Hi everyone.

I'm working with sdRADseq data and I am trying to do the reference assembly pipeline.

At step 3, I got the next error

Step 3: Clustering/Mapping reads within samples
  [####################] 100% 0:28:32 | indexing reference     
  [####################] 100% 0:00:01 | concatenating          
  [####################] 100% 0:00:40 | dereplicating          
  [####################] 100% 0:11:09 | mapping reads          

  Encountered an Error.
  Message: IPyradError: bwa error: None
  Use debug flag (-d) for full code traceback.

I'm working with ipyrad [v.0.7.30] on a HPC cluster. I don't know why I can do to solve that.

using de -d flag I get this:

python2.7/site-packages/bin/bedtools-linux-x86_64', 'bamtobed', '-i', '/panfs/roc/groups/14/mcgaughs/mgarduos/ipyrad/radseq_refmapping/TRIM_T7548_S8001-mapped-sorted.bam'] ['/home/mcgaughs/mgarduos/software/ls/lib/python2.7/site-packages/bin/bedtools-linux-x86_64', 'merge', '-d', '-10', '-i', '-']
2019-10-14 14:45:07,857     pid=24965   [assembly.py]   ERROR   IPyradError(None)
2019-10-14 14:45:08,908     pid=24965   [assembly.py]   INFO    interrupted engine 2 w/ SIGINT to 25036
2019-10-14 14:45:08,937     pid=24965   [assembly.py]   INFO    interrupted engine 12 w/ SIGINT to 25152
2019-10-14 14:45:08,958     pid=24965   [assembly.py]   INFO    interrupted engine 18 w/ SIGINT to 25225
2019-10-14 14:45:09,976     pid=24965   [assembly.py]   INFO      shutting down engines
2019-10-14 14:45:10,029     pid=24965   [assembly.py]   INFO      finished shutdown
2019-10-14 14:45:10,033     pid=24965   [__init__.py]   INFO    debugging turned off

I hope that someone could help me with mi issue.