Generating OTUs with Vesearch

Hi all,
I already generated rep-seq and table after DADA2 in Qiime2! Now, I need to generate OTUs with Vsearch. I used this command but it gives an unknown error!

qiime vsearch cluster-features-de-novo
--i-sequences 3merged-Rep.Seq-mcrA-DNA.qza
--i-table 3merged-Tables-mcrA-DNA.qza
--p-perc-identity 0.9
--p-threads 4
--o-clustered-table 90%-vesearch culstered table-for-mcrA.qza
--o-clustered-sequences 90%-vesearch culstered rep-seq-for-mcrA.qza
--verbose

qiime vsearch cluster-features-de-novo \

--i-sequences 3merged-Rep.Seq-mcrA-DNA.qza
--i-table 3merged-Tables-mcrA-DNA.qza
--p-perc-identity 0.9
--p-threads 4
--o-clustered-table 90%-vesearch culstered table-for-mcrA.qza
--o-clustered-sequences 90%-vesearch culstered rep-seq-for-mcrA.qza
--verbose
Usage: qiime vsearch cluster-features-de-novo [OPTIONS]

Given a feature table and the associated feature sequences, cluster the
features based on user-specified percent identity threshold of their
sequences. This is not a general-purpose de novo clustering method, but
rather is intended to be used for clustering the results of quality-
filtering/dereplication methods, such as DADA2, or for re-clustering a
FeatureTable at a lower percent identity than it was originally clustered
at. When a group of features in the input table are clustered into a
single feature, the frequency of that single feature in a given sample is
the sum of the frequencies of the features that were clustered in that
sample. Feature identifiers and sequences will be inherited from the
centroid feature of each cluster. See the vsearch documentation for
details on how sequence clustering is performed.

Inputs:
--i-sequences ARTIFACT FeatureData[Sequence]
The sequences corresponding to the features in
table. [required]
--i-table ARTIFACT FeatureTable[Frequency]
The feature table to be clustered. [required]
Parameters:
--p-perc-identity PROPORTION Range(0, 1, inclusive_start=False,
inclusive_end=True) The percent identity at which clustering should be
performed. This parameter maps to vsearch's --id
parameter. [required]
--p-threads INTEGER Range(0, 256, inclusive_end=True)
The number of threads to use for computation.
Passing 0 will launch one thread per CPU core.
[default: 1]
Outputs:
--o-clustered-table ARTIFACT FeatureTable[Frequency]
The table following clustering of features.
[required]
--o-clustered-sequences ARTIFACT FeatureData[Sequence]
Sequences representing clustered features.
[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).
--examples Show usage examples 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 arguments (culstered table-for-mcrA.qza culstered
** rep-seq-for-mcrA.qza)**

My table is grouped and merged one! And I am using 2020.08 Qiime2 version.

Please help me how to solve this error!

Thanks

Qiimer

I think the problem here is that you have spaces and non-safe characters (e.g. % in your output file names):

Hence the warning:

Perhaps change your output to:

–o-clustered-table vesearch-90-clustered-table-for-mcrA.qza
–o-clustered-sequences vesearch-90-clustered-rep-seq-for-mcrA.qza
1 Like

Unfortunately it was not the case!

qiime vsearch cluster-features-de-novo \

--i-sequences 3merged-Rep.Seq-mcrA-DNA.qza
--i-table 3merged-Tables-mcrA-DNA.qza
--p-perc-identity 0.99
--p-threads 4
--o-clustered-table 90per-vesearch culstered table-for-mcrA.qza
--o-clustered-sequences 90per-vesearch culstered rep-seq-for-mcrA.qza
--verbose
Usage: qiime vsearch cluster-features-de-novo [OPTIONS]

Given a feature table and the associated feature sequences, cluster the
features based on user-specified percent identity threshold of their
sequences. This is not a general-purpose de novo clustering method, but
rather is intended to be used for clustering the results of quality-
filtering/dereplication methods, such as DADA2, or for re-clustering a
FeatureTable at a lower percent identity than it was originally clustered
at. When a group of features in the input table are clustered into a
single feature, the frequency of that single feature in a given sample is
the sum of the frequencies of the features that were clustered in that
sample. Feature identifiers and sequences will be inherited from the
centroid feature of each cluster. See the vsearch documentation for
details on how sequence clustering is performed.

Inputs:
--i-sequences ARTIFACT FeatureData[Sequence]
The sequences corresponding to the features in
table. [required]
--i-table ARTIFACT FeatureTable[Frequency]
The feature table to be clustered. [required]
Parameters:
--p-perc-identity PROPORTION Range(0, 1, inclusive_start=False,
inclusive_end=True) The percent identity at which clustering should be
performed. This parameter maps to vsearch's --id
parameter. [required]
--p-threads INTEGER Range(0, 256, inclusive_end=True)
The number of threads to use for computation.
Passing 0 will launch one thread per CPU core.
[default: 1]
Outputs:
--o-clustered-table ARTIFACT FeatureTable[Frequency]
The table following clustering of features.
[required]
--o-clustered-sequences ARTIFACT FeatureData[Sequence]
Sequences representing clustered features.
[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).
--examples Show usage examples 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 arguments (culstered table-for-mcrA.qza culstered
rep-seq-for-mcrA.qza)

Incorrect. There are still spaces.

2 Likes

Aha…thanks sir. You rock!

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