Stage 5: Filter Fasta error

[karimi81]

Hi there,
I have got an error at stage 5 indicating that the header of fasta files are not correct:
processing file GCF_014441545.1_ROS_Cfam_1.0_protein.fasta
The ID on def line '>GCF_014441545.1_ROS_Cfam_1.0_protein|NP_001002930.1' is missing the prefix '0_protein|' 'GCF_014441545.1_ROS_Cfam_1.0_protein'

I have downloaded the protein fasta files from the NCBI genome annotation for each species. I wonder if I need to edit these files before processing using pipeline. Can you please let me know which format of fasta file would require for orthomcl-pipeline
Thanks

[apetkau]

Are you using the OrthoMCL software available from https://orthomcl.org/orthomcl/app/downloads/software/ or the version from https://github.com/apetkau/orthomclsoftware-custom? I suspect you are using the version from orthomcl.org, which does not support underscores _ and other special characters in the fasta file name. The version in https://github.com/apetkau/orthomclsoftware-custom contains some modifications I made to support underscores _ and so you may wish to try installing this version instead.