Off topic:Genome Music Path-Scan Negative P-Value?

Question

[John St. John]

Hello,

Genome MuSic path-scan crashes with the following error on one of my datasets, and works fine with another that has identical format. Here is the error from the dataset that crashes out:

...
Skipping Silent mutation in gene POMT1.
Skipping Silent mutation in gene ABCD1.
ERROR: Error running genome music path-scan: '-1.62633954011268e-15' is not a p-val at /usr/share/perl5/Genome/Model/Tools/Music/PathScan/PopulationPathScan.pm line 615
ERROR: Please see 'genome music play --help' for more information.

Has anyone experienced this kind of error before? Unfortunately I am running this on patient data, so I cannot share the dataset that it crashes on.

This is using genome music play version 0.4, and is running on ubuntu version 12.04.

genome music play  \
    --bam-list filelist.bams   \
    --roi-file ensembl_67_cds_ncrna_and_splice_sites_hg19   \
    --genetic-data-type gene   --reference-sequence genome.fa  \
    --pathway-file KEGG.txt    --maf-file VariantCalls.maf   \
    --output-dir VariantCalls_play_out

Edit: this question has been asked and answered before: MuSIC path-scan pvalue error