Opened 4 years ago
Last modified 4 years ago
#1243 closed defect
Improve status checking for NovaSeq — at Initial Version
| Reported by: | Nicklas Nordborg | Owned by: | Nicklas Nordborg |
|---|---|---|---|
| Priority: | major | Milestone: | Reggie v4.27 |
| Component: | net.sf.basedb.reggie | Keywords: | |
| Cc: |
Description
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 flow cells. 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).
