thread.error: can't start new thread

[Nick]

I encounter a problem at the very last step of Humann2 where I get this error:

humann2 --input samp.fastq.gz --output results/samp --threads 24 --verbose --remove-temp-output --memory-use maximum > logs/samp.log 2>&1

...

Computing pathways abundance and coverage ...
Traceback (most recent call last):
  File "/home/nickchengg/anaconda3/envs/humann2/bin/humann2", line 11, in <module>
    sys.exit(main())
  File "/home/nickchengg/anaconda3/envs/humann2/lib/python2.7/site-packages/humann2/humann2.py", line 1066, in main
    gene_scores, reactions_database, pathways_database)
  File "/home/nickchengg/anaconda3/envs/humann2/lib/python2.7/site-packages/humann2/quantify/modules.py", line 154, in identify_reactions_and_pathways
    utilities.command_threading(config.threads,minpath_commands)
  File "/home/nickchengg/anaconda3/envs/humann2/lib/python2.7/site-packages/humann2/utilities.py", line 598, in command_threading
    worker.start()
  File "/home/nickchengg/anaconda3/envs/humann2/lib/python2.7/threading.py", line 736, in start
    _start_new_thread(self.__bootstrap, ())
thread.error: can't start new thread

I've raised my ulimit settings very high so I don't think that's the issue. 

Has anyone encountered this problem? I've tried other samples that work just fine with humann2 but this one refuses to finish running for some reason.

[Lauren McIver]

Hello Nick - It is possible another process is also running on the machine? If you reduce the number of threads it should resolve the issue. 

Thanks!

Lauren

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