I am still trying to run the prokaryotic annotation pipeline and am now stuck
at the overlap_analysis.default component. With Jason's recent post I could fix
the problem which was making this component trying to submit to SGE but now I
have another quite major problem.
First of all I must tell that in order to use the latest Pfam-A and TIGRFAMs HMM
databases (which all require HMM version 3 format) I have replaced the hmmpfam
component with the hmmpfam3 component in that very same pipeline. Btw: for more
information on this please see my previous post on May 5th. So after replacing
hmmpfam with hmmpfam3 component the pipeline worked nicely but now the problem
is that the overlap_analysis.default requires BSML files in order to proceed and
these files should have been outputted by hmmpfam3. Unfortunately, it looks like
hmmpfam3 component doesn't include any processing of the raw result files and as
such doesn't generate any BSML files.
I compared hmmpfam3 component with the older hmmpfam component and noticed that
hmmpfam3 really doesn't include any processing of the raw results as it looks
like the scripts for that are missing (no hmmpfam32bsml.pl script for example).
So I have two questions here: can I assume that the hmmpfam3 component is not
finished yet and shouldn't be used yet? And in the worst case, is there any way
that I can skip the overlap_analysis.default component and if yes how?