Question: (Closed) Genome Music Path-Scan Negative P-Value?
2
gravatar for John St. John
6.0 years ago by
John St. John1.1k
San Francisco, CA, Cancer Therapeutics Innovation Group
John St. John1.1k wrote:

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

music • 2.1k views
ADD COMMENTlink modified 5.4 years ago by Chris Miller20k • written 6.0 years ago by John St. John1.1k
1

This has been asked before at - MuSIC path-scan pvalue error

ADD REPLYlink written 6.0 years ago by Cyriac Kandoth5.2k

Thanks for digging up that post for me!

ADD REPLYlink written 6.0 years ago by John St. John1.1k

Np. Your question contains the actual error message. So folks are more likely to find this post first, rather than that older one.

ADD REPLYlink written 6.0 years ago by Cyriac Kandoth5.2k

Closing as a duplicate, and also marking with the "resolved" tag, in case we ever get around to excluding such posts from automatic bumping.

ADD REPLYlink written 5.4 years ago by Chris Miller20k
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