr/local/packages/transdecoder-5.7.1/util/select_best_ORFs_per_transcript.pl --gff3_file /autofs/projects-t2/SerreDLab-2/fdumetz/Ld_annotation/Transdecoder/Ld1S_3ONT_monocistron.fasta.transdecoder_dir/longest_orfs.gff3 --cds_scores /autofs/projects-t2/SerreDLab-2/fdumetz/Ld_annotation/Transdecoder/Ld1S_3ONT_monocistron.fasta.transdecoder_dir/longest_orfs.cds.scores --min_length_auto_accept 927 --pfam_hits pfam.domtblout --blast_hits blastp.outfmt6 > /autofs/projects-t2/SerreDLab-2/fdumetz/Ld_annotation/Transdecoder/Ld1S_3ONT_monocistron.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3 died with ret 512 No such file or directory at /usr/local/packages/transdecoder-5.7.1/PerlLib/Pipeliner.pm line 187.
Pipeliner::run(Pipeliner=HASH(0x1860e38)) called at /usr/local/packages/transdecoder-5.7.1/TransDecoder.Predict line 369
All the files have been written accept longest_orfs.cds.best_candidates.gff3 that is a 0kb
Hi,
The key error message was:
Error, cannot find file blastp.outfmt6 at
/usr/local/packages/transdecoder-5.7.1/util/select_best_ORFs_per_transcript.pl
line 315.
so it was unable to find the blastp.outfmt6 file provided as an input
parameter. You could try giving it the full path.
Activity
Franck-Dumetz commentedon Oct 23, 2023
I said nothing, fixed it
brianjohnhaas commentedon Oct 24, 2023
chen7567 commentedon Mar 19, 2024
I'm facing a similar issue. Could you kindly share how you resolved it? I'm having trouble locating the blastp.outfmt6 file.