parsnp only recruits a subset of genome fasta files in the directory

[TashyK]

Hi

I am trying to do an alignment of 190 Mycobacterium tuberculosis genome sequences using parsnp. It seems to work fine and creates an .xmfa file. However it doesn't recruit all the genome fasta files into the alignment - only 95 of the total 190. I'm sure why because all of the files are in fasta format, and it doesn't seem to be related to the file name.

Any advice would be greatly appreciated.

Thanks
Tasha

[tseemann]

I think you need to file this at the ParSNP project: https://github.com/marbl/parsnp

FYI - ParSNP will reject any samples from the final output if they are "too distant" from everything else. This is unexpected for Mtb, but maybe you have some NTMs in the mix?