error from fragment-insertion sepp

Hi,

I just run into a similar error. I'm using Qiime2-2020.8 and I have 128GB (and 500GB for hard drive) and 16 CPUs. I'm working with 2 fasta qc files forward and reverse (each file is 25MB on average). All run well including taxonomy classification. The error showed when I run the fragment-insertion sepp. I'm including below the commands I use, the log file error I obtained and the message too.

qiime fragment-insertion sepp
--i-representative-sequences boiling_dada2_rep-seqs.qza
--i-reference-database sepp-refs-silva-128.qza
--o-tree boiling_dada2_tree.qza
--o-placements boiling_tree_dada2_placements.qza
--p-threads 14


Removing /tmp/tmp.MXIwpOlLjy/sepp-tmp-imXUDDyhlE
Traceback (most recent call last):
File "/opt/conda/envs/qiime2-2020.8/lib/python3.6/site-packages/q2cli/commands.py", line 329, in call
results = action(**arguments)
File "", line 2, in sepp
File "/opt/conda/envs/qiime2-2020.8/lib/python3.6/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
output_types, provenance)
File "/opt/conda/envs/qiime2-2020.8/lib/python3.6/site-packages/qiime2/sdk/action.py", line 390, in callable_executor
output_views = self._callable(**view_args)
File "/opt/conda/envs/qiime2-2020.8/lib/python3.6/site-packages/q2_fragment_insertion/_insertion.py", line 77, in sepp
debug)
File "/opt/conda/envs/qiime2-2020.8/lib/python3.6/site-packages/q2_fragment_insertion/_insertion.py", line 53, in _run
subprocess.run(cmd, check=True, cwd=cwd)
File "/opt/conda/envs/qiime2-2020.8/lib/python3.6/subprocess.py", line 438, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run-sepp.sh', '/tmp/qiime2-archive-kwte99ss/3407a126-de9d-4a83-9f9f-93c4b6bd8503/data/dna-sequences.fasta', 'q2-fragment-insertion', '-x', '14', '-A', '1000', '-P', '5000', '-a', '/tmp/qiime2-archive-g8_r8d_m/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/aligned-dna-sequences.fasta', '-t', '/tmp/qiime2-archive-g8_r8d_m/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/tree.nwk', '-r', '/tmp/qiime2-archive-g8_r8d_m/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/raxml-info.txt']' returned non-zero exit status 1.

Would appreciate any help.
Thank you!

Hi @rosave,

Thanks for reaching out! :qiime2:

Can you please try the following:

  • Installing the latest version of QIIME 2 (install guide can be found here)
  • Re-running the same command above, but including the --verbose flag after your last parameter, and copy/pasting the full terminal output in your response.

Thank you! :lizard:

Hi Thanks so much! I downloaded the latest version of qiime 2021.11 and re-run the command including --verbose in the end.
These are errors I get

File "/opt/conda/envs/qiime2-2021.11/lib/python3.8/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
outputs = self.callable_executor(scope, callable_args,
File "/opt/conda/envs/qiime2-2021.11/lib/python3.8/site-packages/qiime2/sdk/action.py", line 391, in callable_executor
output_views = self._callable(**view_args)
File "/opt/conda/envs/qiime2-2021.11/lib/python3.8/site-packages/q2_fragment_insertion/_insertion.py", line 71, in sepp
_run(str(representative_sequences.file.view(DNAFASTAFormat)),
File "/opt/conda/envs/qiime2-2021.11/lib/python3.8/site-packages/q2_fragment_insertion/_insertion.py", line 53, in run
subprocess.run(cmd, check=True, cwd=cwd)
File "/opt/conda/envs/qiime2-2021.11/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['run-sepp.sh', '/tmp/qiime2-archive-pitmg2a
/3407a126-de9d-4a83-9f9f-93c4b6bd8503/data/dna-sequences.fasta', 'q2-fragment-insertion', '-x', '14', '-A', '1000', '-P', '5000', '-a', '/tmp/qiime2-archive-p1ryk7wr/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/aligned-dna-sequences.fasta', '-t', '/tmp/qiime2-archive-p1ryk7wr/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/tree.nwk', '-r', '/tmp/qiime2-archive-p1ryk7wr/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-archive-pitmg2a_/3407a126-de9d-4a83-9f9f-93c4b6bd8503/data/dna-sequences.fasta', 'q2-fragment-insertion', '-x', '14', '-A', '1000', '-P', '5000', '-a', '/tmp/qiime2-archive-p1ryk7wr/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/aligned-dna-sequences.fasta', '-t', '/tmp/qiime2-archive-p1ryk7wr/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/tree.nwk', '-r', '/tmp/qiime2-archive-p1ryk7wr/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/raxml-info.txt']' returned non-zero exit status 1.

