Traceback (most recent call last):
 File "/usr/local/bin/bcbio_nextgen.py", line 226, in <module>
   runfn.process(kwargs["args"])
 File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/distributed/runfn.py", line 57, in process
   out = fn(fnargs)
 File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/utils.py", line 52, in wrapper
   return apply(f, *args, **kwargs)
 File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/distributed/multitasks.py", line 263, in variantcall_batch_region
   return genotype.variantcall_batch_region(*args)
 File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/variation/genotype.py", line 431, in variantcall_batch_region
   [_region_to_coords(r) for r in region_block], out_file)
 File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/variation/gatk.py", line 169, in haplotype_caller
   except (subprocess.CalledProcessError, msg):
NameError: global name 'msg' is not defined


Script:
'bcbio_nextgen.py' 'runfn' 'variantcall_batch_region' 'cwl' 'sentinel_runtime=cores,16,ram,57344' 'sentinel_parallel=batch-parallel' 'sentinel_outputs=vrn_file_region,region_block' 'sentinel_inputs=batch_rec:record,region_block:var'