I am still facing problems in running the I-TASSER program and need help from experts.
I ran a serial run after fixing for the Java Home in the code. Below is the log of the run. Can somebody please help me in fixing the code/program for the errors in bold:
sh: line 1: 31332 Killed /usr/global/java/jdk1.6.0_45/bin/java -Xms2512m -Xmx2512m -jar fNNNd.jar > rst.dat
/bin/cp: cannot stat `pair.3': No such file or directory
/bin/cp: cannot stat `pair.1': No such file or directory
/bin/cp: cannot stat `/gpfs/home/usr123/work/rbseqdata/SEQ1234/pair1.dat': No such file or directory
/bin/cp: cannot stat `/gpfs/home/usr123/work/rbseqdata/SEQ1234/pair3.dat': No such file or directory
Full Log:
[usr123@SERVER rbseqdata]$ $HOME/work/I-TASSER2.1/I-TASSERmod/runI-TASSER.pl -libdir $HOME/work/I-TASSER2.1 -seqname SEQ1234 -datadir $HOME/work/rbseqdata/SEQ1234 -usrname usr123
Your setting is:
-libdir =/gpfs/home/usr123/work/I-TASSER2.1
-seqname =SEQ1234
-datadir =/gpfs/home/usr123/work/rbseqdata/SEQ1234
-usrname =usr123
-runstyle =serial
-idcut =1
-ntemp =20
-nmodel =5
1. make seq.txt and rmsinp
2.1 run Psi-blast
2.2 run PSSpred
2.3 run solve
2.3 run solve
2.4 run pairmod
2.4.1 removing homology templates based on real and 1
2.4.2 running pair ................
/bin/cp: cannot stat `pair.3': No such file or directory
/bin/cp: cannot stat `pair.1': No such file or directory
3.1 do threading
start serial threading PPA
/tmp/usr123/ITSEQ1234
/gpfs/home/usr123/work/rbseqdata/SEQ1234/PPA_SEQ1234
hostname: SERVER.aset.univ.edu
starting time: Sat Nov 16 14:07:00 EST 2013
pwd: /tmp/usr123/ITSEQ1234
running zalign .....
ending time: Sat Nov 16 14:34:49 EST 2013
start serial threading dPPA
/tmp/usr123/ITSEQ1234
/gpfs/home/usr123/work/rbseqdata/SEQ1234/dPPA_SEQ1234
hostname: SERVER.aset.univ.edu
starting time: Sat Nov 16 14:34:51 EST 2013
pwd: /tmp/usr123/ITSEQ1234
running zalign .....
ending time: Sat Nov 16 15:20:53 EST 2013
start serial threading dPPA2
/tmp/usr123/ITSEQ1234
/gpfs/home/usr123/work/rbseqdata/SEQ1234/dPPA2_SEQ1234
hostname: SERVER.aset.univ.edu
starting time: Sat Nov 16 15:20:54 EST 2013
pwd: /tmp/usr123/ITSEQ1234
running zalign .....
ending time: Sat Nov 16 16:07:40 EST 2013
start serial threading sPPA
/tmp/usr123/ITSEQ1234
/gpfs/home/usr123/work/rbseqdata/SEQ1234/sPPA_SEQ1234
hostname: SERVER.aset.univ.edu
starting time: Sat Nov 16 16:07:42 EST 2013
pwd: /tmp/usr123/ITSEQ1234
running zalign .....
ending time: Sat Nov 16 16:59:32 EST 2013
start serial threading MUSTER
/tmp/usr123/ITSEQ1234
/gpfs/home/usr123/work/rbseqdata/SEQ1234/MUSTER_SEQ1234
hostname: SERVER.aset.univ.edu
starting time: Sat Nov 16 16:59:34 EST 2013
pwd: /tmp/usr123/ITSEQ1234
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
==>3dh4A 3dh4A 14.9883548821199 15.1226620332629
3dh4A 3dh4A 14 14
score_flag=1
ending time: Sat Nov 16 18:05:15 EST 2013
start serial threading wPPA
/tmp/usr123/ITSEQ1234
/gpfs/home/usr123/work/rbseqdata/SEQ1234/wPPA_SEQ1234
sh: line 1: 31332 Killed /usr/global/java/jdk1.6.0_45/bin/java -Xms2512m -Xmx2512m -jar fNNNd.jar > rst.dat
hostname: SERVER.aset.univ.edu
starting time: Sat Nov 16 18:05:17 EST 2013
pwd: /tmp/usr123/ITSEQ1234
running Psi-blast .....
