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donovan-h-parks / STAMP

Statistical Analysis of Metagenomic Profiles
GNU General Public License v3.0
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Heatmap crashes, etc. #23

Open riccardoh opened 7 years ago

riccardoh commented 7 years ago

Hello,

I've been trying to plot a heatmap of KEGG pathways using STAMP. My data are from 16s sequences from soil. I used MICCA followed by Picrust to generate .biom files etc. I initially had trouble getting STAMP to import the files, so I had to manually convert the biom files to json and then to spf. When I plot an initial heatmap, I have no problems, but when I try to configure the plot it almost always throws an error. I've tried it on Windows and on Linux. On Linux I got an error saying the distance matrix looked suspiciously uncondensed. On windows I'm getting a "KeyError" which occurred at line 135 of the MultiGroupProfile.pyo. I've found at least one other person online with a somewhat similar issue: https://groups.google.com/forum/#!topic/stamp_help/_VV_8FqUSVw.

Apparently, if I configure the settings and let it crash, I can then restart the program and the changes will have taken place and I have the heatmap I want. However, it will crash again if I try to make changes. Any suggestions? I'm particularly concerned about that "uncondensed distance matrix" error.

Thanks!

riccardoh commented 7 years ago

Update: It appears this only happens when trying to configure the plot when the profile level is set to '3'.

Thanks again :D