Commit 3f898bb9 by Eric Coissac

Catch the brokenPipeError generated when orgasmi stop after reaching the

maximum indexable read count.
parent 9014afff
......@@ -526,25 +526,31 @@ def run(config):
logger.info(" ".join(command))
if fconvert or rconvert:
if nopipe:
logger.info("Writting transformed sequence files...")
writeToFifo(pairs,forward,reverse,logger)
logger.info("Done.")
try:
if fconvert or rconvert:
if nopipe:
logger.info("Writting transformed sequence files...")
writeToFifo(pairs,forward,reverse,logger)
logger.info("Done.")
logger.info("Starting indexing...")
logger.info(" ".join(command))
os.system(" ".join(command))
else:
logger.info("Starting indexing...")
process=Popen(command)
writeToFifo(pairs,forward,reverse,logger)
process.wait()
logger.info('Done.')
else:
logger.info("Starting indexing...")
logger.info(" ".join(command))
os.system(" ".join(command))
else:
logger.info("Starting indexing...")
process=Popen(command)
writeToFifo(pairs,forward,reverse,logger)
process.wait()
logger.info('Done.')
else:
logger.info("Starting indexing...")
logger.info(" ".join(command))
os.system(" ".join(command))
except BrokenPipeError:
logger.warning("Maximum count of read indexed.")
logger.warning("Indexing stopped but the index is usable.")
r=Index(output)
......
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