ending time: Sat Nov 16 19:24:34 EST 2013
start serial threading wdPPA
/tmp/usr123/ITSEQ1234
/gpfs/home/usr123/work/rbseqdata/SEQ1234/wdPPA_SEQ1234
sh: line 1: 32053 Killed /usr/global/java/jdk1.6.0_45/bin/java -Xms2512m -Xmx2512m -jar fGGGd.jar > rst.dat
hostname: SERVER.aset.univ.edu
starting time: Sat Nov 16 19:24:36 EST 2013
pwd: /tmp/usr123/ITSEQ1234
running Psi-blast .....
ending time: Sat Nov 16 20:40:58 EST 2013
start serial threading wMUSTER
/tmp/usr123/ITSEQ1234
/gpfs/home/usr123/work/rbseqdata/SEQ1234/wMUSTER_SEQ1234
sh: line 1: 353 Killed /usr/global/java/jdk1.6.0_45/bin/java -Xms2512m -Xmx2512m -jar fQQQ.jar > rst.dat
hostname: SERVER.aset.univ.edu
starting time: Sat Nov 16 20:40:59 EST 2013
pwd: /tmp/usr123/ITSEQ1234
running Psi-blast .....
running Psi-blast .....
==>3dh4A 3dh4A 20.5367885261286 20.2885694463166
3dh4A 3dh4A 15.19 15.19
score_flag=1
ending time: Sat Nov 16 22:21:16 EST 2013
3.2 make restraints
4.1 run simulation
run 15 serial simulations
run simulation job 1 / 15
/bin/cp: cannot stat `/gpfs/home/usr123/work/rbseqdata/SEQ1234/pair1.dat': No such file or directory
/bin/cp: cannot stat `/gpfs/home/usr123/work/rbseqdata/SEQ1234/pair3.dat': No such file or directory
run simulation job 2 / 15
/bin/cp: cannot stat `/gpfs/home/usr123/work/rbseqdata/SEQ1234/pair1.dat': No such file or directory
/bin/cp: cannot stat `/gpfs/home/usr123/work/rbseqdata/SEQ1234/pair3.dat': No such file or directory
run simulation job 3 / 15
/bin/cp: cannot stat `/gpfs/home/usr123/work/rbseqdata/SEQ1234/pair1.dat': No such file or directory
/bin/cp: cannot stat `/gpfs/home/usr123/work/rbseqdata/SEQ1234/pair3.dat': No such file or directory
run simulation job 4 / 15
/bin/cp: cannot stat `/gpfs/home/usr123/work/rbseqdata/SEQ1234/pair1.dat': No such file or directory
/bin/cp: cannot stat `/gpfs/home/usr123/work/rbseqdata/SEQ1234/pair3.dat': No such file or directory
run simulation job 5 / 15
/bin/cp: cannot stat `/gpfs/home/usr123/work/rbseqdata/SEQ1234/pair1.dat': No such file or directory
/bin/cp: cannot stat `/gpfs/home/usr123/work/rbseqdata/SEQ1234/pair3.dat': No such file or directory
run simulation job 6 / 15
/bin/cp: cannot stat `/gpfs/home/usr123/work/rbseqdata/SEQ1234/pair1.dat': No such file or directory
/bin/cp: cannot stat `/gpfs/home/usr123/work/rbseqdata/SEQ1234/pair3.dat': No such file or directory
run simulation job 7 / 15
/bin/cp: cannot stat `/gpfs/home/usr123/work/rbseqdata/SEQ1234/pair1.dat': No such file or directory
/bin/cp: cannot stat `/gpfs/home/usr123/work/rbseqdata/SEQ1234/pair3.dat': No such file or directory
run simulation job 8 / 15
/bin/cp: cannot stat `/gpfs/home/usr123/work/rbseqdata/SEQ1234/pair1.dat': No such file or directory