See above for debug info.

Would appreciate any advice. Thanks!

Sorry, just noticed the full error wasn't copied. I re-run it and here's the full error.

Traceback (most recent call last):
File "/opt/conda/envs/qiime2-2021.11/lib/python3.8/site-packages/q2cli/commands.py", line 339, in call
results = action(**arguments)
File "", line 2, in sepp
File "/opt/conda/envs/qiime2-2021.11/lib/python3.8/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
outputs = self.callable_executor(scope, callable_args,
File "/opt/conda/envs/qiime2-2021.11/lib/python3.8/site-packages/qiime2/sdk/action.py", line 391, in callable_executor
output_views = self._callable(**view_args)
File "/opt/conda/envs/qiime2-2021.11/lib/python3.8/site-packages/q2_fragment_insertion/_insertion.py", line 71, in sepp
_run(str(representative_sequences.file.view(DNAFASTAFormat)),
File "/opt/conda/envs/qiime2-2021.11/lib/python3.8/site-packages/q2_fragment_insertion/_insertion.py", line 53, in _run
subprocess.run(cmd, check=True, cwd=cwd)
File "/opt/conda/envs/qiime2-2021.11/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['run-sepp.sh', '/tmp/qiime2-archive-mcuo6q2x/3407a126-de9d-4a83-9f9f-93c4b6bd8503/data/dna-sequences.fasta', 'q2-fragment-insertion', '-x', '14', '-A', '1000', '-P', '5000', '-a', '/tmp/qiime2-archive-z45ljmdo/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/aligned-dna-sequences.fasta', '-t', '/tmp/qiime2-archive-z45ljmdo/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/tree.nwk', '-r', '/tmp/qiime2-archive-z45ljmdo/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-archive-mcuo6q2x/3407a126-de9d-4a83-9f9f-93c4b6bd8503/data/dna-sequences.fasta', 'q2-fragment-insertion', '-x', '14', '-A', '1000', '-P', '5000', '-a', '/tmp/qiime2-archive-z45ljmdo/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/aligned-dna-sequences.fasta', '-t', '/tmp/qiime2-archive-z45ljmdo/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/tree.nwk', '-r', '/tmp/qiime2-archive-z45ljmdo/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/raxml-info.txt']' returned non-zero exit status 1.

See above for debug info.
(qiime2-2021.11) [email protected]:/workspace#

Hi @rosave,

Thanks for providing those details! Apologies for making you re-run this command again, but can you try your same command with both the --verbose and --debug flags? The error you are receiving is coming from sepp, so we just need some additional logs to decipher what's causing the problem. Thanks! :lizard:

This is what I get. I run this in screen mode so I can only see this far. I'll try running in the main but it took kinda long and I was afraid it was going to disconnect

File "/opt/conda/envs/qiime2-2021.11/lib/python3.8/site-packages/q2cli/commands.py", line 339, in call
results = action(**arguments)
File "", line 2, in sepp
File "/opt/conda/envs/qiime2-2021.11/lib/python3.8/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
outputs = self.callable_executor(scope, callable_args,
File "/opt/conda/envs/qiime2-2021.11/lib/python3.8/site-packages/qiime2/sdk/action.py", line 391, in callable_executor
output_views = self._callable(**view_args)
File "/opt/conda/envs/qiime2-2021.11/lib/python3.8/site-packages/q2_fragment_insertion/_insertion.py", line 71, in sepp
_run(str(representative_sequences.file.view(DNAFASTAFormat)),
File "/opt/conda/envs/qiime2-2021.11/lib/python3.8/site-packages/q2_fragment_insertion/_insertion.py", line 53, in _run
subprocess.run(cmd, check=True, cwd=cwd)
File "/opt/conda/envs/qiime2-2021.11/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['run-sepp.sh', '/tmp/qiime2-archive-bcz5b8me/4b3d3b64-4723-4b70-8eb7-0cf009dccfc9/data/dna-sequences.fasta', 'q2-fragment-insertion', '-x', '14', '-A', '1000', '-P', '5000', '-a', '/tmp/qiime2-archive-gq3oi4v4/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/aligned-dna-sequences.fasta', '-t', '/tmp/qiime2-archive-gq3oi4v4/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/tree.nwk', '-r', '/tmp/qiime2-archive-gq3oi4v4/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/raxml-info.txt', '-b', '1']' returned non-zero exit status 1.

