MAJIQ 2.0 questions

[Botao]

Dear Biociphers Team,

Thanks a lot for releasing the MAJIQ 2.0. I have the following questions for the new version.

1. You mentioned that one novel function is "Output a negative set: When comparing two conditions MAJIQ can give not only a high confidence set of changing events but also a high confidence set of events that are *not* changing."

How should I achieve this specifically? I could not find any instructions in the documentation or the help.

2. Dose the new "voila view" output all the LSVs without pre-filtering? The job has been stuck at the "Creating index" step for several hours without any new log info or intermediate files. It used to be much faster with the 1.1.x version by setting the threshold. The job is also not using much resources (CPU, MEM). Is it normal? The installation was fine without obvious errors. All the upstream steps are fine, including majiq build (much faster, thanks!), deltapsi, voila tsv. How long does it usually take to complete a voila run for viewing of ~50,000 total LSVs with 12 cores? Any suggestions to fix this issue?

Best,

Botao

[Jordi Vaquero]

Hello Botao, 

About the second point, please send me the text appears in the command screen. 

About the other text, in the tsv part of voila there are two commands that changes the both filters

  --non-changing-threshold NON_CHANGING_THRESHOLD

                        The default is "0.05".

  --probability-threshold PROBABILITY_THRESHOLD

                        This is off by default.

Did you try setting this to your value? 

Thanks

[Caleb Radens]

Hi Botao,

Just to make sure- the voila view command, run locally on your laptop, will print out a link that you then copy paste into your browser. Sometimes I don't notice that the link has been created because it's short.

Best,

Caleb

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[Botao]

HI Caleb and Jordi,

Thanks a lot for the quick response.

1. 1.1.x version has those two options. I did not realize that they are new. I thought the --probability-threshold PROBABILITY_THRESHOLD is for the P(|dPSI|>=0.20). I set it as 0.95.

How should I set the filtering for e.g. P(|dPSI|<=0.05) >0.95 for all junctions? Please let me know if I misunderstood anything.

2. For the voila view command, I mis-understood the instructions and ran the job at the background. When I ran it interactively, I saw the service address. However, I did the analysis on a server remotely. I'm not sure how to access to the webpage in this configuration. Thus, do I need to download the voila files and also install MAJIQ locally on my laptop. Is there a better way?

Thanks,

Botao

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[Botao]

Hi Caleb,

I tried to run voila view command locally. I got errors and the browser only showed the filtering options and the table head. Could you help me with this? Thanks a lot, Botao.

A pop-up error from the browser: DataTables warning: table id=results - Ajax error. For more information about this error, please see http://datatables.net/tn/7.

Errors from the terminal:

/usr/local/lib/python3.5/dist-packages/h5py/_hl/dataset.py:313: H5pyDeprecationWarning: dataset.value has been deprecated. Use dataset[()] instead.

  "Use dataset[()] instead.", H5pyDeprecationWarning)

ERROR:flask.app:Exception on /index-table [POST]

Traceback (most recent call last):

  File "/usr/local/lib/python3.5/dist-packages/flask/app.py", line 2292, in wsgi_app

    response = self.full_dispatch_request()

  File "/usr/local/lib/python3.5/dist-packages/flask/app.py", line 1815, in full_dispatch_request

    rv = self.handle_user_exception(e)

  File "/usr/local/lib/python3.5/dist-packages/flask/app.py", line 1718, in handle_user_exception

    reraise(exc_type, exc_value, tb)

  File "/usr/local/lib/python3.5/dist-packages/flask/_compat.py", line 35, in reraise

    raise value

  File "/usr/local/lib/python3.5/dist-packages/flask/app.py", line 1813, in full_dispatch_request

    rv = self.dispatch_request()

  File "/usr/local/lib/python3.5/dist-packages/flask/app.py", line 1799, in dispatch_request

    return self.view_functions[rule.endpoint](**req.view_args)

  File "/usr/local/lib/python3.5/dist-packages/voila/view/deltapsi.py", line 65, in index_table

    dt.delta_psi_filters()

  File "/usr/local/lib/python3.5/dist-packages/voila/view/datatables.py", line 109, in delta_psi_filters

    self.extra_filter(lambda rs: any(r >= dpsi_thresh for r in json.loads(rs['dpsi_threshold'])))

  File "/usr/local/lib/python3.5/dist-packages/voila/view/datatables.py", line 72, in extra_filter

    self._records = list(r for r in self._records if filter_fn(r))

  File "/usr/local/lib/python3.5/dist-packages/voila/view/datatables.py", line 72, in <genexpr>

    self._records = list(r for r in self._records if filter_fn(r))

  File "/usr/local/lib/python3.5/dist-packages/voila/view/datatables.py", line 109, in <lambda>

    self.extra_filter(lambda rs: any(r >= dpsi_thresh for r in json.loads(rs['dpsi_threshold'])))

  File "/usr/lib/python3.5/json/__init__.py", line 312, in loads

    s.__class__.__name__))

TypeError: the JSON object must be str, not 'bytes_'

On Wednesday, April 3, 2019 at 5:44:55 PM UTC-4, Caleb Radens wrote:

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[Austin Gillen]

Hi Botao and Caleb,

Botao - were you ever able to resolve the voila view error you describe below? I'm getting the same error using voila view on majiq deltapsi output (psi output from the same samples is unaffected and works fine).

Caleb (or other maintainers) - what can I provide to help troubleshoot this?

Cheers,

Austin