/bin/cp: cannot stat `/gpfs/home/usr123/work/rbseqdata/SEQ1234/pair3.dat': No such file or directory
run simulation job 9 / 15
/bin/cp: cannot stat `/gpfs/home/usr123/work/rbseqdata/SEQ1234/pair1.dat': No such file or directory
/bin/cp: cannot stat `/gpfs/home/usr123/work/rbseqdata/SEQ1234/pair3.dat': No such file or directory
run simulation job 10 / 15
/bin/cp: cannot stat `/gpfs/home/usr123/work/rbseqdata/SEQ1234/pair1.dat': No such file or directory
/bin/cp: cannot stat `/gpfs/home/usr123/work/rbseqdata/SEQ1234/pair3.dat': No such file or directory
run simulation job 11 / 15
/bin/cp: cannot stat `/gpfs/home/usr123/work/rbseqdata/SEQ1234/pair1.dat': No such file or directory
/bin/cp: cannot stat `/gpfs/home/usr123/work/rbseqdata/SEQ1234/pair3.dat': No such file or directory
run simulation job 12 / 15
/bin/cp: cannot stat `/gpfs/home/usr123/work/rbseqdata/SEQ1234/pair1.dat': No such file or directory
/bin/cp: cannot stat `/gpfs/home/usr123/work/rbseqdata/SEQ1234/pair3.dat': No such file or directory
run simulation job 13 / 15
/bin/cp: cannot stat `/gpfs/home/usr123/work/rbseqdata/SEQ1234/pair1.dat': No such file or directory
/bin/cp: cannot stat `/gpfs/home/usr123/work/rbseqdata/SEQ1234/pair3.dat': No such file or directory
run simulation job 14 / 15
/bin/cp: cannot stat `/gpfs/home/usr123/work/rbseqdata/SEQ1234/pair1.dat': No such file or directory
/bin/cp: cannot stat `/gpfs/home/usr123/work/rbseqdata/SEQ1234/pair3.dat': No such file or directory
run simulation job 15 / 15
/bin/cp: cannot stat `/gpfs/home/usr123/work/rbseqdata/SEQ1234/pair1.dat': No such file or directory
/bin/cp: cannot stat `/gpfs/home/usr123/work/rbseqdata/SEQ1234/pair3.dat': No such file or directory
5.1 do clustering
No. of trajectory files: 45
8.000000 3.500000 12.00000
5.2 build full-atomic model
/gpfs/home/usr123/work/I-TASSER2.1/I-TASSERmod/EMrefinement.pl /gpfs/home/usr123/work/rbseqdata/SEQ1234 /gpfs/home/usr123/work/I-TASSER2.1/abs/mybin closc1.pdb combo1.pdb SEQ1234 usr123
/gpfs/home/usr123/work/I-TASSER2.1/I-TASSERmod/EMrefinement.pl /gpfs/home/usr123/work/rbseqdata/SEQ1234 /gpfs/home/usr123/work/I-TASSER2.1/abs/mybin closc2.pdb combo2.pdb SEQ1234 usr123
/gpfs/home/usr123/work/I-TASSER2.1/I-TASSERmod/EMrefinement.pl /gpfs/home/usr123/work/rbseqdata/SEQ1234 /gpfs/home/usr123/work/I-TASSER2.1/abs/mybin closc3.pdb combo3.pdb SEQ1234 usr123
/gpfs/home/usr123/work/I-TASSER2.1/I-TASSERmod/EMrefinement.pl /gpfs/home/usr123/work/rbseqdata/SEQ1234 /gpfs/home/usr123/work/I-TASSER2.1/abs/mybin closc4.pdb combo4.pdb SEQ1234 usr123
/gpfs/home/usr123/work/I-TASSER2.1/I-TASSERmod/EMrefinement.pl /gpfs/home/usr123/work/rbseqdata/SEQ1234 /gpfs/home/usr123/work/I-TASSER2.1/abs/mybin closc5.pdb combo5.pdb SEQ1234 usr123
78674[usr123@SERVER rbseqdata]$