Plugin error from fragment-insertion:

Yiggrite · September 15, 2023, 10:04pm

Hi
I am running the Parkison mice sample data, and I have updated the Qiime2, and my computer have enough capacity. But I still met this problem. Could you please help me deal with it?

Command '['run-sepp.sh', '/tmp/qiime2-archive-6m4if51o/a3c55eab-dffc-426e-8521-3d193cab2fc0/data/dna-sequences.fasta', 'q2-fragment-insertion', '-x', '1', '-A', '1000', '-P', '5000', '-a', '/tmp/qiime2-archive-0s212g0k/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/aligned-dna-sequences.fasta', '-t', '/tmp/qiime2-archive-0s212g0k/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/tree.nwk', '-r', '/tmp/qiime2-archive-0s212g0k/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt']' returned non-zero exit status 1.

Debug info has been saved to /tmp/qiime2-q2cli-err-zys3hl94.log
(qiime2) yiggrite@MWMJ07RHBF:~/mouse_tutorial$ conda activate qiime2-2023.7

EnvironmentNameNotFound: Could not find conda environment: qiime2-2023.7
You can list all discoverable environments with conda info --envs.

(qiime2) yiggrite@MWMJ07RHBF:~/mouse_tutorial$ conda activate qiime2-2023.7
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
(qiime2-2023.7) yiggrite@MWMJ07RHBF:~/mouse_tutorial$ ls
dada2_rep_set.qza dada2_stats.qza dada2_table.qza dada2_table.qzv demultiplexed_seqs demultiplexed_seqs.zip demux_seqs.qza demux_seqs.qzv manifest.tsv metadata.qzv metadata.tsv sample_metadata.tsv sepp-refs-gg-13-8.qza
(qiime2-2023.7) yiggrite@MWMJ07RHBF:~/mouse_tutorial$ qiime fragment-insertion sepp
--i-re> --i-representative-sequences ./dada2_rep_set.qza \

--i-reference-database sepp-refs-gg-13-8.qza
--o-tree ./tree.qza
--o-placements ./tree_placements.qza
--p-threads 1
Plugin error from fragment-insertion:

Command '['run-sepp.sh', '/tmp/qiime2/yiggrite/data/a3c55eab-dffc-426e-8521-3d193cab2fc0/data/dna-sequences.fasta', 'q2-fragment-insertion', '-x', '1', '-A', '1000', '-P', '5000', '-a', '/tmp/qiime2/yiggrite/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/aligned-dna-sequences.fasta', '-t', '/tmp/qiime2/yiggrite/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/tree.nwk', '-r', '/tmp/qiime2/yiggrite/data/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt']' returned non-zero exit status 1.

Debug info has been saved to /tmp/qiime2-q2cli-err-ff9fv0o4.log
(qiime2-2023.7) yiggrite@MWMJ07RHBF:~/mouse_tutorial$

5cr34m · September 16, 2023, 10:27pm

Good evening.
Could you please post here cat /tmp/qiime2-q2cli-err-ff9fv0o4.log result?
Regards, sn

lizgehret · September 17, 2023, 2:56am

Hi @Yiggrite,

Can you please re-run your fragment-insertion command with the --debug flag and share the output in your response? Thanks!

Yiggrite · September 18, 2023, 5:00pm

(qiime2-2023.7) yiggrite@MWMJ07RHBF:~/mouse_tutorial$ qiime fragment-insertion sepp
--i-representative-sequences ./dada2_rep_set.qza
--i-reference-database sepp-refs-gg-13-> --i-representative-sequences ./dada2_rep_set.qza \

--i-reference-database sepp-refs-gg-13-8.qza
--o-tree ./tree.qza
--o-placements ./tree_placements.qza
--p-threads 1 \ --debug
Usage: qiime fragment-insertion sepp [OPTIONS]

Perform fragment insertion of sequences using the SEPP algorithm.

Inputs:
--i-representative-sequences ARTIFACT FeatureData[Sequence]
The sequences to insert into the reference tree.
[required]
--i-reference-database ARTIFACT SeppReferenceDatabase
The reference database to insert the representative
sequences into. [required]
Parameters:
--p-alignment-subset-size INTEGER
Each placement subset is further broken into subsets
of at most these many sequences and a separate HMM is
trained on each subset. [default: 1000]
--p-placement-subset-size INTEGER
The tree is divided into subsets such that each subset
includes at most these many subsets. The placement step
places the fragment on only one subset, determined
based on alignment scores. Further reading:
https://github.com/smirarab/sepp/blob/master/tutorial/s
epp-tutorial.md#sample-datasets-default-parameters.
[default: 5000]
--p-threads INTEGER The number of threads to use. [default: 1]
--p-debug / --p-no-debug
Collect additional run information to STDOUT for
debugging. Temporary directories will not be removed if
run fails. [default: False]
Outputs:
--o-tree ARTIFACT The tree with inserted feature data.
Phylogeny[Rooted] [required]
--o-placements ARTIFACT
Placements Information about the feature placements within the
reference tree. [required]
Miscellaneous:
--output-dir PATH Output unspecified results to a directory
--verbose / --quiet Display verbose output to stdout and/or stderr during
execution of this action. Or silence output if
execution is successful (silence is golden).
--example-data PATH Write example data and exit.
--citations Show citations and exit.
--help Show this message and exit.

