ERROR: Could not run: snp-sites -c -o core.aln core.full.aln

[ellisrichardj]

I'm getting the could not run snp-sites error even though like others who have had this issue (e.g. #326) I don't have the warning that I have no SNPs. However, I can successfully run snp-sites outside of the snippy script directly on the output that snippy had produced before it failed.

....
18	AF-21-00169-20	snp=4358589	del=5	ins=58	het=0	unaligned=0
19	AF-21-07705-19	snp=4350978	del=4	ins=72	het=0	unaligned=0
20	AF-21-06823-19	snp=4354593	del=7	ins=59	het=0	unaligned=0
Opening: core.tab
Opening: core.vcf
Processing contig: LT708304-Mycobacteriumbovis-AF2122-97
Generating core.full.aln
Creating TSV file: core.txt
Running: snp-sites -c -o core.aln core.full.aln
ERROR: Could not run: snp-sites -c -o core.aln core.full.aln

Any ideas why snippy causes the error with snp-sites?

[pvanheus]

In my experience this is typically caused by inclusion of poor quality samples or samples with reads that don't map to reference. The snp-sites -c command excludes all columns of the MSA that contain a character other than ACTG, which means that any columns where the sequence is N or - get excluded. If there is a poor quality sequence in the alignment this could cause all variant sites to be removed and then trigger this error.

The solution is to identify and remove the sequences that are causing problems, perhaps by examining the alignment in core.full.aln.