AlleleCall issue - Error on select_representatives, KeyError

[0mician]

Hi there,

I am using your really cool piece of software to analyze a large dataset of genomes from a single species. The SchemaCreation pipeline worked without any issue (output attached), but the AlleleCall pipeline crashes.

CreateSchema.log
AlleleCall.log

Do you know what could be the problem?

Thanks a lot in advance!
0mician

[rfm-targa]

Greetings @0mician,

Sorry for the delay. Thank you for sharing the information printed to the stdout. It seems the AlleleCall module is failing when trying to access the BLASTp raw score for candidate representatives. It tries to select new representative alleles for the schema loci but cannot compute the BSR value to determine if they should be chosen as new representatives. This might be related to issues when running BLASTp to get the self-score.
Can you share the commands used to run both modules? Also, can you share more information about the genome assemblies? (e.g. the list of accession numbers if the data is publicly available).

Kind regards,

Rafael