                There was a problem with the command:

(1/1) Got unexpected extra argument ( --debug)
(qiime2-2023.7) yiggrite@MWMJ07RHBF:~/mouse_tutorial$

Did I do it right?

lizgehret · September 18, 2023, 5:24pm

Hi @Yiggrite,

You'll want to include the --verbose flag on its own line just like the rest of your commands. Here's what your command should look like:

qiime fragment-insertion sepp \
--i-representative-sequences ./dada2_rep_set.qza \
--i-reference-database sepp-refs-gg-13-8.qza \
--o-tree ./tree.qza \
--o-placements ./tree_placements.qza \
--p-threads 1 \
--debug

Cheers

Yiggrite · September 18, 2023, 5:33pm

Here is the result:
(qiime2-2023.7) yiggrite@MWMJ07RHBF:~/mouse_tutorial$ qiime fragment-insertion sepp
i-representative-sequences ./dada2_rep_set.qza
--i-reference-database sepp-refs-gg-13-8.qza
--o-tree ./tree.qza
--o-placements ./tree_placements.qza
--p-threads 1
--debug
Usage: qiime fragment-insertion sepp [OPTIONS]

Perform fragment insertion of sequences using the SEPP algorithm.

Inputs:
--i-representative-sequences ARTIFACT FeatureData[Sequence]
The sequences to insert into the reference tree.
[required]
--i-reference-database ARTIFACT SeppReferenceDatabase
The reference database to insert the representative
sequences into. [required]
Parameters:
--p-alignment-subset-size INTEGER
Each placement subset is further broken into subsets
of at most these many sequences and a separate HMM is
trained on each subset. [default: 1000]
--p-placement-subset-size INTEGER
The tree is divided into subsets such that each subset
includes at most these many subsets. The placement step
places the fragment on only one subset, determined
based on alignment scores. Further reading:
https://github.com/smirarab/sepp/blob/master/tutorial/s
epp-tutorial.md#sample-datasets-default-parameters.
[default: 5000]
--p-threads INTEGER The number of threads to use. [default: 1]
--p-debug / --p-no-debug
Collect additional run information to STDOUT for
debugging. Temporary directories will not be removed if
run fails. [default: False]
Outputs:
--o-tree ARTIFACT The tree with inserted feature data.
Phylogeny[Rooted] [required]
--o-placements ARTIFACT
Placements Information about the feature placements within the
reference tree. [required]
Miscellaneous:
--output-dir PATH Output unspecified results to a directory
--verbose / --quiet Display verbose output to stdout and/or stderr during
execution of this action. Or silence output if
execution is successful (silence is golden).
--example-data PATH Write example data and exit.
--citations Show citations and exit.
--help Show this message and exit.

              There were some problems with the command:

(1/4) Missing option '--i-representative-sequences'.
(2/4) Missing option '--i-reference-database'.
(3/4) Missing option '--o-tree'. ("--output-dir" may also be used)
(4/4) Missing option '--o-placements'. ("--output-dir" may also be used)
(qiime2-2023.7) yiggrite@MWMJ07RHBF:~/mouse_tutorial$ --i-representative-sequences ./dada2_rep_set.qza
--i-representative-sequences: command not found
(qiime2-2023.7) yiggrite@MWMJ07RHBF:~/mouse_tutorial$ --i-reference-database sepp-refs-gg-13-8.qza
--i-reference-database: command not found
(qiime2-2023.7) yiggrite@MWMJ07RHBF:~/mouse_tutorial$ --o-tree ./tree.qza
--o-tree: command not found
(qiime2-2023.7) yiggrite@MWMJ07RHBF:~/mouse_tutorial$ --o-placements ./tree_placements.qza
--o-placements: command not found
(qiime2-2023.7) yiggrite@MWMJ07RHBF:~/mouse_tutorial$ --p-threads 1
--p-threads: command not found
(qiime2-2023.7) yiggrite@MWMJ07RHBF:~/mouse_tutorial$ --debug
--debug: command not found
(qiime2-2023.7) yiggrite@MWMJ07RHBF:~/mouse_tutorial$

lizgehret · September 18, 2023, 7:33pm

@Yiggrite,

My apologies - I was careless in my copy/paste of your commands

For multi-line commands, you'll need to include a \ at the end of each line, like so:

qiime fragment-insertion sepp \
--i-representative-sequences ./dada2_rep_set.qza \
--i-reference-database sepp-refs-gg-13-8.qza \
--o-tree ./tree.qza \
--o-placements ./tree_placements.qza \
--p-threads 1 \
--p-debug

