Vsearch returned non-zero exit status -9 (probably due to trying to use too many threads)

User Support
1

Hi community =)

I recently ran the command; qiime vsearch cluster-features-de-novo --i-table table.qza --i-sequences rep-seqs.qza --o-clustered-table table-dn-99.qza --o-clustered-sequences rep-seqs-dn-99.qza --p-perc-identity 0.99 --p-threads 256 --verbose
on my nanopore data, im assuming the following went wrong because I assigned more threads than available to the process. Could anyone confirm/ suggest otherwise so I can be sure?

https://github.com/torognes/vsearch

Reading file /tmp/tmps5m1t0mi 100%  
57344087 nt in 40174 seqs, min 156, max 32769, avg 1427
Sorting by abundance 100%
Counting k-mers 100%  
Clustering 1%Traceback (most recent call last):
  File "/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/q2cli/commands.py", line 274, in __call__
    results = action(**arguments)
  File "<decorator-gen-120>", line 2, in cluster_features_de_novo
  File "/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/sdk/action.py", line 231, in bound_callable
    output_types, provenance)
  File "/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/sdk/action.py", line 362, in _callable_executor_
    output_views = self._callable(**view_args)
  File "/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/q2_vsearch/_cluster_features.py", line 193, in cluster_features_de_novo
    run_command(cmd)
  File "/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/q2_vsearch/_cluster_features.py", line 33, in run_command
    subprocess.run(cmd, check=True)
  File "/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/subprocess.py", line 398, in run
    output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['vsearch', '--cluster_size', '/tmp/tmps5m1t0mi', '--id', '0.99', '--centroids', '/tmp/q2-DNAFASTAFormat-wdqvhtkd', '--uc', '/tmp/tmpa6ngq1n7', '--qmask', 'none', '--xsize', '--threads', '256']' returned non-zero exit status -9

Plugin error from vsearch:

  Command '['vsearch', '--cluster_size', '/tmp/tmps5m1t0mi', '--id', '0.99', '--centroids', '/tmp/q2-DNAFASTAFormat-wdqvhtkd', '--uc', '/tmp/tmpa6ngq1n7', '--qmask', 'none', '--xsize', '--threads', '256']' returned non-zero exit status -9```


Thankyou!

Gus
2

hi all, as suspected it was too many threads and too little memory

I’ll leave this for anyone who has the same issue in the future

I ramped the memory up to 27gb of RAM with 10 cores and dropped the threads to 100

3 Likes
3

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