Opened 5 years ago

Closed 5 years ago

#1171 closed enhancement (fixed)

Hisat alignment stops without error if the genotype VCF file can't be parsed

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: minor Milestone: Reggie v4.23
Component: net.sf.basedb.reggie Keywords:


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.

Change History (1)

comment:1 by Nicklas Nordborg, 5 years ago

Resolution: fixed
Status: newclosed

In 5579:

Fixes #1171: Hisat alignment stops without error if the genotype VCF file can't be parsed

If this happens an exception is thrown and the job is ended with status=ERROR.

Just in case, the Hisat confirmation wizard was also updated to display a warning icon in case the is no genotype counts.

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