Music Path-Scan Problem

Question

[zhouyunyun11]

I got the following problem from Pathscan:

Can't call method "print" on an undefined value at /usr/local/share/perl/5.14.2/Genome/Model/Tools/Music/PathScan.pm line 403.

Here is my input file:

genome music path-scan --bam-list ~/music/mus.hg19 --gene-covg-dir ~/music/0927_test_smg/gene_covgs/ --maf-file ~/music/pathscan_0928.maf --output-file ~/music/sm_pathways --pathway-file ~/music/downloaded_pathway/GO_101008 -bmr 1.8E-6

There shouldn't be any problem from my input file. bam-list, maf-file are all been successfully used by music bmr calc-bmr before. And the gene_covgs are the outputs from bmr calc-bmr,

the GO_101008 is downloaded from Ding-lab parsed file.

Any possible reason might cause this problem?

And also, if I set -bmr 1E-06, I got the following error:

-1.73933694703631e-14' in cdf pair 3 is not a p-val at /usr/local/share/perl/5.14.2/Genome/Model/Tools/Music/PathScan/PopulationPathScan.pm line 655.

Meanwhile, the most important thing: any one knows how to debug this prackage?

I know in perl, we can debug like perl -d test.pl, and watch the intermediate value from the outputs, but for music, the command line likes : Genome Music Path-scan **

Then how do I watch the intermediate value from this package?

Thanks so much for help.

Sorry, I'm very new to perl script and unix environment.

Answer 1

[Cyriac Kandoth]

The two errors you see at PathScan.pm #403 and PopulationPathScan.pm #655 are related. #655 is a known/unsolved error that is mentioned in the following posts: MuSIC path-scan pvalue error question about the MuSiC pathscan FDR value Genome MuSic path-scan negative p-value?

If you are familiar with Perl, you can find the code here: https://github.com/genome/gms-core/blob/master/lib/perl/Genome/Model/Tools/Music/

Running genome music ... is the same as running perl /usr/local/bin/genome music ..., because genome is just a perl script that you can debug.