From: Diane Trout <diane@caltech.edu>
Date: Mon, 2 Dec 2013 19:24:43 +0000 (-0800)
Subject: Catch and report another class of exception
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=commitdiff_plain;h=a116f737719d577bc5846eea895f6b159ad08430

Catch and report another class of exception
---

diff --git a/htsworkflow/pipelines/runfolder.py b/htsworkflow/pipelines/runfolder.py
index 7c06e21..da1bbe6 100644
--- 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)
-            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):