RUN genome music (MuSiC2) error

Question

[Haitao]

Dear All,

From Install to run, I took almost one and half week, but still can not run MuSiC2 successfully.

Here is my install log and run command:

INSTALL log: (non-root install)

1. For low version of samtools-0.1.19, can not install, shown error, I have got the way to solve the problem: download the zlib; cd zlib-1.2.8/; make; Change samtools Makefile: CFLAGS="-O3 -fPIC" ./configure # --prefix=/home/haitaowang/zlib-1.2.8/; make; make install
2. calcRoiCovg: copy zlib-1.2-8/lib to samtools-0.1.19/; then cd calcRoiCovg/; make
3. Joinx I can easily to install, no any error
4. Change .bashrc put $PATH samtools, calcRoiCovg, Joinx
5. Use cpanm install MuSiC2

Then: I can active music2 Program: music2 - Mutational Significance in Cancer (Cancer Mutation Analysis) version 2. Version: v0.1

Author: Beifang Niu && Cyriac Kandoth Usage: music2 <command> [options]

Key commands: bmr ...........

I prepared my bam-list, ROI, reference

bam-list like:

417T_GATK_Variants_filtered /home//kumar/C059.bam   /home/kumar/417T.bam
C059_GATK_Variants_filtered     /home/kumar/E717.bam    /home/kumar/C059.bam

ROI

1       3073251 3074324 4933401J01Rik
1       3102014 3102127 Gm26206
1       3205899 3207319 Xkr4
1       3213437 3216970 Xkr4
1       3252755 3253238 Gm18956

reference

>1 dna:chromosome chromosome:GRCm38:1:1:195471971:1 REF
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

music command

music2 bmr calc-covg \ 
--bam-list /home/haitaowang/Project/Wenhui_DNA/music/list.txt \
--roi-file /home/haitaowang/Database/roi_file_for_music \
--reference-sequence /home/haitaowang/Database/Mus_musculus.GRCm38.fa \
--output-dir /home/haitaowang/Project/Wenhui_DNA/music/output

then I got such error

417T_GATK_Variants_filtered.covg not found in /home/haitaowang/Project/Wenhui_DNA/music/output/roi_covgs. please make a command list file to run calcRoiCovg !

then I checked created output file:

1. total_covgs: (only show header) Sample Covered_Bases AT_Bases_Covered CpG_Bases_Covered CG_Bases_Covered

2. roi_covgs (empty)

3. gene_covgs (empty)

If I changed the command like this:

music2 bmr calc-covg \
--bam-list /home/haitaowang/Project/Wenhui_DNA/music/list.txt \
--roi-file roi_file_for_music \
--reference-sequence mm10.fa \
--output-dir output/417T_GATK_Variants_filtered.covg \
--normal-min-depth 6 \
--tumor-min-depth 8 \
--min-mapq 20 \
--bp-class-types AT,CpG,CG

then the error show like this: Can't call method "print" on an undefined value at /home/haitaowang/.perlbrew/libs/perl-5.24.0@lib001/lib/perl5/TGI/MuSiC2/CalcCovg.pm line 108.

Thanks in advance if any one can help this! Haitao

[Cyriac Kandoth]

1. What are the instructions you are following? Have you seen this: Installation of the MuSiC suite on unsupported Linux distributions
2. Does your system have docker installed? This will nearly obsolete the need for installation.
3. "zlib" is a popular development library, so it makes sense for a root user to install it system-wide. You should not need to compile it from scratch for samtools.
4. What is the operating system you are using? Run command cat /etc/*release to find out.
5. If it is a cluster of compute nodes, what job scheduler does it use? E.g. LSF, SGE, PBS/Torque, etc?

[Haitao]

1. I'm following the instructions from MuSiC2 github: https://github.com/ding-lab/MuSiC
2. We don't have docker been installed.
3. NA
4. CentOS release 6.6 (Final) LSB_VERSION=base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch CentOS release 6.6 (Final) Rocks release 6.2 (SideWinder) CentOS release 6.6 (Final)
5. Yes. it is a cluster of compute nodes, but I'm not familiar with scheduler things.

I also try to install the old version (genome-music-0.4.1), before yesterday it is can not be installed, still have problem when I build music, the error like this:

failed to extract pod: : Error while autoloading with 'use Genome::Model::Tools::Music::Survival': Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at /home/haitaowang/.cpanm/work/1476924800.15296/genome-music-0.4.1/blib/lib/Genome/Model/Tools/Music/Survival.pm line 336.

Later, I download "Genome/Model/Tools/Music/Survival.pm" from github, and modify the script:

#check to see if this gene is on the list (if there is a list at all)
        if( defined @{$mutated_genes_to_include} ) {
            next unless (scalar grep { m/^$gene$/ } @{$mutated_genes_to_include});
        }

to

  #check to see if this gene is on the list (if there is a list at all)
            if( defined **() and** @{$mutated_genes_to_include} ) {
                next unless (scalar grep { m/^$gene$/ } @{$mutated_genes_to_include});
            }

then, It is work.

[Haitao]

Thanks, Cyriac. I'm still think why MuSiC2 not run in our HPC_jade, I try to run calcRoiCovg independently, It is work well, so I don't know if there are any library problem? (coz i didn't follow to install libbz2-dev and libgtest-dev, honestly, our manager didn't install apt-get function on HPC, I don't know how to install without root privileges)

the old version now running.

Thanks again, Haitao