tamuanand

Hi Milot, Thanks for taking the time to respond. I have some follow up questions 1. I am building a customized database with sequences from ~20 species. Do you still...

Thanks Milot. I have used this as the guide (Section 3.5 - Building Customized Databases) https://github.com/soedinglab/hh-suite/blob/master/hhsuite- userguide.pdf and I have been able to run the first 2 steps (split fasta...

This step worked mpirun -np 16 ffindex_apply_mpi ecoli.fa.ff{data,index} -i ecoli_a3m_wo_ss.ffindex -d ecoli_a3m_wo_ss.ffdata -- hhblits -d uniprot20_2016_02 -i stdin -oa3m stdout -n 3 -cpu 1 -v 0 This step errs out...

Hi Milot I downloaded psipred from here: http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/old_versions/psipred.4.0.tar.gz Then did a tar -xzvf and then changed the paths within runpsipred to point to my blast install All the errors in...

Thanks Milot - that seemed to take care of the errors. However, the *_a3m.ffdata file produced at this step is empty - is that expected? The *_a3m.ffindex seems to have...

I keep getting errors about makemat. Do I have to download makemat separately - I do not find it within my blast suite (2.2.25). This is the log /CentOS_6.4/hhsuite/r-3.0-beta.3/scripts/reformat.pl -v...

ok - do you recommend 2.2.24 or any other version. thanks in advance

Hi I downloaded legacy blast, changed the relevant variables/paths etc When I run mpirun -np 16 ffindex_apply_mpi ecoli_a3m_wo_ss.ff{data,index} -i ecoli_a3m.ffindex -d ecoli_a3m.ffdata -- addss.pl -v 0 stdin stdout these are...

Hi Andrea and Milot, No I have not been able to resolve this - I have paused working on this temporarily after several tries. I would start re-work on this...

Hello Andrea, I see that you mentioned that you have been trying to get HHSuite to work on AWS. If so, would you be willing to share the AWS blueprint...