Opened 4 weeks ago

Closed 4 weeks ago

Last modified 3 weeks ago

#1243 closed defect (fixed)

Improve status checking for NovaSeq

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v4.27
Component: net.sf.basedb.reggie Keywords:
Cc:

Description (last modified by Nicklas Nordborg)

This is related to #1242. The novaseq_status.sh script doesn't include enough information for Reggie (in NovaSeqSignalHandler class) to be able determine how many *.cbcl files to expect when the sequencing has been completed. The RunInfo.xml file have the same numbers for LaneCount (=2), SurfaceCount (=2), SwathCount (=2) and TileCount (=78) for both SP and S2 flow cells. This causes Reggie to expect 436 cbcl files (for 218 cycles) in both cases. In reality the S1 flow cell creates 872 cbcl files. The only visible difference in RunInfo.xml is the number of <Tile> tags which is 312 for SP and 624 for S1 flow cells. There is also a <FlowCellMode> tag in RunParameters.xml which can be used (the value is either SP or S1).

Change History (3)

comment:1 Changed 4 weeks ago by Nicklas Nordborg

In 5934:

References #1243: Improve status checking for NovaSeq?

Updated the novaseq_status.sh script to include:

  • FlowCellMode: (eg. SP or S1, etc.)
  • RunInfoDate: Date value from RunInfo.xml converted to same date format as other dates
  • TileTags: Number of <Tile> tags in RunInfo.xml

comment:2 Changed 4 weeks ago by Nicklas Nordborg

Resolution: fixed
Status: newclosed

In 5935:

Fixes #1243: Improve status checking for NovaSeq?

The new values from novaseq_status.sh are now used by Reggie to generate the status.

comment:3 Changed 3 weeks ago by Nicklas Nordborg

Description: modified (diff)
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