How to run the programme at local compute

[GuoHao150]

First, I found your paper is so inspiring and I'm trying to run the omixer-rpm-1.1.jar with my local compute. and my command is java -jar omixer-rpm-1.1.jar -a demo_data/dataset.tsv -d GBMs/GBM.inputfile.txt -o test it just return me Annotation (demo_data/dataset.tsv) is not a valid annotation. So How can I run this demo properly?

[omixer]

Hello,

Could you please try running the demo with the following command?

java -jar omixer-rpm-1.1.jar -a 1 -d GBMs/GBM.inputfile.txt -i demo_data/dataset.tsv -o test

The -a option is to specify the format of the input file. For example if you are using a file with KO annotation only (e.g. https://raw.githubusercontent.com/raeslab/omixer-rpm/master/src/test/resources/matrix.tsv) you should use -a 1. If you have taxonomic information as well (e.g. https://raw.githubusercontent.com/raeslab/omixer-rpm/master/src/test/resources/taxon_matrix.tsv) please use -a 2.

I hope this solves your problem.

[bartns]

Hi,

I had the same issue / error with running the example-data.

The error message: ERROR - InferenceApp.main(292) | Exception while reading input. Please make sure you are using the correct annotation value (cf. --annotation description) for your input.

Sent me in the wrong direction towards annotation file.. However turned out my database was on the wrong format. Maybe this helps anyone.

Kind regards, Bart.