Pfam searching is taking a really long time. Why?
In order to better mirror the results of the Pfam server, InterProScan now searches both LS and FS models (for more information on LS and FS models, see the Pfam website). This means that the number of models which need searching is doubled and hence so is the search time. If you do not wish to search the FS models (you will not miss too many hits if you don’t) you can do this by replacing the file that comes wih InterProScan (“Pfam”) with a file from the Pfam ftp site (Pfam_ls). Rename Pfam_ls so that it is called “Pfam” and put it in the iprscan/data directory. You will then need to run bin/index_data.pl -inx -bin -f Pfam in order to index the file for InterProScan and convert it into the HMMER binary format. The binary conversion uses hmmconvert, if not present into your bin archive, please download the hmmer package from http://hmmer.wustl.edu/ for your platform and copy it into iprscan/bin/binaries.
