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sanger-pathogens / companion

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion
http://companion.sanger.ac.uk
ISC License
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SNAP error #100

Open WanessaMGoes opened 3 years ago

WanessaMGoes commented 3 years ago

Hello everyone.!!

I did not understand the error that Companion is presenting and I did not find the motivation for it. What should I do to fix it?

Error executing process > 'run_snap'

Caused by: Process run_snap terminated with an error exit status (2)

Command executed:

echo '##gff-version 3' > snap.gff3 snap -gff -quiet snap.hmm pseudo.pseudochr.fasta > snap.tmp snap_gff_to_gff3.lua snap.tmp > snap.tmp.2 if [ -s 1 ]; then gt gff3 -sort -tidy -retainids snap.tmp.2 > snap.gff3; fi

Command exit status: 2

Command output: (empty)

Command error: ZOE ERROR (from snap): error opening file ((null)/HMM/snap.hmm) ZOE library version 2013-02-16

Work dir: /home/wanessa/work/6b/94be813b401ee67df7d4ab7bbc0277

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line

satta commented 3 years ago

(Warning; I haven't looked at the Companion codebase in a while now)

Looks like you are trying to run SNAP within Companion with a reference for which there is not trained model for SNAP. You might be able to just deactivate run_snap in your params config file, it usually does not help much with gene calling accuracy but may add false positives. So you should be fine without.