Cheers

Yiggrite · September 20, 2023, 9:27pm

lizgehret:

qiime fragment-insertion sepp \
--i-representative-sequences ./dada2_rep_set.qza \
--i-reference-database sepp-refs-gg-13-8.qza \
--o-tree ./tree.qza \
--o-placements ./tree_placements.qza \
--p-threads 1 \
--debug

(qiime2-2023.7) yiggrite@MWMJ07RHBF:~/mouse_tutorial$ ls
dada2_rep_set.qza dada2_stats.qza dada2_table.qza dada2_table.qzv demultiplexed_seqs demultiplexed_seqs.zip demux_seqs.qza demux_seqs.qzv manifest.tsv metadata.qzv metadata.tsv sample_metadata.tsv sepp-refs-gg-13-8.qza
(qiime2-2023.7) yiggrite@MWMJ07RHBF:~/mouse_tutorial$ qiime fragment-insertion sepp \

--i-representative-sequences ./dada2_rep_set.qza
--i-reference-database sepp-refs-gg-13-8.qza
--o-tree ./tree.qza
--o-placements ./tree_placements.qza
reads 1 > --p-threads 1
--debug
Usage: qiime fragment-insertion sepp [OPTIONS]

Perform fragment insertion of sequences using the SEPP algorithm.

Inputs:
--i-representative-sequences ARTIFACT FeatureData[Sequence]
The sequences to insert into the reference tree.
[required]
--i-reference-database ARTIFACT SeppReferenceDatabase
The reference database to insert the representative
sequences into. [required]
Parameters:
--p-alignment-subset-size INTEGER
Each placement subset is further broken into subsets
of at most these many sequences and a separate HMM is
trained on each subset. [default: 1000]
--p-placement-subset-size INTEGER
The tree is divided into subsets such that each subset
includes at most these many subsets. The placement step
places the fragment on only one subset, determined
based on alignment scores. Further reading:
https://github.com/smirarab/sepp/blob/master/tutorial/s
epp-tutorial.md#sample-datasets-default-parameters.
[default: 5000]
--p-threads INTEGER The number of threads to use. [default: 1]
--p-debug / --p-no-debug
Collect additional run information to STDOUT for
debugging. Temporary directories will not be removed if
run fails. [default: False]
Outputs:
--o-tree ARTIFACT The tree with inserted feature data.
Phylogeny[Rooted] [required]
--o-placements ARTIFACT
Placements Information about the feature placements within the
reference tree. [required]
Miscellaneous:
--output-dir PATH Output unspecified results to a directory
--verbose / --quiet Display verbose output to stdout and/or stderr during
execution of this action. Or silence output if
execution is successful (silence is golden).
--example-data PATH Write example data and exit.
--citations Show citations and exit.
--help Show this message and exit.

                There was a problem with the command:

(1/1?) No such option: --debug Did you mean --p-debug?
(qiime2-2023.7) yiggrite@MWMJ07RHBF:~/mouse_tutorial$

lizgehret · September 20, 2023, 9:57pm

Hi @Yiggrite,

You'll need to include --p-debug, not --debug - that's my mistake, my original suggestion just included --debug. Here's the full command again so you can copy-paste:

qiime fragment-insertion sepp \
--i-representative-sequences ./dada2_rep_set.qza \
--i-reference-database sepp-refs-gg-13-8.qza \
--o-tree ./tree.qza \
--o-placements ./tree_placements.qza \
--p-threads 1 \
--p-debug

Cheers

Yiggrite · September 27, 2023, 12:39am

Hi
It has been running for four days and still no response.
There was a problem with the command:
(1/1?) No such option: --debug Did you mean --p-debug?
(qiime2-2023.7) yiggrite@MWMJ07RHBF:~/mouse_tutorial$ qiime fragment-insertion sepp \

--i-representative-sequences ./dada2_rep_set.qza
--i-reference-database sepp-refs-gg-13-8.qza
--o-tree ./tree.qza
--o-placements ./tree_placements.qza
--p-threads 1
--p-debug

lizgehret · September 27, 2023, 9:04pm

Hi @Yiggrite,

If it's been running for that long, you may want to kill it and re-run with additional threads to improve on processing time. Cheers

lizgehret · September 28, 2023, 5:53pm

2 off-topic replies have been split into a new topic: error while running fragment-insertion

Please keep replies on-topic in the future.

Yiggrite · October 8, 2023, 2:03pm

Hey, I closed the WSL window, and now I can not open it again. How should I do?

cherman2 · October 10, 2023, 10:35pm

Hi @Yiggrite,
I am not sure what you mean that WSL wont open. Here are the WSL install docs and tutorials: Install WSL | Microsoft Learn. Hopefully something there can help!

system · November 11, 2023, 4:36am

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