fragment insertion plug in error

Technical Support
1

Hi everyone
I have seen other posts on this matter but I don't think the issue was resolved in those cases. I am running qiime2-2022.11 in conda on a macbook pro MacOS Big Sur 11.3.1, Intel Core i9 with 64GB of RAM.
I ran the fragment insert plugin:

(qiime2-2022.11) [email protected] Abeni % qiime fragment-insertion sepp
--i-representative-sequences ./complete-rep-seqs.qza
--i-reference-database sepp-refs-gg-13-8.qza
--o-tree ./HHS_preterm_tree.qza
--o-placements ./HHS_preterm_tree_placements.qza
--p-threads 1

Here is the input file:
complete-rep-seqs.qza (2.0 MB)

After four days of processing I got this error:

Plugin error from fragment-insertion:

Command '['run-sepp.sh', '/var/folders/sh/bt1662zx00j4d45h9855jqy00000gn/T/qiime2/fernandonieto/data/8218c03b-568f-41dd-ac4a-e2f0e6b6d3cc/data/dna-sequences.fasta', 'q2-fragment-insertion', '-x', '1', '-A', '1000', '-P', '5000', '-a', '/var/folders/sh/bt1662zx00j4d45h9855jqy00000gn/T/qiime2/fernandonieto/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/aligned-dna-sequences.fasta', '-t', '/var/folders/sh/bt1662zx00j4d45h9855jqy00000gn/T/qiime2/fernandonieto/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/tree.nwk', '-r', '/var/folders/sh/bt1662zx00j4d45h9855jqy00000gn/T/qiime2/fernandonieto/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt']' returned non-zero exit status 1.

Debug info has been saved to /var/folders/sh/bt1662zx00j4d45h9855jqy00000gn/T/qiime2-q2cli-err-o1qcbq_s.log

Here is the debug info:

"Traceback (most recent call last):
File "/Users/fernandonieto/opt/miniconda3/envs/qiime2-2022.11/lib/python3.8/site-packages/q2cli/commands.py", line 352, in call
results = action(**arguments)
File "", line 2, in sepp
File "/Users/fernandonieto/opt/miniconda3/envs/qiime2-2022.11/lib/python3.8/site-packages/qiime2/sdk/action.py", line 234, in bound_callable
outputs = self.callable_executor(scope, callable_args,
File "/Users/fernandonieto/opt/miniconda3/envs/qiime2-2022.11/lib/python3.8/site-packages/qiime2/sdk/action.py", line 381, in callable_executor
output_views = self._callable(**view_args)
File "/Users/fernandonieto/opt/miniconda3/envs/qiime2-2022.11/lib/python3.8/site-packages/q2_fragment_insertion/_insertion.py", line 71, in sepp
(qiime2-2022.11) [email protected] Abeni % less /var/folders/sh/bt1662zx00j4d45h9855jqy00000gn/T/qiime2-q2cli-err-o1qcbq_s.log

Removing /var/folders/sh/bt1662zx00j4d45h9855jqy00000gn/T/sepp-tmp-XXXXXXXXXX.e6995Csp
Traceback (most recent call last):
File "/Users/fernandonieto/opt/miniconda3/envs/qiime2-2022.11/lib/python3.8/site-packages/q2cli/commands.py", line 352, in call
results = action(**arguments)
File "", line 2, in sepp
File "/Users/fernandonieto/opt/miniconda3/envs/qiime2-2022.11/lib/python3.8/site-packages/qiime2/sdk/action.py", line 234, in bound_callable
outputs = self.callable_executor(scope, callable_args,
File "/Users/fernandonieto/opt/miniconda3/envs/qiime2-2022.11/lib/python3.8/site-packages/qiime2/sdk/action.py", line 381, in callable_executor
output_views = self._callable(**view_args)
File "/Users/fernandonieto/opt/miniconda3/envs/qiime2-2022.11/lib/python3.8/site-packages/q2_fragment_insertion/_insertion.py", line 71, in sepp
_run(str(representative_sequences.file.view(DNAFASTAFormat)),
File "/Users/fernandonieto/opt/miniconda3/envs/qiime2-2022.11/lib/python3.8/site-packages/q2_fragment_insertion/_insertion.py", line 53, in _run
subprocess.run(cmd, check=True, cwd=cwd)
File "/Users/fernandonieto/opt/miniconda3/envs/qiime2-2022.11/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['run-sepp.sh', '/var/folders/sh/bt1662zx00j4d45h9855jqy00000gn/T/qiime2/fernandonieto/data/8218c03b-568f-41dd-ac4a-e2f0e6b6d3cc/data/dna-sequences.fasta', 'q2-fragment-insertion', '-x', '1', '-A', '1000', '-P', '5000', '-a', '/var/folders/sh/bt1662zx00j4d45h9855jqy00000gn/T/qiime2/fernandonieto/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/aligned-dna-sequences.fasta', '-t', '/var/folders/sh/bt1662zx00j4d45h9855jqy00000gn/T/qiime2/fernandonieto/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/tree.nwk', '-r', '/var/folders/sh/bt1662zx00j4d45h9855jqy00000gn/T/qiime2/fernandonieto/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt']' returned non-zero exit status 1."

Any help will be greatly appreciated.
Thank you
Fernando

2

Hi @nietof,

Thanks for reaching out!

Can you please try re-running your command with the --debug flag included? This will give us better debugging info do help determine where the source of the issue is coming from. Thanks! :lizard:

3

Ok will do, it took four days to run, should I increase the number of threads? will that speed it up?
Thank you regards
Fernando

4
5

Hi @nietof,

Yes, increasing threads should speed things up! Cheers :lizard:

6
7

Hi lizgehret
It worked this time. I think increasing the threads to 3 made it work.
thank you
Fernando

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8

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