search

sanger-pathogens / seroba

k-mer based Pipeline to identify the Serotype from Illumina NGS reads
https://sanger-pathogens.github.io/seroba/
Other
19 stars 16 forks source link

After kmc, error "Stopping! Signal received: 13" #43

Open tseemann opened 5 years ago

tseemann commented 5 years ago

I was wondering what this error means?

<snip>
0.02010796221322537
19A
cluster detected 1 threads available to it
cluster reported completion
Stopping! Signal received: 13
tseemann commented 5 years ago

I get pred.tsv but detailed_serogroup_info.txt is missing :(

eppinglen commented 5 years ago

Hi @tseemann

this error was already discussed in: https://github.com/sanger-pathogens/ariba/issues/238. Unfortunately there is no solution available at the moment, however I think this should not effect the serotype prediction.

The detailed_serogroup_info.txt is not created for all serotypes, due the construction of the PneumoCaT database. This file will only be printed if there is information available on presence/absence of allelic variants or SNPs for a specific serotype. So, if SeroBA predicts a serotype just based on the sequence identity this file is not created.

However, to avoid further confusion the detailed_serogroup_info.txt should probably be created for all serotypes in future versions.