thread.error: can't start new thread

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Nick

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Nov 14, 2019, 3:53:19 AM11/14/19
to HUMAnN Users
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

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Nov 14, 2019, 4:24:58 PM11/14/19
to HUMAnN Users
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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