Plugin error from fragment-insertion:

Command '['run-sepp.sh', '/tmp/qiime2-archive-bcz5b8me/4b3d3b64-4723-4b70-8eb7-0cf009dccfc9/data/dna-sequences.fasta', 'q2-fragment-insertion', '-x', '14', '-A', '1000', '-P', '5000', '-a', '/tmp/qiime2-archive-gq3oi4v4/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/aligned-dna-sequences.fasta', '-t', '/tmp/qiime2-archive-gq3oi4v4/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/tree.nwk', '-r', '/tmp/qiime2-archive-gq3oi4v4/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/raxml-info.txt', '-b', '1']' returned non-zero exit status 1.

See above for debug info.

Hi @rosave,

I'm still not seeing anything in this traceback that indicates where this error is coming from. If you run this command again without the --verbose and --debug flags, the full error log should be saved to a file on your machine. Can you re-run and then share the associated debug file with me? You can attach it to your subsequent message, or in a private message with me directly - whichever you prefer!

You mean just running the command as original (see below)? I don't need to include something else for the full error log to be created? Because if so maybe I can go to my older files and see if it's still there. Under what name does this error log typically gets created?

qiime fragment-insertion sepp
--i-representative-sequences boiling_dada2_rep-seqs.qza
--i-reference-database sepp-refs-silva-128.qza
--o-tree boiling_dada2_tree.qza
--o-placements boiling_tree_dada2_placements.qza
--p-threads 14

Hi @rosave,

Yes, that's correct - the file will always have a different name, so I would just recommend re-running the command. When it fails, the terminal output will include the name of the associated file with the error log, so you'll know its name from there.

Cheers :lizard:

Will this also be the case if I run it on screen?

Hi @lizgehret
This is the error file I obtained. Thanks SO much for your help! I'll send you the actual log file privately. Thanks!

Removing /tmp/tmp.BpqWDmfL9I/sepp-tmp-vlgloemUuM
Traceback (most recent call last):
File "/opt/conda/envs/qiime2-2021.11/lib/python3.8/site-packages/q2cli/commands.py", line 339, in call
results = action(**arguments)
File "", line 2, in sepp
File "/opt/conda/envs/qiime2-2021.11/lib/python3.8/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
outputs = self.callable_executor(scope, callable_args,
File "/opt/conda/envs/qiime2-2021.11/lib/python3.8/site-packages/qiime2/sdk/action.py", line 391, in callable_executor
output_views = self._callable(**view_args)
File "/opt/conda/envs/qiime2-2021.11/lib/python3.8/site-packages/q2_fragment_insertion/_insertion.py", line 71, in sepp
_run(str(representative_sequences.file.view(DNAFASTAFormat)),
File "/opt/conda/envs/qiime2-2021.11/lib/python3.8/site-packages/q2_fragment_insertion/_insertion.py", line 53, in _run
subprocess.run(cmd, check=True, cwd=cwd)
File "/opt/conda/envs/qiime2-2021.11/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['run-sepp.sh', '/tmp/qiime2-archive-qvyfoss9/3407a126-de9d-4a83-9f9f-93c4b6bd8503/data/dna-sequences.fasta', 'q2-fragment-insertion', '-x', '14', '-A', '1000', '-P', '5000', '-a', '/tmp/qiime2-archive-8i7awzcw/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/aligned-dna-sequences.fasta', '-t', '/tmp/qiime2-archive-8i7awzcw/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/tree.nwk', '-r', '/tmp/qiime2-archive-8i7awzcw/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/raxml-info.txt']' returned non-zero exit status 1.

@rosave,

Thanks for sending over your error log! I'm checking in with a few other folks on this, so hang tight. I appreciate your patience! :lizard:

@rosave,

Thanks again for your patience here! I have a couple of things I'd like you to try - can you download the latest references (from our 2022.2 release) for silva-128 and greengenes, and try using both of those as your --i-reference-database (on separate runs) and see if you are successful? I'm wondering if the issue is potentially a bad ref database.

Please copy/paste the full output from your terminal if you are still running into an error, and we'll go from there!

Cheers :lizard:

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