Error when creating data/all.gff file

[anttonalberdi]

Hi! I have run the entire pipeline but found that it failed in the data/all.gff file creation step and thus all downstream steps.

Writing all.gff file to 7-Metaerg/data
print() on closed filehandle $all_gff_fh at metaerg/bin/metaerg.pl line 637.
print() on closed filehandle $all_gff_fh at metaerg/bin/metaerg.pl line 647.
print() on closed filehandle $all_gff_fh at metaerg/bin/metaerg.pl line 647.
... (the same error many times)
could not open 7-Metaerg/data/all.gff to read, No such file or directory
Could not run command:perl metaerg/bin/output_reports.pl -g 7-Metaerg/data/all.gff -o 7-Metaerg -f 7-Metaerg/metaerg.pl_05182020.fna, Bad file descriptor

Any idea why this could have happened? Do I need to rerun the entire analysis or is there any way to use the generated data. These are the files that I have in the tmp folder:

3.0K | 8S_rRNA.ffn 37K | arc.tblout 34K | bac.tblout 566K | casgenes.hmm.tblout 38M | cds.faa 43M | cds.faa.temp.1 82M | cds.ffn 89M | cds.ffn.temp.1 64M | cds.gff.temp.1 413 | crisprs.temp 30K | euk.tblout 123M | features.annot.gff 14M | features.gff 31M | FOAM1.hmm.tblout 34M | FOAM2.hmm.tblout 36M | FOAM3.hmm.tblout 40M | FOAM4.hmm.tblout 44M | FOAM5.hmm.tblout 183M | FOAM-hmm_rel1a.hmm.tblout 11M | genomedb.blasttable 687K | metabolic.hmm.tblout 86M | metaerg.pl_05182020.crispr.masked.fna 87M | metaerg.pl_05182020.fna 86M | metaerg.pl_05182020.rRNA.masked.fna 86M | metaerg.pl_05182020.tRNA.masked.fna 30M | Pfam-A.hmm.tblout 44K | rRNA.ffn 12K | rRNA.gff 3.7M | TIGRFAMs.hmm.tblout 3.5M | tRNA.temp 5.9M | uniprot_sprot.blasttable

Thanks a lot!