search

oschwengers / bakta

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
GNU General Public License v3.0
432 stars 53 forks source link

PSC failed! diamond-error-code=-11 #290

Closed DariaGI closed 2 months ago

DariaGI commented 3 months ago

Hello, please help me to resolve the problem below. Where to find information about the -11 diamond error.

15:11:43.788 - INFO - CDS - contig=contig_16, start=1047, stop=2303, strand=+, nt=[TTGCAAAAAT..CGGCTCTTAA] 15:11:43.789 - INFO - CDS - contig=contig_17, start=897, stop=1418, strand=-, frame=3, truncated=no, start-type=ATG, RBS-motif=None 15:11:43.789 - INFO - CDS - contig=contig_17, start=1544, stop=2563, strand=+, frame=2, truncated=no, start-type=ATG, RBS-motif=None 15:11:43.789 - INFO - CDS - contig=contig_17, start=2560, stop=2781, strand=-, frame=2, truncated=no, start-type=ATG, RBS-motif=None 15:11:43.789 - INFO - CDS - contig=contig_17, start=897, stop=1418, strand=-, nt=[ATGAAATATA..CGTACAATGA] 15:11:43.789 - INFO - CDS - contig=contig_17, start=1544, stop=2563, strand=+, nt=[ATGATAATAG..AAGTAGCTAA] 15:11:43.789 - INFO - CDS - contig=contig_17, start=2560, stop=2781, strand=-, nt=[ATGGACAGAG..AAGTCTTTAG] 15:11:43.789 - INFO - CDS - contig=contig_18, start=357, stop=1025, strand=-, frame=1, truncated=no, start-type=GTG, RBS-motif=GGA/GAG/AGG 15:11:43.789 - INFO - CDS - contig=contig_18, start=357, stop=1025, strand=-, nt=[GTGTCTGCGG..AAAGAAGTAA] 15:11:43.789 - INFO - CDS - contig=contig_19, start=101, stop=454, strand=+, frame=2, truncated=no, start-type=TTG, RBS-motif=GGA/GAG/AGG 15:11:43.789 - INFO - CDS - contig=contig_19, start=101, stop=454, strand=+, nt=[TTGCAAAAAA..TAAAAAATAG] 15:11:43.789 - INFO - CDS - contig=contig_21, start=56, stop=550, strand=-, frame=2, truncated=no, start-type=TTG, RBS-motif=None 15:11:43.789 - INFO - CDS - contig=contig_21, start=56, stop=550, strand=-, nt=[TTGTCTAAAA..TACAACATAA] 15:11:43.839 - INFO - CDS - predicted=689 15:11:43.841 - INFO - ORF - write internal aa seqs: # seqs=689, path=/tmp/tmpr2ni0o/cds.spurious.faa 15:11:44.355 - INFO - ORF - discarded=0 15:11:44.411 - INFO - UPS - looked-up=0 15:11:44.412 - INFO - IPS - looked-up=0 15:11:44.412 - INFO - ORF - write internal aa seqs: # seqs=689, path=/tmp/tmpr2ni0o/cds.psc.faa 15:11:52.909 - WARNING - PSC - PSC failed! diamond-error-code=-11 15:11:52.911 - INFO - MAIN - removed tmp dir: /tmp/tmpr2ni0o

I tried to start the annotation with different genomes and the result is the same, so the issie is not related with data. And the diamond itself works fine.

kiranpatil222 commented 3 months ago

I also have same Error

oschwengers commented 3 months ago

Hi and thanks for reporting, this is a known bug caused by Diamond introduced in the latest version v2.1.9. This has already been reported multiple times by other users (https://github.com/oschwengers/bakta/issues/271, https://github.com/oschwengers/bakta/issues/272) and is already validated and reported in the upstream Diamond repository: https://github.com/bbuchfink/diamond/issues/785.

Best thing to circumvent is to downgrade Diamond to v2.1.8 which solves the issue until this bug is fixed upstream.