Music Bmr Calc-Bmr: Division By Zero Error

Question

[cfan2004]

Hi,

I am using genome music bmr calc-bmr

music bmr calc-bmr \
    --bam-list input_dir/bam_list \
    --maf-file input_dir/myMAF.tsv \
    --output-dir output_dir/ \
    --reference-sequence input_dir/all_sequences.fa \
    --roi-file input_dir/all_coding_exons.tsv

Got this error message:

Loading per-sample coverages stored in /home/user/Music/total_covgs
Loading per-gene coverage files stored under /home/user/Music/gene_covgs/
Running 'joinx1.6 ref-stats' to read reference FASTA and identify SNVs at AT, CG, CpG sites
Parsing MAF file to classify mutations
Finished Parsing the MAF file to classify mutations
Skipped 290472 mutation(s) that belong to unrecognized samples
ERROR: Illegal division by zero at /usr/share/perl5/Genome/Model/Tools/Music/Bmr/CalcBmr.pm line 488.

Does anyone know where did the error come from and how to fix it?

Thank you. FC

Answer 1

[Istvan Albert]

Well it pretty much looks like you have a naming problem perhaps the chromosomes are named differently that leads to an empty set.

Answer 2

[Cyriac Kandoth]

Istvan is right. More specifically, notice the message that says "Skipped 290472 mutation(s) that belong to unrecognized samples". My guess is that 290472 is the total number of mutations in your MAF file. They were all skipped because the sample IDs in the MAF (column 16) do no match the sample IDs listed in the BAM list. This is required, as per the documentation.

~Cyriac