Problem in music bmr coverage

Question

[Nitish Mishra]

Hi,

I am using this command in music

genome music bmr calc-covg \
  --bam-list /shared/unmc1/unmc_gudalab/nitish123/DbGAP/Reference-Platypus/TumorVsNormal/BAM_list \
  --output-dir /shared/unmc1/unmc_gudalab/nitish123/DbGAP/Reference-Platypus/TumorVsNormal/coverage/ \
  --gene-covg-dir /shared/unmc1/unmc_gudalab/nitish123/DbGAP/Reference-Platypus/TumorVsNormal/coverage/ \
  --reference-sequence /shared/unmc1/unmc_gudalab/nitish123/DbGAP/Pancreatic/hg19-Pancreatic/hg19_UCSC.fa \
  --roi-file /shared/unmc1/unmc_gudalab/nitish123/Tools/music/roi_Ensemble_Homo_sapiens.hg38.77.tsv

Whenever I am giving this command getting same error (given below). I would be happy if anyone suggest me what exactly I have to do to solve this problem.

Can't exec "calcRoiCovg": No such file or directory at /home/unmc_gudalab/nitish123/perl5/lib/perl5/Genome/Model/Tools/Music/Bmr/CalcCovgHelper.pm line 183.
Failed to execute: calcRoiCovg /shared/unmc1/unmc_gudalab/nitish123/DbGAP/Reference-Platypus/TumorVsNormal/PACA104/Normal.bam /shared/unmc1/unmc_gudalab/nitish123/DbGAP/Reference-Platypus/TumorVsNormal/PACA104/Tumor.bam /shared/unmc1/unmc_gudalab/nitish123/Tools/music/roi_Ensemble_Homo_sapiens.hg38.77.tsv /shared/unmc1/unmc_gudalab/nitish123/DbGAP/Pancreatic/hg19-Pancreatic/hg19_UCSC.fa /shared/unmc1/unmc_gudalab/nitish123/DbGAP/Reference-Platypus/TumorVsNormal/coverage/roi_covgs/PACA-104-TUMOR.covg 6 8 20
Failed to execute: 'gmt music bmr calc-covg-helper --normal-tumor-bam-pair "PACA-104-TUMOR      /shared/unmc1/unmc_gudalab/nitish123/DbGAP/Reference-Platypus/TumorVsNormal/PACA104/Normal.bam  /shared/unmc1/unmc_gudalab/nitish123/DbGAP/Reference-Platypus/TumorVsNormal/PACA104/Tumor.bam" --roi-file "/shared/unmc1/unmc_gudalab/nitish123/Tools/music/roi_Ensemble_Homo_sapiens.hg38.77.tsv" --reference-sequence "/shared/unmc1/unmc_gudalab/nitish123/DbGAP/Pancreatic/hg19-Pancreatic/hg19_UCSC.fa" --output-file "/shared/unmc1/unmc_gudalab/nitish123/DbGAP/Reference-Platypus/TumorVsNormal/coverage/roi_covgs/PACA-104-TUMOR.covg"'

Thanks

Answer 1

[Cyriac Kandoth]

The command calcRoiCovg is not found in your PATH. Try Installation of the MuSiC suite on unsupported Linux distributions.