plug in error from demux

Hi this is what I got!

Usage: qiime demux summarize [OPTIONS]
Try “qiime demux summarize --help” for help.

Error: Got unexpected extra arguments ( de-demux-paired-end.qza de-demux.qzv flag)

Oops, looks like you accidentally removed the flag --o-visualization from the command. Please go back to the original command and append the --verbose flag to the end of it, like this:

qiime demux summarize --i-data de-demux-paired-end.qza --o-visualization de-demux.qzv --verbose

Make sense?

Hi @thermokarst this is what I got back !

s/decorator.py:decorator-gen-425>", line 2, in summarize
File “/home/smith5mr/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 231, in bound_callable
output_types, provenance)
File “/home/smith5mr/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 427, in callable_executor
ret_val = self._callable(output_dir=temp_dir, **view_args)
File “/home/smith5mr/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_demux/_summarize/_visualizer.py”, line 165, in summarize
forward_stats = _compute_stats_of_df(forward_scores)
File “/home/smith5mr/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_demux/_summarize/_visualizer.py”, line 92, in _compute_stats_of_df
percentiles=[0.02, 0.09, 0.25, 0.5, 0.75, 0.91, 0.98])
File “/home/smith5mr/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/pandas/core/generic.py”, line 8500, in describe
raise ValueError(“Cannot describe a DataFrame without columns”)
ValueError: Cannot describe a DataFrame without columns

Plugin error from demux:

Cannot describe a DataFrame without columns

See above for debug info.

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Problem solved just reimported my fast q files and ran the script on the server!

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I imagine there was some kind of issue the first time you imported --- that error message seems to indicate that there was an "empty" list of things somewhere. Not sure if that was an empty sample with no sequences in it, or, if the list of samples was empty. If you still have the offending artifact around feel free to message me a download link to it, I would love to take a closer look!
:qiime2: :t_rex:

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@thermokarst thank you so much you guys are amazing and super speedy with helping!

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This is the error I'm getting when I attempt to run the following command

qiime demux summarize
--i-data cnn-paired-end-demux.qza
--o-visualization cnn-demux.qzv

any ideas on what is happening here?

garter.csv (3.8 KB)

I also attached my .csv and here is the previous command I used to import the data that worked succesfully

qiime tools import
--type 'SampleData[PairedEndSequencesWithQuality]'
--input-path garter.csv
--output-path cnn-paired-end-demux.qza
--input-format PairedEndFastqManifestPhred33

This is a previously unreported error message - can you please share a download link to the file cnn-paired-end-demux.qza (okay to send in a direct message). Thanks! :qiime2:

I am having trouble finding the file on my MAC , how should I locate it. I searched in finder and it didn’t show up, but I know it is on the computer somewhere

Hmm, I don’t think we can help with that - do you have someone local to you that can help show you around on your computer? Maybe an IT department, or a colleague?

Actually, wait a minute, is it on your mac? I thought I saw some discussion yesterday that mentioned you were logging into a remote server. Either way, maybe you can get some help with this from someone more familiar with your computing environment?

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Thanks for sharing that file with me in a DM! Well, the problem is pretty clear — every one of your files is completely empty. Are the original files empty, too? Maybe double check that everything downloaded from your sequencing center completely. If they did, maybe check in with your sequencing center?

Just to clarify, I am talking about the fastq.gz files — if you open any of them up (after exporting the Artifact), they have no reads in them.

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