q2-itsxpress: can we visualize the outputs as a QZV?

Community Plugin Support
1

Hi @Adam_Rivers,
I was wondering if we could visualize “trimmed.qza” file in “.qzv” form. Visualization of the trimmed sequences with their quality can be helpful in truncating the sequences using DADA2.

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2

Hi @Ishwora_Dhungana,

Can you double check the semantic type of the trimmed.qza file? I’m guessing that it’s a SampleData[SequencesWithQuality] Artifact (or a SampleData[PairedEndSequencesWithQuality]). If that’s the case, you could try qiime demux summarize to generate the visualisation.

Best,
Justine

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3

Yes, you should be able to visualize the output with qiime demux summarize. Are there specific plots you would like to see or specific questions you would want to assess looking at a .qza report that are not included in the general summary above?

ITSxpress is due for a bigger release that incorporates several new feature requests. I would like to include your suggestions.

Adam

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4

Hi @jwdebelius and @Adam_Rivers,

Thank you for your help. I tried visualizing using the following command and got plugin error.
qiime demux summarize
–i-data demux-trimmed-ITS.qza
–o-visualization demux-trimmed-ITS.qzv

Plugin error from demux:

list index out of range

Debug info has been saved to /var/folders/g7/18xrfw8d5_1fx8n9vfd5c78w0000gp/T/qiime2-q2cli-err-t6lxut9v.log

Can you help me to figure out this error.

Best,
Ishwora

5

Hi @Ishwora_Dhungana,

This may be related to another issue we’ve seen with demux summarize, but its hard to tell. Could you provide the log file indicated in that error?

Thanks!

6

Some issues with our manifest files were fixed in q2_itsxpress version 1.7.4 released today. You may want to try upgrading:

Upgrade the Qiime 2 plugin q2_itsxpress to v1.7.4 using pip

pip install update q2_itsxpress

You should also verify that the stand-alone program itsxpress is up to date too (v 1.7.2)

conda update itsxpress
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7

I have the same problem
Im trying to visualize my trimmed seqs and get an error: “Cannot describe a DataFrame without columns”
the type of output trimmed.qza is:

  • type:“SampleData[PairedEndSequencesWithQuality]”
  • format:“SingleLanePerSamplePairedEndFastqDirFmt”

I ran this on a server:

qiime demux summarize --i-data trimmed.qza --o-visualization trimmed.qzv --verbose

Traceback (most recent call last):
File “/Local/gcf/anaconda2/envs/qiime2-2019.4/lib/python3.6/site-packages/q2cli/commands.py”, line 311, in call
results = action(**arguments)
File “</Local/gcf/anaconda2/envs/qiime2-2019.4/lib/python3.6/site-packages/decorator.py:decorator-gen-440>”, line 2, in summarize
File “/Local/gcf/anaconda2/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 231, in bound_callable
output_types, provenance)
File “/Local/gcf/anaconda2/envs/qiime2-2019.4/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 “/Local/gcf/anaconda2/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_demux/_summarize/_visualizer.py”, line 165, in summarize
forward_stats = _compute_stats_of_df(forward_scores)
File “/Local/gcf/anaconda2/envs/qiime2-2019.4/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 “/Local/gcf/anaconda2/envs/qiime2-2019.4/lib/python3.6/site-packages/pandas/core/generic.py”, line 9721, 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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8

Hi @Sheli_Ostrow - this error happens when there are no sequences in the artifact being visualized. This likely means that trimming/demuxing didn’t go as planned.

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