`DRAM` running time

[ZeroDesigner]

Hi, I am racently using DRAMv and follow this protocol https://www.protocols.io/view/viral-sequence-identification-sop-with-virsorter2-btv8nn9w?step=1. Could you tell how much time DRAMv will take ? How can I estimate the time?

[shafferm]

How long DRAM-v will take to run depends on your data set size. Usually a virus takes about 5-10 minutes with 20 processors and we are looking into ways to speed up DRAM-v all the time!

[hyphaltip]

Have you explored hmmsearch + MPI for another speedup? - I am happy to try to help @shafferm eg based on http://cryptogenomicon.org/hmmscan-vs-hmmsearch-speed-the-numerology.html simple cmndline differences https://github.com/ucr-hpcc/hpcc_slurm_examples/tree/master/hmmer

[shafferm]

I have had bad experiences getting MPI to work in the past so I have tried to avoid it. Do you only need to add the --mpi flag. What other dependencies does it introduce and what happens if you use the flag and don't have MPI set up?

[rmFlynn]

Worth looking into again