Error In Genome Music Path-Scan

Question

[Andreas Weller]

I'm using Genome Music 0.4.1 on an Ubuntu 10.04 server. Most functions work fine, so I guess my installation and my input files are generally ok.

However, "genome music path-scan" throws the following error:

Use of uninitialized value $diseases in string eq at /usr/share/perl5/Genome/Model/Tools/Music/PathScan.pm line 250, <GEN161> line 674.
Use of uninitialized value $drugs in string eq at /usr/share/perl5/Genome/Model/Tools/Music/PathScan.pm line 251, <GEN161> line 674.
Use of uninitialized value $description in string eq at /usr/share/perl5/Genome/Model/Tools/Music/PathScan.pm line 252, <GEN161> line 674.
...
(this repeats hundreds of times)
...
ERROR: '3' is not a hit number at /usr/share/perl5/Genome/Model/Tools/Music/PathScan.pm line 382

I tried it without success on 2 different pathway files provided in this thread: Pathway file generation for path-scan under Genome Music using KEGGREST under R.

Any ideas?

Thanks!

Answer 1

[Cyriac Kandoth]

This is just a warning, not an error... courtesy of unhandled exceptions in the code. In this case, many of the pathway files, like this one, do not have those 3 fields defined: DISEASES, DRUGS, DESCRIPTION. The code does not check whether they are properly defined in the pathway file before trying to use them. That's the reason for the warning. But since it's not an error, you should get your results just fine. Let me know otherwise. And for now, to avoid the message, you can append your command with 2> /dev/null. :)

[Andreas Weller]

Thanks for your quick reply! Unfortunately the last line of error seems to stop the script, as I don't see the output file I specified.

I tried path-scan with a different input dataset. This time I don't get the "uninitialized value" message, but a different error that again stops the script without output: """ ERROR: '-1.3253284061131e-17' in cdf pair 111 is not a p-val at /usr/share/perl5/Genome/Model/Tools/Music/PathScan/PopulationPathScan.pm line 618"""