IOError: [Errno 2] No such file or directory: 'p2g_18546/diamond.matches.tab'

[sophietandonnet]

IOError: [Errno 2] No such file or directory: 'p2g_18546/diamond.matches.tab'

[reslp]

Hi Sophie,

Looks like something is wrong with the paths (and maybe also the funannotate database). Does it work if you specify the full path to the output directory? Also I would specify the path to the funannotate database as a seperate bindpoint (the real path to the funannotate database needs to be changed).

Does this work?

docker run --rm -it -v /local/path/to/database:/data/database -v $(pwd):/data reslp/funannotate:1.7.4 predict -i JU1783-k35_Gapclosed_v1.fa.masked.cleanfun.sorted --species "Rhabditis sp. JU1783" --transcript_evidence Trinity.fasta.clean --rna_bam JU1783-RNA-reads-aln-sortedgenome.bam --protein_evidence metazoa-and-Arh-proteins.fasta --pasa_gff sample_mydb_pasa.sqlite.valid_gmap_alignments.gff3 --organism other --ploidy 2  --busco_db nematoda --strain JU1783 -o /data/JU1783-funannotate1

cheers,

Philipp

[sophietandonnet]

Dear Philipp, Thanks for your quick response and sorry for taking so long to answer. Our server has had some serious hardware problems and I haven't yet been able to try your suggestions yet. As soon as everything is back to normal I will come back to running funannotate. Thanks again!! Sophie Em ter., 9 de fev. de 2021 às 07:40, Philipp Resl <[email protected]> escreveu:

…

Hi Sophie, Looks like something is wrong with the paths (and maybe also the funannotate database). Does it work if you specify the full path to the output directory? Also I would specify the path to the funannotate database as a seperate bindpoint (the real path to the funannotate database needs to be changed). Does this work? docker run --rm -it -v /local/path/to/database:/data/database -v $(pwd):/data reslp/funannotate:1.7.4 predict -i JU1783-k35_Gapclosed_v1.fa.masked.cleanfun.sorted --species "Rhabditis sp. JU1783" --transcript_evidence Trinity.fasta.clean --rna_bam JU1783-RNA-reads-aln-sortedgenome.bam --protein_evidence metazoa-and-Arh-proteins.fasta --pasa_gff sample_mydb_pasa.sqlite.valid_gmap_alignments.gff3 --organism other --ploidy 2 --busco_db nematoda --strain JU1783 -o /data/JU1783-funannotate1 cheers, Philipp — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#2 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABTMN6QQX4A3SZKSD5GBTPTS6EGI7ANCNFSM4XJM2ZZQ> .