I have run the q2-sample-classifier and am receiving an error that for such option for the output visualization. Any thoughts on why this might be occurring?
qiime sample-classifier classify-samples --i-table C:\Users\kjharris\Desktop\crayfishmicrobiome2018\rep-seqs.qza --m-metadata-file “C:\Users\kjharris\Desktop\crayfishmicrobiome2018\metadata April 16 2019 - Editable.txt” --p-optimize-feature-selection --p-parameter-tuning --p-estimator RandomForestClassifier --p-n-estimators 100 --o-visualization crayfishmicrobiome2018\rep-seqs.qzv
Usage: qiime sample-classifier classify-samples [OPTIONS]
Try “qiime sample-classifier classify-samples --help” for help.
Error: no such option: --o-visualization
Hey there @mudbugecology!
Yes indeed - the information is all right there, ripe for the picking!
Let's start with the error message:
Okay, so so looks like this part of your command is causing the problem:
--o-visualization crayfishmicrobiome2018\rep-seqs.qzv. So, if we double check the docs (trimmed to just the output section):
--o-sample-estimator ARTIFACT PATH SampleEstimator[Classifier]
Trained sample estimator. [required if not
--o-feature-importance ARTIFACT PATH FeatureData[Importance]
Importance of each input feature to model
accuracy. [required if not passing
--o-predictions ARTIFACT PATH SampleData[ClassifierPredictions]
Predicted target values for each input
sample. [required if not passing --output-
--o-model-summary VISUALIZATION PATH
Summarized parameter and (if enabled)
feature selection information for the
trained estimator. [required if not passing
--o-accuracy-results VISUALIZATION PATH
Accuracy results visualization. [required
if not passing --output-dir]
So, the first thing I notice is that there is no
--o-visualization option in this command. Okay, so moving forward --- double check the
--help text for the command to make sure that you are providing all the required options to the command, then try it again! Good luck!
Thanks for the quick reply! I will give this a try!
Just to clarify: “visualization” was an output in an old version of q2-sample-classifier. You must have been using some old docs or copying/pasting from an old collection of scripts. So you are not going crazy — but as @thermokarst recommends whenever you see an error like that it is best to check the help documentation since parameter names do change from time to time!
An off-topic reply has been split into a new topic: How to use metadata in q2-sample-classifier
Please keep replies on-topic in the future.
I am attempting to run this in Linux as a subsystem on a new pc and I have the most recent release of q2, I have also been attempting this on my mac, but I am still having some difficultly getting the directory to output:
(qiime2-2019.4) [email protected]:/mnt/c/Users/kjharris/Desktop$ qiime diversity alpha-group-significance --i-table C:\Users\kjharris\Desktop\crayfishmicrobiome2018\table.qza --m-metadata-file “C:\Users\kjharris\Desktop\crayfishmicrobiome2018\metadata may 1 2019 modified.txt” --m-metadata-column SampleType “C:\Users\kjharris\Desktop\crayfishmicrobiome2018\metadata may 1 2019 modified.txt” --p-optimize-feature-selection --p-parameter-tuning --p-estimator RandomForestClassifier --p-n-estimators 100 --output-dir SampleTypeMicrobiome
Usage: qiime diversity alpha-group-significance [OPTIONS]
Visually and statistically compare groups of alpha diversity values.
–i-alpha-diversity ARTIFACT SampleData[AlphaDiversity]
Vector of alpha diversity values by sample. [required]
(multiple The sample metadata.
be merged) [required]
–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:
(1/6?) no such option: --i-table
(2/6?) no such option: --m-metadata-column
(3/6?) no such option: --p-optimize-feature-selection
(4/6?) no such option: --p-parameter-tuning
(5/6?) no such option: --p-estimator
(6/6?) no such option: --p-n-estimators
(qiime2-2019.4) [email protected]:/mnt/c/Users/kjharris/Desktop$
not sure why I started it that way since the current doc on the tutorial https://docs.qiime2.org/2019.4/tutorials/sample-classifier/#best-practices-things-you-should-not-do-with-q2-sample-classifier suggests this:
qiime sample-classifier classify-samples
I think the issue is you need to prefix your paths with
/mnt/c/<normal path here, but with / not \>. That being said, the parser shouldn’t really be complaining about those options not existing, as obviously they do. So there’s an interesting edge case here (and not your fault).
Regardless of that, I think if you update your paths, the command should start working correctly.
inside the linux subsystem.
Let me know if that works! I’ll look into why the
no such option: is happening with the Windows style paths…
thanks, Evan!! I will give this a go and let you know if it works
working on a new error message, but this seems to be moving in the right direction: qiime sample-classifier classify-samples --i-table /mnt/c/Users/kjharris/Desktop/crayfishmicrobiome2018/table/qza --m-metadata-file /mnt/c/Users/kjharris/Desktop/crayfishmicrobiome2018/metadata may 1 2019 modified.txt --m-metadata-column SampleType /mnt/c/Users/kjharris/Desktop/crayfishmicrobiome2018/metadata may 1 2019 modified.txt --p-optimize-feature-selection --p-parameter-tuning --p-estimator RandomForestClassifier --p-n-estimators 100 --output-dir SampleTypecrayfishmicrobiome
There was an issue with loading the file /mnt/c/Users/kjharris/Desktop/crayfishmicrobiome2018/metadata as metadata:
Metadata file path doesn’t exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): /mnt/c/Users/kjharris/Desktop/crayfishmicrobiome2018/metadata
There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org
Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2019.4/tutorials/metadata/
Yep! The issue this time is one of path quoting, to be honest, I’m taking notes here, as this is another common problem that ideally the parser should be handling more gracefully (so thanks!)
To solve this one you have two options:
/mnt/c/Users/kjharris/Desktop/crayfishmicrobiome2018/metadata may 1 2019 modified.txt
should be written as either:
/mnt/c/Users/kjharris/Desktop/crayfishmicrobiome2018/metadata\ may\ 1\ 2019\ modified.txt
'/mnt/c/Users/kjharris/Desktop/crayfishmicrobiome2018/metadata may 1 2019 modified.txt'
(note the single-quotes around the path)
Space is considered a special character to most command line tools, so it doesn’t realize
2019, etc are part of the file. Most people just avoid space all-together in their filenames as it makes life much easier.
bingo! you all are the best
qiime sample-classifier classify-samples --i-table /mnt/c/Users/kjharris/Desktop/crayfishmicrobiome2018/table-rarefy-to-12000.qza --m-metadata-file /mnt/c/Users/kjharris/Desktop/crayfishmicrobiome2018/metadata\ April\ 30\ 2019.t
xt --m-metadata-column SampleType --p-optimize-feature-selection --p-parameter-tuning --p-estimator RandomForestClassifier --p-n-estimators 10
0 --output-dir SampleTypecrayfishmicrobiome
Saved SampleEstimator[Classifier] to: SampleTypecrayfishmicrobiome/sample_estimator.qza
Saved FeatureData[Importance] to: SampleTypecrayfishmicrobiome/feature_importance.qza
Saved SampleData[ClassifierPredictions] to: SampleTypecrayfishmicrobiome/predictions.qza
Saved Visualization to: SampleTypecrayfishmicrobiome/model_summary.qzv
Saved Visualization to: SampleTypecrayfishmicrobiome/accuracy_results.qzv
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