Run-sepp.sh returned non-zero exit status 1

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1

Hello all,

I have been trying to run some sequences through fragment-insertion sepp. I get the same error when running on mac osx and linux. It is running on a qza I created from a fasta rep set file generated in a custom qiime 1 analysis where OTUs were picked on DADA2 sequences. The full error from running on a linux system is below.

Removing /tmp/tmp.6ekomwa03h/sepp-tmp-bSNAB
Traceback (most recent call last):
  File "/Users/mish0397/miniconda3/envs/qiime2-2018.4/lib/python3.5/site-packages/q2cli/command
s.py", line 274, in __call__
    results = action(**arguments)
  File "<decorator-gen-382>", line 2, in sepp
  File "/Users/mish0397/miniconda3/envs/qiime2-2018.4/lib/python3.5/site-packages/qiime2/sdk/action.py", line 366, in _callable_executor_
    output_views = self._callable(**view_args)
  File "/Users/mish0397/miniconda3/envs/qiime2-2018.4/lib/python3.5/site-packages/q2_fragment_insertion-2018.2.0.dev0-py3.5.egg/q2_fragment_insertion/_insertion.py", line 184, in sepp
    reference_alignment, reference_phylogeny, reference_info)
  File "/Users/mish0397/miniconda3/envs/qiime2-2018.4/lib/python3.5/site-packages/q2_fragment_insertion-2018.2.0.dev0-py3.5.egg/q2_fragment_insertion/_insertion.py", line 136, in _run
    subprocess.run(cmd, check=True, cwd=cwd)
  File "/Users/mish0397/miniconda3/envs/qiime2-2018.4/lib/python3.5/subprocess.py", line 398, in run
    output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run-sepp.sh', '/tmp/qiime2-archive-z99a0cb4/5d99e020-3075-4171-bac3-82b695fe4055/data/dna-sequences.fasta', 'q2-fragment-insertion', '-x', '3', '-A', '1000', '-P', '5000']' returned non-zero exit status 1

Plugin error from fragment-insertion:

  Command '['run-sepp.sh', '/tmp/qiime2-archive-z99a0cb4/5d99e020-3075-4171-bac3-82b695fe4055/data/dna-sequences.fasta', 'q2-fragment-insertion', '-x', '3', '-A', '1000', '-P', '5000']' returned non-zero exit status 1

See above for debug info.
2

Hi Michael,

Danger - please do not run the commands listed in this "detail" section

unfortunately, the error message is not too speaking. Thus, my first step would be to modify SEPP to report a little more verbose error messages. You should find the according run-sepp.sh script in /Users/mish0397/miniconda3/envs/qiime2-2018.4/bin/run-sepp.sh

Use your favourite text editor. Search for the line trap cleanup EXIT and comment it our, i.e. add a # in front of the line. Re-run qiime and hope that the error message is more verbose.

How many CPU cores do you have on your system? Looks like you specified to use 3 threads. You could try to reduce to just 1.

3

Hello Stefan,

I commented out that line and reran. When I run via qiime2 with one or more cores I still get a crash and the error message is about the same.

I also tried running the command that the plugin is calling directly and had a successful run when not providing the -x parameter but got errors when running with -x 1 and -x 10. I have attached error logs from running the commands run-sepp.sh rep_set/dna-sequences.fasta q2-fragment-insertion -A 1000 -P 5000, run-sepp.sh rep_set/dna-sequences.fasta q2-fragment-insertion -A 1000 -P 5000 -x 1 and run-sepp.sh rep_set/dna-sequences.fasta q2-fragment-insertion -A 1000 -P 5000 -x 10 with name based on the x parameter provided. I can reproduce this on mac as well.

qiime2 always runs with the x parameter so that looks like a problem here.

Mike

sepp-q2-fragment-insertion-err.x0.txt (157.8 KB)
sepp-q2-fragment-insertion-err.x1.txt (330.5 KB)
sepp-q2-fragment-insertion-err.x10.txt (1.1 MB)

4

Hi Mike,

I looked through your error files and saw error message that I don’t really understand. I notified the main developer about your issues.
Looks to me like there is at some point a problem with the distribution of the parallel processes. Are you sure you have enough disk space on your system(s). How many different sOTU sequences are in your input?

Best,
Stefan

5

Hi Stefan,

Thanks for bringing in the main developer. I definitely have enough disk space. There are 1660 sequences.

Mike

6

Hi Mike,

turns out your problem isn’t that easy to solve. Would you mind sending us your input for further debugging to my email address: sjanssen@ucsd.edu

Thanks
Stefan

1 Like
7

I sent it to you via email. Thanks for looking into this Stefan.

Mike

8

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