#1339 closed defect (fixed)

ReadLengthAvg annotations are -1

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: critical Milestone: Reggie v4.33.1
Component: net.sf.basedb.reggie Keywords:
Cc:

Description

For the latest sequencing run, there is only one merged item that has a value for the ReadLengthAvgR1 and ReadLengthAvgR2 annotations. All other merged items have -1.

The output file from the job scripts contain values for all items.

The catalina.out log file has a few error message like:

10:53:49,865 ERROR DemuxJobCreator:820 - At line 5: Found readlength data #3 for library xxxxxxxx.1.l.r.n.m.c.lib.g
10:53:49,865 ERROR DemuxJobCreator:820 - At line 6: Found readlength data #4 for library xxxxxxxx.1.l.r.n.m.c.lib.g
...

The first line is for read #3 and it continues with 2 error messages per merged item up to #48. The problem seems to be that the counter for the read number is not reset for each new merged item, but continues to increase for each data line in the result file.

Change History (3)

comment:1 Changed 12 months ago by Nicklas Nordborg

Milestone: Reggie v4.xReggie v4.33.1

comment:2 Changed 12 months ago by Nicklas Nordborg

The items that have -1 need to be updated manually and the results in the Legacy pipeline should be deleted and new jobs should be started.

comment:3 Changed 12 months ago by Nicklas Nordborg

Resolution: fixed
Status: newclosed

In 6430:

Fixes #1339: ReadLengthAvg? annotations are -1

Also modified the code so that if no value is found the annotation is not set at all.

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