Error from fragment-insertion

[Lisou]

Hello Qiime2 forum community! Qiime2 beginner here. I've been receiving an error when using the fragment-insertion plugin:

(qiime2-2022.8) lisou@DESKTOP-OO5NL0A:~/EMW2022bees$ qiime fragment-insertion sepp
--i-representative-sequences EW_rep_seqs.qza
--i-reference-database sepp-refs-silva-128.qza
--o-tree $output/EW_sepp_tree.qza
--o-placements $output/EW_sepp_placements.qza
--verbose
--p-threads 16

Removing /tmp/tmp.tAoEddVqNR/sepp-tmp-1BAl9bds7E
Traceback (most recent call last):
File "/home/lisou/anaconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2cli/commands.py", line 339, in call
results = action(**arguments)
File "", line 2, in sepp
File "/home/lisou/anaconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/qiime2/sdk/action.py", line 234, in bound_callable
outputs = self.callable_executor(scope, callable_args,
File "/home/lisou/anaconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/qiime2/sdk/action.py", line 381, in callable_executor
output_views = self._callable(**view_args)
File "/home/lisou/anaconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2_fragment_insertion/_insertion.py", line 71, in sepp
_run(str(representative_sequences.file.view(DNAFASTAFormat)),
File "/home/lisou/anaconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2_fragment_insertion/_insertion.py", line 53, in _run
subprocess.run(cmd, check=True, cwd=cwd)
File "/home/lisou/anaconda3/envs/qiime2-2022.8/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['run-sepp.sh', '/tmp/qiime2/lisou/data/b4ddb03a-b161-4ea5-8123-309e86595f69/data/dna-sequences.fasta', 'q2-fragment-insertion', '-x', '16', '-A', '1000', '-P', '5000', '-a', '/tmp/qiime2/lisou/data/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/aligned-dna-sequences.fasta', '-t', '/tmp/qiime2/lisou/data/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/tree.nwk', '-r', '/tmp/qiime2/lisou/data/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/raxml-info.txt']' returned non-zero exit status 1.

Plugin error from fragment-insertion:
**> **
> Command '['run-sepp.sh', '/tmp/qiime2/lisou/data/b4ddb03a-b161-4ea5-8123-309e86595f69/data/dna-sequences.fasta', 'q2-fragment-insertion', '-x', '16', '-A', '1000', '-P', '5000', '-a', '/tmp/qiime2/lisou/data/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/aligned-dna-sequences.fasta', '-t', '/tmp/qiime2/lisou/data/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/tree.nwk', '-r', '/tmp/qiime2/lisou/data/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/raxml-info.txt']' returned non-zero exit status 1.
**> **
> See above for debug info.

Could anyone share what this error means?
I downloaded 'sepp-refs-silva-128.qza' from docs/source/data-resources.rst at master · qiime2/docs · GitHub

Thank you!

[lizgehret]

Hi @Lisou,

Thanks for reaching out! Can you please re-run your command with the --p-debug flag included? This will give us some additional details on this error message. Thanks!

[Lisou]

debug fragment-insertion 6-10-2022.txt (695.0 KB)

In a whooping 272 pages, here is the debug report!

[lizgehret]

Hi @Lisou,

Thanks for re-running and sharing your debug file - I did find something in there that gave me a good lead:

 return code: -11

How are you running QIIME 2 (conda, virtual machine, etc)? And what machine/OS are you using?

I found another forum post from a WSL user that references this same return code that may have a few helpful things for you to try:

fragment-insertion sepp debug help

Running this command qiime fragment-insertion sepp \ --i-representative-sequences output/representative_sequences.qza \ --i-reference-database input/sepp-refs-silva-128.qza \ --o-tree output/rooted_tree \ --o-placements output/placements \ --p-threads 12 \ --verbose \ --p-debug with the edit to run-sepp.sh mentioned here (is this the same as the debug flag?) yields the following message: File "/home/dylan/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/q2cli/commands.py", line…

Take a look and see if that's helpful - otherwise we'll keep digging! Cheers

[Lisou]

Hi Liz!

I think we're onto something here - looks like I do have the same problem as what was discussed in this forum. I am also running WSL with Ubuntu 20.04, with a 12 core processor and 32 gigs of RAM.

I don't see a solution on the forum post, except that they changed over to using OS ... :S

[lizgehret]

Hi @Lisou,

There were a couple of suggestions in this reply, but if those don't work it may be just as Matt mentions at the end of that post:

Sounds to me like maybe you didn’t have enough memory allocated in WSL

If possible, try allocating more memory within WSL - or try running this command on a different machine (again, if possible) to see if that changes things.

Cheers