I'm using a python package with python subprocessing command. When I qsub several jobs in parallel, it shows the error: subprocess.CalledProcessError: died with
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/anaconda3/envs/lib/python3.6/multiprocessing/pool.py", line 119, in worker
result = (True, func(*args, **kwds))
File "/anaconda3/envs/syniu/lib/python3.6/subprocess.py", line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['bismark', '/fasta', '--bowtie2', 'R1.trimed.fq.gz', '--pbat', '-o', '/M1-1-2-A3', '--temp_dir', '/M1-1-2-A3']' died with <Signals.SIGPIPE: 13>.
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/anaconda3/envs/bin/yap", line 11, in <module>
sys.exit(main())
File "/anaconda3/envs/lib/python3.6/site-packages/__main__.py", line 970, in main
func(**args_vars)
File "/anaconda3/envs/lib/python3.6/site-packages/mapping/pipeline.py", line 263, in pipeline
bismark_df = bismark(fastq_final_df, out_dir, config)
File "/anaconda3/envs/lib/python3.6/site-packages/mapping/bismark.py", line 135, in bismark
result.get()
File "/anaconda3/envs/lib/python3.6/multiprocessing/pool.py", line 670, in get
raise self._value
subprocess.CalledProcessError: Command '['bismark', '/fasta', '--bowtie2', 'R1.trimed.fq.gz', '--pbat', '-o', '/M1-1-2-A3', '--temp_dir', '/M1-1-2-A3']' died with <Signals.SIGPIPE: 13>.
Any good suggestion?