One or more keys necessary for output format <0> are missing.
Closed this issue · 3 comments
jose-martinez-fignoni commented
Hi guys! I am getting a missing keys error for some predictors. Below is the command and error message. I have changed nothing in the config.ini file, which was working before. Any ideas how to fix it? tks!
Command: python3 bin/mobidb/2.0/mobidb_lite.py /mnt/efs/genomes/results/SYM57343/WGS18118/ASM-txvdzN/annotation/ANN-79MFN4JTs/iprscan_822/temp/ip-172-60-37-232.ec2.internal_20221007_025458642_kvow//jobMobiDBLite/000000000001_000000000492.fasta
Error output from binary:
| ERROR | One or more keys necessary for output format <0> are missing. Check your config.ini and make sure that all necessary keys are present. | MISSING KEY(S): ._disembl; ._espritz; ._iupred; ._globplot
The content from my config.ini file:
# absolute path to the predictor folder
# ! DONT DELETE UNASSIGNED KEYS !
anchor=
disembl=
dynamine=
espritz=
fess=
globplot=
iupred=
jronn=
pfilt=
seg=
vsl2=
[thresholds]
mdb=0.625
anchor=0.5
dis465=0.5
disHL=0.086
dynamine_coil=0.5
espD=0.5072
espN=0.3089
espX=0.1434
iupl=0.5
iups=0.5
glo=0.0
jronn=0.5
pfilt=0.5
seg=0.5
vsl=0.5
fess_helix=0.5
fess_sheet=0.5
fess_coil=0.5
[outfmt_groups]
0=main
1=main
2=mobidb3
3=allid
damianopiovesan commented
Hi Jose. Can you share the input sequence? Do you have Python2 installed? Have you tried running mobidb_lite.py from its folder?
jose-martinez-fignoni commented
Hi Damiano! Tks for your quick reply. I am running this through the InterproScan, in Python3. It was working fine until I upgraded the InterproScan version because of a different issue.
I don't think I can get the input sequence easily, I am not using the software myself but just trying to fix it for a different team.
Sorry for being so little helpful, any idea what this can be related to? Will try getting an input sequence in case it's needed for solving this.
tks!
…________________________________
From: Damiano Piovesan ***@***.***>
Sent: Monday, October 10, 2022 12:50 PM
To: BioComputingUP/MobiDB-lite ***@***.***>
Cc: Jose Martinez ***@***.***>; Author ***@***.***>
Subject: Re: [BioComputingUP/MobiDB-lite] One or more keys necessary for output format <0> are missing. (Issue #2)
Hi Jose. Can you share the input sequence? Do you have Python2 installed? Have you tried running mobidb_lite.py from its folder?
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matthiasblum commented
We replied to your issue in ebi-pf-team/interproscan#294. Briefly, MobiDB-lite cannot find the path to predictor executables if [bin_directories] is missing in the config.ini file.