X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=blobdiff_plain;f=htsworkflow%2Fpipelines%2Frunfolder.py;h=669c5f03363dfc8c647730133af71678319d0336;hp=26c592ce5f7eb6d65175031f9c9010dc400d9410;hb=86dc57e6227c79cd3f599e3d8bac46a44f961607;hpb=805338420063c86eda5fe13c566b7eb8c2a650b7

diff --git a/htsworkflow/pipelines/runfolder.py b/htsworkflow/pipelines/runfolder.py
index 26c592c..669c5f0 100644
--- 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):