MuSic Pfam file path in Linux RHEL

Question

[Nitish Mishra]

Hi,

I am trying to use MuSic for pfam annotation on Linux RHEL system. I already downloaded pfam, cosmic-omim data (genome-databases_1-1.tar.gz) in my home directory from http://apt.genome.wustl.edu/ubuntu/pool/main/g/genome-databases/ (as explained in Tutorial: Installation of the MuSiC suite on unsupported Linux distributions). I don't know how I can use pfam data in genome music pfam.

Command:

music pfam --maf-file Total_fpfilter.maf --output-file Total_fpfilter.maf.pfam
ERROR: Cannot find the pfam db path. at /usr/local/share/perl5/Genome/Model/Tools/Music/Pfam.pm line 89, <GEN5> line 3.

Can I just give the path at line 89 of Pfam.pm

my $db_path = Genome::Sys->dbpath( 'pfam', 'latest' ) or die "Cannot find the pfam db path.";

I am not sure I can give my pfam data path. Let I have pfam data at /shared/unmc1/unmc_gudalab/nitish123/Tools/music/genome-databases-1/db/pfam/latest. So I can change line 89 of Pfam.pm (my $db_path = Genome::Sys->dbpath( 'pfam', 'latest' ) or die "Cannot find the pfam db path.";)

By using:

Option1::

my $db_path = '/shared/unmc1/unmc_gudalab/nitish123/Tools/music/genome-databases-1/db/pfam/latest';

Option2::

$path=/shared/unmc1/unmc_gudalab/nitish123/Tools/music/genome-databases-1/db/pfam/latest';
my $db_path = Genome::Sys->dbpath('$path') or die "Cannot find the pfam db path.";

Option3::

my $db_path = Genome::Sys->dbpath('/shared/unmc1/unmc_gudalab/nitish123/Tools/music/genome-databases-1/db/pfam/latest') or die "Cannot find the pfam db path.";

Answer 1

[nnutter]

I think you need to set the GENOME_DB environment variable. For example,

$ export GENOME_DB='/shared/unmc1/unmc_gudalab/nitish123/Tools/music/genome-databases-1/db'
$ perl -MGenome -e 'print Genome::Sys->dbpath(qw(pfam latest)), qq(\n)'
/shared/unmc1/unmc_gudalab/nitish123/Tools/music/genome-databases-1/db/pfam/latest

[Nitish Mishra]

Thanks for reply. I just export the path of pfam database. I am getting result file but same time I am getting this error

[tabix] the index file either does not exist or is older than the vcf file. Please reindex.

[nnutter]

You'll need to generate an index for the VCF file with tabix. However, I don't know the exact command to accomplish that.

Edit: It looks like there are tabix-related questions asked here, for example, Question: Generate Vcf.Gz File And Its Index File Vcf.Gz.Tbi.