Hisat alignment stops without error if the genotype VCF file can't be parsed
After a Hisat alignment job has been completed some of the data files are parsed and information is imported to BASE as annotations. If all seems good, and auto-confirmation has been selected, the next step should be started, otherwise it is expected that an error message or something else is indicating that there was a problem.
There seems to be issue if the VCF file for genotype qc can't be parsed. The job ends without any error. Auto-confirmation stops further analysis since a HET percentage is missing, but there is no notion that this is the case. A sharp-eyed user can see that the job status is missing a number for the HET percentage:
Done: 0.5M reads after mask; 0.5M reads after alignment; 3.6% duplicates; % HET
Note! In this case, the reason for not being able to parse the VCF file was that the SSH fingerprint for the ProjectArchive server had changed due to an update of the SSH library.