Warning: No SNPs were detected so there is nothing to output

sanger-pathogens / snp-sites

Finds SNP sites from a multi-FASTA alignment file

http://sanger-pathogens.github.io/snp-sites/

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Warning: No SNPs were detected so there is nothing to output #112

Open sreerampeela opened 1 year ago

sreerampeela commented 1 year ago

Hi, My issue is similar to https://github.com/sanger-pathogens/snp-sites/issues/96 only that when I manually look at the alignment file, I can find many mutations. The attached file is one such example generated using EMBL Clustal Omega (I had to convert as a text file to upload here, but was using the aln file). I even tried with MAFFT, but the issue remains the same.

I am running the following command:

/usr/bin/snp-sites -v -o msrR.vcf MsrR_aligned.aln

MsrR_aligned_aln.txt

JMiguelRamirez commented 4 months ago

Hi,

I had the same problem and fixed it by changing the output format of clustal omega. I was using "clustalo -outfmt=a2m" to get the same output format as you shared in the .aln file. I then removed the "-outfmt=a2m" to get the default multi fasta in the .aln file. With this change snp-sites worked.

I hope it helps,

José