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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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Job runs for 17+ hours without completion #70

Open emmadoughty opened 1 year ago

emmadoughty commented 1 year ago

Hi there,

I have run a few hundred samples through SeroBA v1.0.2 using the sangerpathogens/seroba docker image. Of these, 6 of them have failed to complete the job, producing the following the log files and continuing to run for 17+ hours before I aborted the job. QC of reads and assemblies from these samples have looked fine. Do you know what might be causing this issue and how we might avoid it?

Thanks in advance, Emma

Stage 1: 0% Stage 1: 26% Stage 1: 52% Stage 1: 78% Stage 1: 100%
Stage 2: 100%
1st stage: 3.11065s
2nd stage: 0.071989s
Total : 3.18264s
Tmp size : 0MB

Stats:
No. of k-mers below min. threshold : 0
No. of k-mers above max. threshold : 0
No. of unique k-mers : 0
No. of unique counted k-mers : 0
Total no. of k-mers : 0
Total no. of reads : 1476720
Total no. of super-k-mers : 0
in1: 0% in1: 0% in2: 0%