Run-sepp.sh error again

Hey there,
this issue is related/similar to the following but there was no follow up on the forum so I m afraid I have to bug you again:

I downloaded the latest qiime2 version (qiime2-2018.6) , activated qiime 2 environment and then installed fragment-insertionn using:

conda install -c https://conda.anaconda.org/biocore q2-fragment-insertion
qiime dev refresh-cache

I ran into the issue described on the website with PackageNotfound error, which I also solved as described on the github page (https://github.com/biocore/q2-fragment-insertion) - thank you for that…

conda install -c anaconda -c defaults -c conda-forge -c bioconda -c https://conda.anaconda.org/biocore q2-fragment-insertion
qiime dev refresh-cache

I tried running the following command on the rep-seqs output from dada2 in the moving pictures tutorial (ignore the joining of the dashes in the copied command):

qiime fragment-insertion sepp
–i-representative-sequences Downloads/rep-seqs.qza
–o-tree i-tree.qza
–o-placements insertion-placements.qza

and received the following error:

Plugin error from fragment-insertion:
Command ‘[‘run-sepp.sh’, ‘/var/folders/my/pq46r9ts5ns4b7xlvm1sk7m40000gn/T/qiime2-archive-ewpmr_fy/33e6372d-fab7-460b-89aa-b42b83262e03/data/dna-sequences.fasta’, ‘q2-fragment-insertion’, ‘-x’, ‘1’, ‘-A’, ‘1000’, ‘-P’, ‘5000’]’ returned non-zero exit status 1
Debug info has been saved to /var/folders/my/pq46r9ts5ns4b7xlvm1sk7m40000gn/T/qiime2-q2cli-err-wdv4qamf.log

less on the output file gives the following, which does not change after adding # to trap cleanup EXIT:

ages/q2cli/commands.py", line 274, in __call__
    results = action(**arguments)
  File "<decorator-gen-252>", line 2, in sepp
  File "/Users/rimachakaroun/anaconda/envs/qiime2-2018.6/lib/python3.5/site-packages/qiime2/sdk/action.py", line 232, in bound_callable
    output_types, provenance)
  File "/Users/rimachakaroun/anaconda/envs/qiime2-2018.6/lib/python3.5/site-packages/qiime2/sdk/action.py", line 367, in _callable_executor_
    output_views = self._callable(**view_args)
  File "/Users/rimachakaroun/anaconda/envs/qiime2-2018.6/lib/python3.5/site-packages/q2_fragment_insertion/_insertion.py", line 179, in sepp
    reference_alignment, reference_phylogeny, debug)
  File "/Users/rimachakaroun/anaconda/envs/qiime2-2018.6/lib/python3.5/site-packages/q2_fragment_insertion/_insertion.py", line 137, in _run
    subprocess.run(cmd, check=True, cwd=cwd)
  File "/Users/rimachakaroun/anaconda/envs/qiime2-2018.6/lib/python3.5/subprocess.py", line 398, in run
    output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run-sepp.sh', '/var/folders/my/pq46r9ts5ns4b7xlvm1sk7m40000gn/T/qiime2-archive-tbv78tgl/33e6372d-fab7-460b-89aa-b42b83262e03/data/dna-sequences.fasta', 'q2-fragment-insertion', '-x', '1', '-A', '1000', '-P', '5000']' returned non-zero exit status 1

thanks for the help in advance!
Rima

1 Like

This came up at STAMPS and I wasn’t able to figure out what was going on. @Stefan, any thoughts?

Hi Rima,

I just ran fragment-insertion on the freshly downloaded DADA2 rep-seqs and executed this command

qiime fragment-insertion sepp --i-representative-sequences rep-seqs-dada2.qza --o-tree i-tree.qza --o-placements insertion-placements.qza --p-debug --verbose 2> err.txt > out.txt

in a qiime2-2018.6 conda environment, which produces the artifacts without errors (placements are too large to upload). The file "err.txt" is empty (as expected) and the content of "out.txt" is attached.

i-tree.qza (2.3 MB)
out.txt (2.0 KB)

Can you copy and paste the result of conda list | grep frag?

@Stefan
just discovered the notification for this in my SPAM. sorry :S will get cracking and update this week.
Thanks for taking the time to reply and sorry again for not noticing earlier.
Rima

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