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