vsearch unrecognized option '--qseqout'

Technical Support
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1

Running qiime2 2022.2 (because of old processors that are not compatible with later versions). Running qiime rescript extract-seq-segments and I get an error with vsearch that the --qsegout parameter does not exist. Is this a problem with mismatched vsearch and qiime2 versions? vsearch is v2.7.0_linux_x86_64 .

Here's the code and error:

qiime rescript extract-seq-segments \
--i-input-sequences musselnd1-ref-database-derep-seqs.qza \
--i-reference-segment-sequences musselnd1-ref-database-derep2x-culled-filtered-seqs.qza \
--p-perc-identity 0.7 \
--p-min-seq-len 10 \
--p-threads 10 \
--o-extracted-sequence-segments musselnd1-ref-database-extracted-filtered-seqs-01.qza \
--o-unmatched-sequences musselnd1-ref-database-unmatched-sequences-01.qza \
--verbose

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: vsearch --usearch_global /scratch/tangled/tmp/qiime2-archive-06q0mw51/61ca6db3-a86f-4a0d-9003-e134ca3b9b15/data/dna-sequences.fasta --db /scratch/tangled/tmp/qiime2-archi
ve-fg4addqm/e507ad96-eae8-4b8d-be5c-d4104b73b679/data/dna-sequences.fasta --id 0.7 --strand plus --threads 10 --qmask none --qsegout /scratch/tangled/tmp/q2-DNAFASTAFormat-6k3hsz2
e --notmatched /scratch/tangled/tmp/q2-DNAFASTAFormat-5cmdsrtt --minseqlength 10

vsearch: unrecognized option '--qsegout'
Traceback (most recent call last):
  File "/home/tangled/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2cli/commands.py", line 339, in __call__
    results = action(**arguments)
  File "<decorator-gen-513>", line 2, in extract_seq_segments
  File "/home/tangled/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
    outputs = self._callable_executor_(scope, callable_args,
  File "/home/tangled/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 391, in _callable_executor_
    output_views = self._callable(**view_args)
  File "/home/tangled/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/rescript/extract_seq_segments.py", line 50, in extract_seq_segments
    run_command(cmd)
  File "/home/tangled/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/rescript/_utilities.py", line 99, in run_command
    subprocess.run(cmd, check=True)
  File "/home/tangled/miniconda3/envs/qiime2-2022.2/lib/python3.8/subprocess.py", line 516, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['vsearch', '--usearch_global', '/scratch/tangled/tmp/qiime2-archive-06q0mw51/61ca6db3-a86f-4a0d-9003-e134ca3b9b15/data/dna-sequences.fasta
', '--db', '/scratch/tangled/tmp/qiime2-archive-fg4addqm/e507ad96-eae8-4b8d-be5c-d4104b73b679/data/dna-sequences.fasta', '--id', '0.7', '--strand', 'plus', '--threads', '10', '--q
mask', 'none', '--qsegout', '/scratch/tangled/tmp/q2-DNAFASTAFormat-6k3hsz2e', '--notmatched', '/scratch/tangled/tmp/q2-DNAFASTAFormat-5cmdsrtt', '--minseqlength', '10']' returned
 non-zero exit status 1.

Plugin error from rescript:

  Command '['vsearch', '--usearch_global', '/scratch/tangled/tmp/qiime2-archive-06q0mw51/61ca6db3-a86f-4a0d-9003-e134ca3b9b15/data/dna-sequences.fasta', '--db', '/scratch/tangled/
tmp/qiime2-archive-fg4addqm/e507ad96-eae8-4b8d-be5c-d4104b73b679/data/dna-sequences.fasta', '--id', '0.7', '--strand', 'plus', '--threads', '10', '--qmask', 'none', '--qsegout', '
/scratch/tangled/tmp/q2-DNAFASTAFormat-6k3hsz2e', '--notmatched', '/scratch/tangled/tmp/q2-DNAFASTAFormat-5cmdsrtt', '--minseqlength', '10']' returned non-zero exit status 1.

See above for debug info.
2

HI @alexkrohn,

The processors have little to do with compatibility in this case. I am able to run this code on computer hardware as far back as 2012. :man_technologist:

EDIT: unless related to the Intel to ARM processor. transition.

That version of QIIME 2 is likely too old. We added extract-seq-segments ~ late 2022, when the vsearch --qsegout option was added to vsearch 2.21 in January 2022, see their manual. Even though that version of QIIME 2 is from 2022, we could not immediately update the QIIME 2 vsearch version due to compatibility conflicts with other plugins at the time. So you'd have to install at least a late 2022 version of QIIME 2. Though I'd recommend just installing the latest version of QIIME 2.

2 Likes
3

That solved it. Thank you. I had tried to update a few years ago, but I think the ARM or Linux + ARM chips were unsupported at that time. Anyway, it appears the issue has been fixed and now my machine can run 2024.*

Thanks again!

2 Likes
4

Oh that's right! I forgot I was spoiled with OS X and Rosetta. But they've indeed updated things on the Linux side since then... I am even running a virtual Ununtu on my Mac arm chip via Rosetta.

1 Like