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
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
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.