Hello,
I have installed I-Tasser on the compute cluster here at Oregon State University. I have recently run into some problems concerning the JAVA_HOME variable. Basically, runI-TASSSER.pl doesn't seem to be able to find the JAVA_HOME directory despite it being set using the -java_home flag. When the -java_home flag is set, it eliminates some of the instances of this problem, but the program still stalls. Do you have any advice on this? I have attached a screen log of the latest run.
Thanks,
Zachary Landry
Graduate Research Assistant
Department of Microbiology
Oregon State University
[landryz@bact0 CO]$ runI-TASSER.pl -seqname 2521609321 -datadir /ubique2/landryz/proj/SAR202/itasser/CO/ -usrname landryz -java_home /usr/bin/java -libdir /raid1/home/micro/landryz/local/src/I-TASSER2.1/
Your setting is:
-libdir =/raid1/home/micro/landryz/local/src/I-TASSER2.1/
-seqname =2521609321
-datadir =/ubique2/landryz/proj/SAR202/itasser/CO/
-usrname =landryz
-runstyle =serial
-idcut =1
-ntemp =20
-nmodel =5
1. make seq.txt and rmsinp
2.1 run Psi-blast
2.3 run solve
2.4 run pairmod
2.4.1 removing homology templates based on and 1
2.4.2 running pair ................
FORTRAN STOP
3.1 do threading
start serial threading PPA
/tmp/landryz/IT2521609321
/ubique2/landryz/proj/SAR202/itasser/CO//PPA_2521609321
hostname: bact0.cgrb.oregonstate.local
starting time: Fri Feb 22 16:41:27 PST 2013
pwd: /tmp/landryz/IT2521609321
running zalign .....
ending time: Fri Feb 22 17:01:25 PST 2013
start serial threading dPPA
/tmp/landryz/IT2521609321
/ubique2/landryz/proj/SAR202/itasser/CO//dPPA_2521609321
hostname: bact0.cgrb.oregonstate.local
starting time: Fri Feb 22 17:01:27 PST 2013
pwd: /tmp/landryz/IT2521609321
running zalign .....
ending time: Fri Feb 22 17:29:27 PST 2013
start serial threading dPPA2
/tmp/landryz/IT2521609321
/ubique2/landryz/proj/SAR202/itasser/CO//dPPA2_2521609321
hostname: bact0.cgrb.oregonstate.local
starting time: Fri Feb 22 17:29:28 PST 2013
pwd: /tmp/landryz/IT2521609321
running zalign .....
ending time: Fri Feb 22 17:52:33 PST 2013
start serial threading sPPA
/tmp/landryz/IT2521609321
/ubique2/landryz/proj/SAR202/itasser/CO//sPPA_2521609321
hostname: bact0.cgrb.oregonstate.local
starting time: Fri Feb 22 17:52:35 PST 2013
pwd: /tmp/landryz/IT2521609321
running zalign .....
ending time: Fri Feb 22 18:26:05 PST 2013
start serial threading MUSTER
/tmp/landryz/IT2521609321
/ubique2/landryz/proj/SAR202/itasser/CO//MUSTER_2521609321
hostname: bact0.cgrb.oregonstate.local
starting time: Fri Feb 22 18:26:06 PST 2013
pwd: /tmp/landryz/IT2521609321
running Psi-blast .....
running zalign .....
./zalign 7.01 0.55 0.66 1.6 -0.99 0.31 0.19 0 1.0 0.39 0.19
==>1sb3D 1sb3D 30.7685949723897 29.738338738654
1sb3D 1sb3D 29 29
score_flag=1
ending time: Fri Feb 22 19:35:47 PST 2013
start serial threading wPPA
/tmp/landryz/IT2521609321
/ubique2/landryz/proj/SAR202/itasser/CO//wPPA_2521609321
hostname: bact0.cgrb.oregonstate.local
starting time: Fri Feb 22 19:35:48 PST 2013
pwd: /tmp/landryz/IT2521609321
running Psi-blast .....
JAVA_HOME setting is not correct
start serial threading wdPPA
/tmp/landryz/IT2521609321
/ubique2/landryz/proj/SAR202/itasser/CO//wdPPA_2521609321
hostname: bact0.cgrb.oregonstate.local
starting time: Fri Feb 22 20:33:16 PST 2013
pwd: /tmp/landryz/IT2521609321
running Psi-blast .....
JAVA_HOME setting is not correct
start serial threading wMUSTER
/tmp/landryz/IT2521609321
/ubique2/landryz/proj/SAR202/itasser/CO//wMUSTER_2521609321
hostname: bact0.cgrb.oregonstate.local
starting time: Fri Feb 22 21:30:06 PST 2013
pwd: /tmp/landryz/IT2521609321
running Psi-blast .....
running Psi-blast .....
JAVA_HOME setting is not correct