search

EBI-Metagenomics / workflow-is-cwl

This repository contains CWL descriptions of the various tools which will allow you to build workflows for the annotation of transcripts
https://www.elixir-europe.org/
Apache License 2.0
6 stars 7 forks source link

BUSCO: Backslash char is not supported in FASTA header - Add FASTA header cleaning step #18

Closed mscheremetjew closed 5 years ago

mscheremetjew commented 5 years ago

While running the annotation pipeline on a full transcriptome assembly, the assembly assessment step (BUSCO) failed, complaining about unsupported characters in the FASTA header

INFO    Configuration loaded from /software/applications/busco/3.0.2/scripts/../config/config.ini
INFO    Init tools...
INFO    Check dependencies...
INFO    Check input file...
ERROR   The character '/' is present in the fasta header >MMETSP0795-doi:10.5281/zenodo.249982-Transcript_0, which will crash Reader. Please clean the header of your input file.
ERROR   BUSCO analysis failed !
ERROR   Check the logs, read the user guide, if you still need technical support, then please contact mailto:support@orthodb.org
mscheremetjew commented 5 years ago

That's in now. FASTA header cleaning step added. There are are more issues with the FASTA header though. The length of the FASTA header should be restricted too as BUSCO complains about it.