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wdecoster / NanoPlot

Plotting scripts for long read sequencing data
http://nanoplot.bioinf.be
MIT License
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NanoPlot 1.39 crashes halfway - ValueError raised from plotly #283

Closed landmanf closed 2 years ago

landmanf commented 2 years ago

Hi Wouter, I'm trying to get NanoPlot to work in a environment with several other dependencies and it crashes halfway before finishing all of the .html it raises an ValueError from plotly

I tried several versions of NanoPlot

Versions (1.35.5, 1.36.1,1.37.0, 1.38.0) gave " scatter() missing 1 required positional argument: 'data_frame' " which I saw in an previous issue (#268 and was fixed in 1.38.1) so I tried those newer versions (1.38.1, 1.39.0) but they gave the ValueError from plotly

Hopefully it's an easy fix :)

Added the logfile: NanoPlot_20211202_0943.log

wdecoster commented 2 years ago

Hi, that seems to be a duplicate of https://github.com/wdecoster/NanoPlot/issues/278, which is unfortunately unsolved as the one who reported that didn't follow up.

My first idea is that you might have an outdated plotly module, could you check the version? python -c "import plotly ; print(plotly.version)"

landmanf commented 2 years ago

Thank you for the quick reply. This is the output: <module 'plotly.version' from 'path/to/conda/envs/test_nanoplot2/lib/python3.8/site-packages/plotly/version.py'> output to your previous command in #278 gave me a version number which is 4.1.0 I noticed now, that the underscores got formatted :)

wdecoster commented 2 years ago

Glad you caught my error in copy-pasting the command :-)

Could you just try upgrading plotly? At least that gives me a starting point on how to reproduce this...

landmanf commented 2 years ago

Upgraded plotly to 5.4.0 and now NanoPlot 1.38.1 works perfect without errors. In the process of upgrading through pip it revealed the program holding plotly back which is PycoQC and says it requires plotly 4.1.0.

wdecoster commented 2 years ago

Aha, that is remarkable but very good to know. I will change the minimal required version for NanoPlot then to 5.4.0... Thanks for the quick feedback!

landmanf commented 2 years ago

Interestingly/luckily enough PycoQC (v2.5.2) still works in this environment as well when only supplying the --summary_file and --output. Thank you for your help :)!