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sanger-pathogens / seroba

k-mer based Pipeline to identify the Serotype from Illumina NGS reads
https://sanger-pathogens.github.io/seroba/
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No detailed output file #44

Open andersgs opened 5 years ago

andersgs commented 5 years ago

Hello.

Nice tool! Thank you.

I seem to have run in to an unexpected behaviour. When I run version 1.0.1 on a my test case, I only get a pred.tsv file with three columns. I see no detailed_serogroup_info.txt. Admittedly, I have only run it on a single sample, and the third column suggests it might be contaminated. I am wondering if I missed out on the detailed_serogroup_info because the sample appears contaminated.

Thank you.

Anders.

tseemann commented 5 years ago

Is the problem related to this? https://github.com/sanger-pathogens/seroba/issues/43

andersgs commented 5 years ago

Possibly. I did not get a Signal 13 error. But, the sample is of the same Serotype...