define PFAM dir in get_homologues perl script

Question

[dago]

I think this is really a trivial question but I am stuck on it.

I would like to use get_homologues to perform a comparative genomic analysis. It requires some dependencies, such as MCL, Blast, hmmer. I am using Biolinux 8 and most of them are installed already.

I follow the installation instructions. When checking the binaries needed I got the following:

 perl get_homologues.pl -v

Checking required binaries and data sources, all set in phyTools.pm :
        EXE_BLASTP : OK (path:/usr/local/lib/get_homologues-x86_64-20140930/bin/ncbi-blast-2.2.27+/bin/blastp)
        EXE_BLASTN : OK (path:/usr/local/lib/get_homologues-x86_64-20140930/bin/ncbi-blast-2.2.27+/bin/blastn)
      EXE_FORMATDB : OK (path:/usr/local/lib/get_homologues-x86_64-20140930/bin/ncbi-blast-2.2.27+/bin/makeblastdb)
           EXE_MCL : OK (path:/usr/local/lib/get_homologues-x86_64-20140930//bin/mcl-02-063/shmcl/mcl)
      EXE_MAKEHASH : OK (path:/usr/local/lib/get_homologues-x86_64-20140930//bin/COGsoft/COGmakehash/COGmakehash )
     EXE_READBLAST : OK (path:/usr/local/lib/get_homologues-x86_64-20140930//bin/COGsoft/COGreadblast/COGreadblast )
        EXE_COGLSE : OK (path:/usr/local/lib/get_homologues-x86_64-20140930//bin/COGsoft/COGlse/COGlse )
        EXE_COGTRI : OK (path:/usr/local/lib/get_homologues-x86_64-20140930//bin/COGsoft/COGtriangles/COGtriangles )
       EXE_HMMPFAM : Pfam-A.hmm file needs to be installed (ftp://ftp.sanger.ac.uk/pub/databases/Pfam/)

        EXE_INPARA : OK (path:/usr/local/lib/get_homologues-x86_64-20140930/_cluster_makeInparalog.pl)
         EXE_ORTHO : OK (path:/usr/local/lib/get_homologues-x86_64-20140930/_cluster_makeOrtholog.pl)
         EXE_HOMOL : OK (path:/usr/local/lib/get_homologues-x86_64-20140930/_cluster_makeHomolog.pl)
    EXE_SPLITBLAST : OK (path:/usr/local/lib/get_homologues-x86_64-20140930/_split_blast.pl)
  EXE_SPLITHMMPFAM : OK (path:/usr/local/lib/get_homologues-x86_64-20140930/_split_hmmscan.pl)

So I just needed to install PFAM. I downloaded as follow:

wget -N ftp://ftp.sanger.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz
gunzip Pfam-A.hmm.gz

I then changed the directory in the appropriate perl scipt to my actual dir where I have the Pfam-A.hmm, which is /usr/local/lib/Pfam-A.hmm

However, when I check again the binaries needed I still get the same message as above, telling me that Pfam-A is not installed.

Anyone can help me with this?

uname -a                                                                                                                                           [ 3:20PM]
Linux bl8vbox 3.13.0-39-generic #66-Ubuntu SMP Tue Oct 28 13:30:27 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux

Update

I downloaded again the Pfam-A.hmm.gz and this time it worked.

I run the get_homologues.pl with the option -D for Pfam search and I do not get any error. However, when I open the file resulted from the analysis XXX.fasta.pfam I do not have any data, but this message:

Error: Unrecognized format, trying to open hmm file /usr/local/lib/get_homologues-x86_64-20140930/db/Pfam-A.hmm for reading.

Any idea?

[komal.rathi]

Did you follow all the instructions given here? Did you install HMMER3? Did you run the commands given below:

Generate binary files for Pfam-A.hmm using

/your/path/hmmer-3.0/src/hmmpress Pfam-A.hmm

Edit file lib/phyTools.pm and modify the relevant line to:

if( ! defined($ENV{"PFAMDB"}) ){ $ENV{"PFAMDB"} = "db/Pfam-A.hmm"; }

[dago]

Thanks a lot.

Hmmer Is already installed in Biolinux. I followed the instruction as in the manual.

Answer 1

[b.contreras.moreira]

Hi Dago,

get_homologues is bundled with all the required sources/binaries, so after running install you should be ready to go if all you get are OKs. The install.pl script will also take care of pressing the PfamA.hmm file located at the $ENV{"PFAMDB"} location, as mentioned above. I do recommend proceeding this way, as thus the software is using compatible hmmpress and then hmmscan binaries. If you choose to press the hmms yourself then you should check that the hmmpress binary in biolinux is compatible with the bundled hmmscan binary,

Hope this helps

Bruno