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wdecoster / NanoPlot

Plotting scripts for long read sequencing data
http://nanoplot.bioinf.be
MIT License
413 stars 47 forks source link

NanoPlot crash with a small file containing a few whales #231

Closed tchrisboles closed 3 years ago

tchrisboles commented 3 years ago

Hi Wouter, We're trying a new sample prep aimed at long reads. I created a new AWS instance (ubuntu) and installed minimap2, samtools, and Nanoplot using conda. The fast-basecalled passed output was not large (2 fastq's total about 760mbytes), but there are a good number of very long reads (>700kb, some 1Mb reads). I ran minimap2 with the -L option because of this. Minknow thought the N50 readlength is 160kb.

Caution: I used the fast-basecaller on the minit only. (I know -lazy - but I just wanted to see if the long reads were total junk.)

Hope you are weathering the pandemic in good health and tolerable good spirits. Chris NanoPlot_20210305_2012.log Nanoplot_crash_screen

wdecoster commented 3 years ago

Hi Chris,

Hope to catch up with you at some conference as soon that is possible again.

Sorry for the inconvenience here, this seems to be the same problem as https://github.com/wdecoster/NanoPlot/issues/201. Downgrading seaborn should fix it.

I'm having some trouble updating the bioconda recipe to take care of that incompatibility, I should really look into that soon...

Hope that helps, Wouter

wdecoster commented 3 years ago

Hi Chris,

Please let me know if this has to be reopened!

Thanks, Wouter