Hello,
I am running ITASSER Suite on a computing network and it never gets past step 4a "run I-TASSER simulation". Before it even runs the first simulation, it times out. I have tried running one node with 24 processors for twenty hours and on two nodes with 48 processors for four hours. The output file reads:
"1. make seq.txt and rmsinp
Your protein contains 283 residues:
> Protein
MALKDDAVLIAARGYVYTAAVGTAAPTPSQLKLIDLEHPEAWDRTGWDLVGHTSEDDLPE
FGFDGGDSEVRGSWQKKKLREVETEEIADYVVINLTQFDESALELYFGPNQSATPGIFGV
KSGSVVNERALLIVIVDNDVRLGFHARKASLKREDAISLATDEFGALPVRATFLDYQSYN
LYEWIEEDWFNAADAPVVYLLDLGGATGGDYTLLVGGKSTGDIAYNANASAIKTAIGAVD
DGVAESAWTVTADGSDFEISGPLAVALGVDSTTGGSGVTVDVA
2.1 run Psi-blast
2.2 Secondary structure prediction was done before.
2.3 Predict solvent accessibility...
2.4 run pairmod
pair exist
3.1 do threading
/home/ek/ProteinSeq/Protein/init.PPAS exists
/home/ek/ProteinSeq/Protein/init.dPPAS exists
/home/ek/ProteinSeq/Protein/init.dPPAS2 exists
/home/ek/ProteinSeq/Protein/init.Env-PPAS exists
/home/ek/ProteinSeq/Protein/init.MUSTER exists
/home/ek/ProteinSeq/Protein/init.wPPAS exists
/home/ek/ProteinSeq/Protein/init.wdPPAS exists
/home/ek/ProteinSeq/Protein/init.wMUSTER exists
3.2 make restraints
4.1 run simulation
run 14 parallel simulations
run the first simulation job Proteinsim_1A"
I'm not sure if I'm doing something wrong. My command line is: "runI-TASSER.pl -libdir /depot/mylab/itasserlib -seqname Protein -datadir /home/ek/ProteinSeq/Protein".
Should I just keep trying for longer amounts of time? Or is there likely something wrong with my code?