Error When Running The Music Bmr

Question

[yliubu]

I am now using MuSiC to calculate BMR, but there is an error. The command I use is

> genome music bmr calc-wig-covg --wig-list=/home/share/input/wig_list.txt --output-dir=/home/share/output --reference-sequence=/home/share/input/allgenome_hg18.fa --roi-file=/home/share/input/roi_sorted.tsv

And the error message is:

killed

Use of uninitialized value $cg_covd in addition (+) at /usr/share/perl5/Genome/Model/Tools/Music/Bmr/CalcWigCovg.pm line 222, <GEN8> line 4775.
Use of uninitialized value $at_covd in addition (+) at /usr/share/perl5/Genome/Model/Tools/Music/Bmr/CalcWigCovg.pm line 222, <GEN8> line 4775.
Use of uninitialized value $cpg_covd in addition (+) at /usr/share/perl5/Genome/Model/Tools/Music/Bmr/CalcWigCovg.pm line 222, <GEN8> line 4775.
Use of uninitialized value $at_covd in addition (+) at /usr/share/perl5/Genome/Model/Tools/Music/Bmr/CalcWigCovg.pm line 223, <GEN8> line 4775.
Use of uninitialized value $cg_covd in addition (+) at /usr/share/perl5/Genome/Model/Tools/Music/Bmr/CalcWigCovg.pm line 224, <GEN8> line 4775.
Use of uninitialized value $cpg_covd in addition (+) at /usr/share/perl5/Genome/Model/Tools/Music/Bmr/CalcWigCovg.pm line 225, <GEN8> line 4775.

Anybody know how to solve this problem? Even I got such message, I can still get the folders of gene_covg and roi_covgs, and a total_covgs file. Can I use these files to do following path-scan analysis? Thanks in advance!

[yliubu]

The input file is like this: roi_sorted.tsv: 1 69090 70008 OR4F5 1 861120 879961 SAMD11 1 879582 894679 NOC2L 1 895966 901095 KLHL17

wig_list.txt: TCGA-A1-A0SD-01 /home/share/input/BRCA/Coverage/TCGA-A1-A0SD-01.wig

Answer 1

[Christian]

I encounted the same problem and found its cause. The joinx1.6 command in the script CalcWigCovg.pm removes the 'chr' chromosome name prefix by default, and this results in zero coverage values in the output if your other input files do have the 'chr' prefix. Unforunately, there is currently no parameter of genome music bmr calc-wig-covg to change this default behaviour.

To fix this problem, I removed the -c parameter from the two joinx1.6 commands in the file CalcWigCovg.pm (i.e. change from joinx1.6 wig2bed -Zc to joinx1.6 wig2bed -Z). I guess alternatively you could remove the chr prefix from all your input files.

Answer 2

[yliubu]

I extracted only one sample from wig.list and extracted all genes in this sample in roi_sorted.tsv, perform BMR with the above command, it works well without any error. But as long as I include all genes (around 10000) in roi_sorted.tsv, it is killed.

And when I use correctly generated gene_covgs files from that single sample to run path-scan, I always got error message like this:

skipping silent mutation in gene *.

skipping silent mutation in gene *. ...

Error: Can’t call method “print” on an undefined value at /usr/share/perl5/Genome/Model/Tools/Music/PathScan.pm line 403

Is there anybody know how to fix this problem? Thanks so much!

Answer 3

[Cyriac Kandoth]

Here are a few suggestions of where to check for problems:

1. Make sure that you have properly installed joinx and the other dependencies, per the instructions at - /post 62793
2. Ensure that the MAF file, reference fasta, BAM files, and ROI file, all use the same chromosome naming conventions and the same genomic bounds. For example, if your BAMs and reference fasta use the chr-prefix for chromosome names, then the MAF and ROI files should use the same. And definitely make sure you don't mix hg18 with hg19. MAF column 4 specifies which reference build is in use
3. Ensure that all your files are properly tab-delimited, and are using the UNIX formatted newlines "\n" rather than the Windows newlines "\r\n"
4. bmr calc-bmr uses the gene names in column 1 of the MAF to match variants to their respective ROIs. So ensure that the annotation database used to construct your ROI file is the same database used to annotate your MAF file