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Ecogenomics / BamM

Metagenomics-focused BAM file manipulation
http://ecogenomics.github.io/BamM/
GNU Lesser General Public License v3.0
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bamm make crashes if bwa is not on the system path #8

Closed donovan-h-parks closed 9 years ago

donovan-h-parks commented 9 years ago

Calling bamm make causes a system crash if bwa is not on the system path:

/bin/sh: 1: bwa: not found Traceback (most recent call last): File "/srv/sw/BamM/1.0.0/bin/bamm", line 433, in doWork(args) File "/srv/sw/BamM/1.0.0/bin/bamm", line 102, in doWork BS.BMs[0].makeDatabase() File "/srv/sw/BamM/1.0.0/lib/python2.7/site-packages/bamm/bamMaker.py", line 460, in makeDatabase shell=True) File "/srv/sw/python/2.7.4/lib/python2.7/subprocess.py", line 542, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command 'bwa index ../../binning/bins_refined/bin_9.fna' returned non-zero exit status 127

donovan-h-parks commented 9 years ago

The same issue exists for samtools.

minillinim commented 9 years ago

Fixed for both. Now it crashes early, and nicely.