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Merge branch 'django1.4' of mus.cacr.caltech.edu:htsworkflow into django1.4
author
Diane Trout
<diane@caltech.edu>
Thu, 5 Dec 2013 23:06:14 +0000
(15:06 -0800)
committer
Diane Trout
<diane@caltech.edu>
Thu, 5 Dec 2013 23:06:14 +0000
(15:06 -0800)
htsworkflow/pipelines/runfolder.py
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diff --git
a/htsworkflow/pipelines/runfolder.py
b/htsworkflow/pipelines/runfolder.py
index 26c592ce5f7eb6d65175031f9c9010dc400d9410..669c5f03363dfc8c647730133af71678319d0336 100644
(file)
--- a/
htsworkflow/pipelines/runfolder.py
+++ b/
htsworkflow/pipelines/runfolder.py
@@
-363,12
+363,12
@@
def build_hiseq_runs(image_analysis, runs, datadir, runfolder, flowcell_id):
p.suffix = suffix
p.image_analysis = image_analysis
p.bustard = bustard.bustard(unaligned)
- assert p.bustard
if aligned:
p.gerald = gerald.gerald(aligned)
runs.append(p)
- except IOError, e:
- LOGGER.error("Ignoring " + str(e))
+ except (IOError, RuntimeError) as e:
+ LOGGER.error("Exception %s", str(e))
+ LOGGER.error("Skipping run in %s", flowcell_id)
return len(runs) - start
def hiseq_match_aligned_unaligned(aligned, unaligned):