Error while runing music2

Question

[arsenew2012]

hello everybody,

I am using music2 to find significantly mutated gene in a cancer dataset.

After I ran this command:

music2 smg \
      --gene-mr-file output_dir/gene_mrs \
      --output-file output_dir/smgs

I have this error which I can't figure out where it is comming from

#More CG_Transitions seen in PLOD2 than there are bps with sufficient coverage!
#More CG_Transitions seen in POLA1 than there are bps with sufficient coverage!
#More CG_Transitions seen in PPOX than there are bps with sufficient coverage!
#More CG_Transitions seen in PPP1R1B than there are bps with sufficient coverage!
#More CG_Transversions seen in PRAMENP than there are bps with sufficient coverage!
#More CG_Transversions seen in PRRC2C than there are bps with sufficient coverage!
#More CG_Transversions seen in PUS3 than there are bps with sufficient coverage!
#More CG_Transversions seen in RBBP4 than there are bps with sufficient coverage!

Although the I have this error the software still give me some results.

Could someone help me to find the reason for this?

Thank you in advance

[Bastien Hervé]

In the code it is a warning (maybe you will have trouble, maybe not) not an error.

if ( $type ne "Overall" and $covd_bps < $mut_cnt ) { warn "#More $type seen in $gene than there are bps with sufficient coverage!\n"; }

It is your job to detect if this warning is significant in your study or not

Answer 1

[arsenew2012]

I made further investigations regarding the warning above and I discovered another problem.

In the file gene_mrs (which is generated from music2 after step 2: music bmr calc-bmr) in my output-dir, the numbers in lines CpG_Transitions (Covered_Bases) and CG_Transitions (Covered_Bases) are reversed.

For instance in my data set: CpG_Transitions (Covered_Bases) = 0, CpG_Transversion (Covered_Bases) = 0, CG_Transitions (Covered_Bases) = 40230

But the music2 execution gives me: CpG_Transitions (Covered_Bases) = 40230, CpG_Transversion (Covered_Bases) = 40230, CG_Transitions (Covered_Bases) = 0

And because I have 1 mutation in CG but 0 CG_Transitions (covered bases), the warning shows. Which is actually wrong because in my data set I have 40230 CG_Transition (covered_bases)

This bug is coming from file CalcBmr.pm in music2 code. While reading the sample_covg_file at line 265:

my ( $gene, undef, $covd_bases, $covd_at_bases, $covd_cg_bases, $covd_cpg_bases ) = split( /\t/, $line );

They are reading $covd_cg_bases before $covd_cpg_bases although in the header of the file sample_covg_file generated from the software, CpG_Bases_Covered is listed before CG_Bases_Covered.

This is probably a bug, causing the warning I get and probably causing erroneous results.

Please is there someone who knows itself with music2?
I am not sure how to fix this. I was thinking about just change it in the pat of the code but I am not sure if there will be any aftermath regarding the execution of the rest.

I would be glad for any help