I've had some problems running in other species

lh3 / pangene

Constructing a pangenome gene graph

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I've had some problems running in other species #9

Closed Fight-a-tiger-in-the-mountain closed 3 months ago

Fight-a-tiger-in-the-mountain commented 4 months ago

Hello Professor Li, I have deployed the server locally according to your process, as shown in the picture below ${{9OCS)76(H6OL%4C_KST7I$ After I opened the web page locally, I got the information as shown in the following picture, which is the content of the previous gfa file. (YU{3~DLLIV2EYXISJYDKBX XASP$}2(V9O)Y88PBG@HKND

I didn't get a picture when I searched for some genes. I don't know why I tried a lot of genes and didn't see any pangenegraph, whereas typing any gene into your website will bring up a picture (This is my analysis from other species following your process) the genes may be different, I hope you can shed some light Here is your web interface UXKQCLC7J{90YF1DV%VW~FX Thank you very much

Evenlyeven commented 3 months ago

I am experiencing the same issue. Have you figured out why? Thanks!

I also tried the gfa files in the test folder of pangene, same thing happened.

Fight-a-tiger-in-the-mountain commented 3 months ago

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lh3 commented 3 months ago

You may uncheck "filter fragmented contigs" and try again.

Evenlyeven commented 3 months ago

You may uncheck "filter fragmented contigs" and try again.

Thank you for looking it this! I tried it, there's still no plot. Attached is the test MT.gfa file from gfatools.

lh3 commented 3 months ago

I see the issue. You need to run it in the "pangene-1.1-bin" directory as the README shows:

# Deploy the GFA server on the C4 example; require pangene-1.1-bin
cd pangene-1.1-bin                         # run gfa-server in this directory
bin_arm64-mac/gfa-server /path/to/C4.gfa   # or use bin_linux-x64 on x64-linux

Also, gfa-server is developed for pangene graphs and won't plot anything for MT.gfa anyway.