Catch and report another class of exception

diff --git a/htsworkflow/pipelines/runfolder.py b/htsworkflow/pipelines/runfolder.py
index 7c06e217de63d5733e524ae551f06eea40528e11..da1bbe636bccdf359616c3b69e4a5963a5e32370 100644 (file)
--- a/htsworkflow/pipelines/runfolder.py
+++ b/htsworkflow/pipelines/runfolder.py
@@ -361,12 +361,12 @@ def build_hiseq_runs(image_analysis, runs, datadir, runfolder, flowcell_id):
             p.suffix = suffix
             p.image_analysis = image_analysis
             p.bustard = bustard.bustard(unaligned)
             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)
             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):
     return len(runs) - start
 
 def hiseq_match_aligned_unaligned(aligned, unaligned):