-> When i was running I-TASSER program i got errors in the simulation step , following is the output I got :
perl runI-TASSER.pl -pkgdir /sivatop/I-TASSER4.1 -libdir /sivatop -java_home /usr -seqname example -datadir /sivatop/I-TASSER4.1/example
Your setting for running I-TASSER is:
-pkgdir = /sivatop/I-TASSER4.1
-libdir = /sivatop
-java_home = /usr
-seqname = example
-datadir = /sivatop/I-TASSER4.1/example
-outdir = /sivatop/I-TASSER4.1/example
-runstyle = serial
-homoflag = real
-idcut = 1
-ntemp = 20
-nmodel = 5
-light = false
-hours = 50
-LBS = false
-EC = false
-GO = false
1. make seq.txt and rmsinp
Your protein contains 143 residues:
> example
MYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLA
LQDSGLEVNIVTDSQYALGIITQWIHNWKKRGWPVKNVDLVNQIIEQLIKKEKVYLAWVP
AHKGIGGNEQVDKLVSAGIRKVL
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
/sivatop/I-TASSER4.1/example/init.PPAS exists
start serial threading dPPAS
/tmp/siva123/ITexample
/sivatop/I-TASSER4.1/example/dPPAS_example
hostname: sivatop
starting time: Wed Oct 15 12:07:00 IST 2014
pwd: /tmp/siva123/ITexample
running zalign .....
ending time: Wed Oct 15 12:36:30 IST 2014
start serial threading dPPAS2
/tmp/siva123/ITexample
/sivatop/I-TASSER4.1/example/dPPAS2_example
hostname: sivatop
starting time: Wed Oct 15 12:36:31 IST 2014
pwd: /tmp/siva123/ITexample
running zalign .....
ending time: Wed Oct 15 13:06:28 IST 2014
/sivatop/I-TASSER4.1/example/init.Env-PPAS exists
start serial threading MUSTER
/tmp/siva123/ITexample
/sivatop/I-TASSER4.1/example/MUSTER_example
At line 522 of file zal33.f
Fortran runtime error: End of file
Illegal division by zero at /sivatop/I-TASSER4.1/example/MUSTER_example line 599.
hostname: sivatop
starting time: Wed Oct 15 13:06:29 IST 2014
pwd: /tmp/siva123/ITexample
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
/sivatop/I-TASSER4.1/example/init.wPPAS exists
start serial threading wdPPAS
/tmp/siva123/ITexample
/sivatop/I-TASSER4.1/example/wdPPAS_example
hostname: sivatop
starting time: Wed Oct 15 13:09:15 IST 2014
pwd: /tmp/siva123/ITexample
running Psi-blast .....
ending time: Wed Oct 15 14:03:04 IST 2014
start serial threading wMUSTER
/tmp/siva123/ITexample
/sivatop/I-TASSER4.1/example/wMUSTER_example
hostname: sivatop
starting time: Wed Oct 15 14:03:06 IST 2014
pwd: /tmp/siva123/ITexample
running Psi-blast .....
running Psi-blast .....
==>1rilA 1rilA 23.6948176102306 16.9602408201085
1rilA 1rilA 26.57 26.57
score_flag=1
ending time: Wed Oct 15 15:05:48 IST 2014
3.2 make restraints
without init: /sivatop/I-TASSER4.1/example/init.MUSTER
type= easy, n_good=35, M0= 7, M1_for_medm=1.4, n_sg= 7 role=SEQ
domain2=no
type=easy----n_temp_use_for_restraints=20
4.1 run simulation
run 14 serial simulations
run simulation job 1 / 14
At line 1714 of file cas.f
Fortran runtime error: End of file
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 2 / 14
At line 1714 of file cas.f
Fortran runtime error: End of file
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 3 / 14
At line 1714 of file cas.f
Fortran runtime error: End of file
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 4 / 14
At line 1714 of file cas.f
Fortran runtime error: End of file
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 5 / 14
At line 1714 of file cas.f
Fortran runtime error: End of file
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 6 / 14
At line 1714 of file cas.f
Fortran runtime error: End of file
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 7 / 14
At line 1714 of file cas.f
Fortran runtime error: End of file
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 8 / 14
At line 1714 of file cas.f
Fortran runtime error: End of file
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 9 / 14
At line 1714 of file cas.f
Fortran runtime error: End of file
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 10 / 14
At line 1714 of file cas.f
Fortran runtime error: End of file
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 11 / 14
At line 1714 of file cas.f
Fortran runtime error: End of file
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 12 / 14
At line 1714 of file cas.f
Fortran runtime error: End of file
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 13 / 14
At line 1714 of file cas.f
Fortran runtime error: End of file
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 14 / 14
At line 1714 of file cas.f
Fortran runtime error: End of file
bzip2: Can't open input file rep*.tra: No such file or directory.
5.1 do clustering
No. of trajectory files: 0
-> I followed instructions from this post : http://zhanglab.ccmb.med.umich.edu/bbs/?q=node/3464 .
-> As you suggested, " Some input files for running cas program are wrong. You can manually delete the file init.dat and re-run the program.", I couldn't delete init.dat. (I used rm -f -r init.dat )
-> I checked tar -jxvf wgt.tar.bz2 and ./solve , they are working.
-> By running one of the simulations manually I got the following output :
[root@sivatop example]# ./examplesim_1A
hostname: sivatop
starting time: Thu Oct 16 12:01:44 IST 2014
pwd: /sivatop/I-TASSER4.1/example
hostname: sivatop
starting time: Thu Oct 16 12:01:44 IST 2014
pwd: /tmp/siva123/examplesim_1A
starting time: Thu Oct 16 12:01:44 2014
At line 1714 of file cas.f
Fortran runtime error: End of file
bzip2: Can't open input file rep*.tra: No such file or directory.
ending time: Thu Oct 16 12:01:45 IST 2014
-> examplesim_1A folder also not created in tmp/siva123 directory.
This is the whole thing I did. I think now you can trace out my problem and suggest me to resolve.
Thank you,
siva.