GOMO read_cisml error

[cywhale Weng]

Hi All,

I executed command-line GOMO on two computers(both BioLinux 8), one got correct GO analysis result, but the other didn't. The following is the command and error message:
===========================
$gomo -o GO ./gomo_databases/mammal_homo_sapiens_1000_199.na.csv meme.xml

Starting gomo
Loading map from "./gomo_databases/mammal_homo_sapiens_1000_199.na.csv".
Loaded 11794 unique GO terms (IDs) with 1 or more annotations and 18587 annotating sequence IDs.
Loading scores from "meme.xml".
gomo: cisml.c:2973: read_cisml: Assertion `xpath_obj->nodesetval->nodeNr == 1' failed.
zsh: abort      gomo -o GO ../meme_src/gomo_databases/mammal_homo_sapiens_1000_199.na.csv

===========================
Could anyone please to help me figure out how to solve this error message?

Any suggestions are welcome
Thanks~

[James Johnson]

I suspect you have the arguments wrong as GOMo should not be reading anything from a MEME motif file which is what I suspect "meme.xml" is. The error message is terrible unfortunately so I will try to fix that for a future release.

GOMo is designed to work with AMA. The idea is that you scan the sequences with AMA and pass the output CISML file to GOMo.
http://meme.ebi.edu.au/meme/doc/gomo.html

[cywhale Weng]

Hi James,

It's work after using AMA and pass the output to GOMO !

Thanks a lot~