Error on assign_allele_ids in AlleleCall module

[artmisk13]

Hi there,

I encountered an error when running the AlleleCall module. These are the details that might be relevant:

• The schema is prepped using PrepExternalSchema and for each locus in the schema, there is only one allele sequence (this went OK)
• Below is the command I used:
  chewBBACA.py AlleleCall -i /dir/fasta -g /dir/chewbbaca_schema -o ./chewbbaca_allele_call --cpu 6 --output-novel >> output.log

I also tried without --output-novel and it gave me the exact error. Can you please look into this? Is there anything I can do to overcome the error?

Many thanks, appreciate your help!

output.log

[rfm-targa]

Hello @artmisk13,

Based on what's in the log, it appears that the allele identifiers do not end with an integer. chewBBACA expects the sequence headers in the loci FASTA files to be in the format >locusID_int (e.g. >LM2010_1). However, based on the log, you seem to have sequence headers that terminate in strings, such as VFG000326.
I recommend you check the sequence headers to make sure they end with an integer and not with a string.

Kind regards,

Rafael