Question: Music Path-Scan Problem
gravatar for zhouyunyun11
6.5 years ago by
zhouyunyun110 wrote:

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/ 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/ 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, 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.

music • 2.3k views
ADD COMMENTlink modified 3.1 years ago by Biostar ♦♦ 20 • written 6.5 years ago by zhouyunyun110
gravatar for Cyriac Kandoth
6.5 years ago by
Cyriac Kandoth5.5k
Memorial Sloan Kettering, New York, USA
Cyriac Kandoth5.5k wrote:

The two errors you see at #403 and #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:

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.

ADD COMMENTlink written 6.5 years ago by Cyriac Kandoth5.5k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1353 users visited in the last hour