Hello, i am running qiime2 on conda (HPC), analyzing ITS fungi.
everything is fine until the Assign taxonomy command:
qiime feature-classifier classify-sklearn
–i-reads reads rep-seqs-dada2.qza
i have tried two published trained classifiers, with no help.
i get the error:
srun: fatal: No command given to execute.
Usage: qiime feature-classifier classify-sklearn [OPTIONS]
Classify reads by taxon using a fitted classifier.
–i-reads ARTIFACT FeatureData[Sequence]
The feature data to be classified. [required]
TaxonomicClassifier The taxonomic classifier for classifying the reads.
Range(0, None) Number of reads to process in each batch. If “auto”,
this parameter is autoscaled to min( number of query
sequences / n-jobs, 20000). [default: 0]
–p-n-jobs INTEGER The maximum number of concurrently worker processes.
If -1 all CPUs are used. If 1 is given, no parallel
computing code is used at all, which is useful for
debugging. For n-jobs below -1, (n_cpus + 1 + n-jobs)
are used. Thus for n-jobs = -2, all CPUs but one are
used. [default: 1]
–p-pre-dispatch TEXT “all” or expression, as in "3n_jobs". The number of
batches (of tasks) to be pre-dispatched.
–p-confidence VALUE Float % Range(0, 1, inclusive_end=True) | Str %
Choices(‘disable’) Confidence threshold for limiting taxonomic depth.
Set to “disable” to disable confidence calculation,
or 0 to calculate confidence but not apply it to
limit the taxonomic depth of the assignments.
–p-read-orientation TEXT Choices(‘same’, ‘reverse-complement’, ‘auto’)
Direction of reads with respect to reference
sequences. same will cause reads to be classified
unchanged; reverse-complement will cause reads to be
reversed and complemented prior to classification.
“auto” will autodetect orientation based on the
confidence estimates for the first 100 reads.
–o-classification ARTIFACT FeatureData[Taxonomy]
–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).
–citations Show citations and exit.
–help Show this message and exit.
There were some problems with the command:
(1/3) Missing option “–i-reads”.
(2/3) Missing option “–i-classifier”.
(3/3) Missing option “–o-classification”. ("–output-dir" may also be used)