Dear All,

for Getting calculate coverage,music2 bmr calc-covg command failed;but it is ok when i run calcRoiCovg command to get calculate coverage one by one.

Here is my run command:

1.music2 command:

music2 bmr calc-covg --roi-file /home/yuting/yuting/BreastCancer/SMGfolderrename/hg38.roi_file --reference-sequence /home/yuting/yuting/BreastCancer/SMGfolderrename/genome.fa --bam-list /home/yuting/yuting/BreastCancer/SMGfolderrename/renamebamlist --output-dir /home/yuting/yuting/BreastCancer/SMGfolderrename --cmd-list-file example.run-coverage-command

me/yuting/yuting/BreastCancer/SMGfolderrename --cmd-list-file example.run-coverage-command

bash example.run-coverage-command

it is fail to run,and showed this:

example.run-coverage-command: line 1: music2 bmr calc-covg-helper --normal-tumor-bam-pair="BC17preD /home/yuting/yuting/BreastCancer/SMGfolderrename/BC17conD.bam /home/yuting/yuting/BreastCancer/SMGfolderrename/BC17preD.bam" --roi-file=/home/yuting/yuting/BreastCancer/SMGfolderrename/hg38.roi_file --reference-sequence=/home/yuting/yuting/BreastCancer/SMGfolderrename/genome.fa --output-file=/home/yuting/yuting/BreastCancer/SMGfolderrename/roi_covgs/BC17preD.covg --normal-min-depth=6 --tumor-min-depth=8 --min-mapq=20 --bp-class-types=AT,CG,CpG: No such file or directory

2.when i run "music2 bmr calc-covg-helper", Again failed

music2 bmr calc-covg-helper command:

music2 bmr calc-covg-helper --normal-tumor-bam-pair="BC17preD /home/yuting/yuting/BreastCancer/SMGfolderrename/BC17conD.bam /home/yuting/yuting/BreastCancer/SMGfolderrename/BC17preD.bam" --roi-file=/home/yuting/yuting/BreastCancer/SMGfolderrename/hg38.roi_file --reference-sequence=/home/yuting/yuting/BreastCancer/SMGfolderrename/genome.fa --output-file=/home/yuting/yuting/BreastCancer/SMGfolderrename/roi_covgs/BC17preD.covg --normal-min-depth=6 --tumor-min-depth=8 --min-mapq=20 --bp-class-types=AT,CG,CpG

it is fail to run,and showed this:

: No such file or directory Use of uninitialized value $normal_bam in -s at /usr/local/share/perl5/TGI/MuSiC2/CalcCovgHelper.pm line 54. Use of uninitialized value $normal_bam in concatenation (.) or string at /usr/local/share/perl5/TGI/MuSiC2/CalcCovgHelper.pm line 54. Normal BAM file not found or is empty: Use of uninitialized value $tumor_bam in -s at /usr/local/share/perl5/TGI/MuSiC2/CalcCovgHelper.pm line 55. Use of uninitialized value $tumor_bam in concatenation (.) or string at /usr/local/share/perl5/TGI/MuSiC2/CalcCovgHelper.pm line 55. Tumor BAM file not found or is empty: Use of uninitialized value $normal_bam in -s at /usr/local/share/perl5/TGI/MuSiC2/CalcCovgHelper.pm line 56.

3.when i run "calcRoiCovg", it is ok

calcRoiCovg command:

calcRoiCovg /home/yuting/yuting/BreastCancer/SMGfolderrename/BC17conD.bam /home/yuting/yuting/BreastCancer/SMGfolderrename/BC17preD.bam /home/yuting/yuting/BreastCancer/SMGfolderrename/hg38.roi_file /home/yuting/yuting/BreastCancer/SMGfolderrename/genome.fa /home/yuting/yuting/BreastCancer/SMGfolderrename/roi_covgs/BC17preD.covg

it is ok. But I have to create an empty file named "BC17preD.covg" first, then run "calcRoiCovg", the result will be written in it.

4.I prepared bam-list using VIM.It is tab-delimited and like this:

BC17preD    /home/yuting/yuting/BreastCancer/SMGfolderrename/BC17conD.bam   /home/yuting/yuting/BreastCancer/SMGfolderrename/BC17preD.bam

I don't really know what's causing the error. Does any of you know where this is the problem? Thanks a lot,

Gengshen Yin