Dear discussion board,
I've got I-TASSER installed on the Orchestra cluster where the Linux distribution is CentOS 6.6. I've run I-TASSER with:
bsub -W 12:00 -q short -R "rusage[mem=8000]" './runI-TASSER.pl -pkgdir /groups/alquraishi/Protein-DNA/Xide/I_TASSER/I-TASSER4.3 -libdir /groups/alquraishi/Protein-DNA/Xide/I_TASSER/I-TASSER4.3/ITLIB -java_home /opt/java/jdk1.6.0_45 -seqname seq -datadir /groups/alquraishi/Protein-DNA/Xide/I_TASSER/I-TASSER4.3/example/seq.fasta -outdir /groups/alquraishi/Protein-DNA/Xide/I_TASSER/I-TASSER4.3/example'
I get the following output:
Your setting for running I-TASSER is:
-pkgdir = /groups/alquraishi/Protein-DNA/Xide/I_TASSER/I-TASSER4.3
-libdir = /groups/alquraishi/Protein-DNA/Xide/I_TASSER/I-TASSER4.3/ITLIB
-java_home = /opt/java/jdk1.6.0_45
-seqname = seq
-datadir = /groups/alquraishi/Protein-DNA/Xide/I_TASSER/I-TASSER4.3/example
-outdir = /groups/alquraishi/Protein-DNA/Xide/I_TASSER/I-TASSER4.3/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:
> seq
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
2.4.1 Use all templates
2.4.2 running pair ................
FORTRAN STOP
30000 6379375 total lib str & residues
number of observations 27.03459 1658491.
pair done
3.1 do threading
start serial threading PPAS
/tmp/xx40/ITseq
/groups/alquraishi/Protein-DNA/Xide/I_TASSER/I-TASSER4.3/example/PPAS_seq
open: No such file or directory
apparent state: unit 30 named /groups/alquraishi/Protein-DNA/Xide/I_TASSER/I-TASSER4.3/ITLIB/summary/AAA.sec
last format: list io
lately reading sequential formatted external IO
Illegal division by zero at /groups/alquraishi/Protein-DNA/Xide/I_TASSER/I-TASSER4.3/example/PPAS_seq line 354.
hostname: clarinet001-219
starting time: Mon Aug 24 14:57:51 EDT 2015
pwd: /tmp/xx40/ITseq
running zalign .....
start serial threading dPPAS
/tmp/xx40/ITseq
/groups/alquraishi/Protein-DNA/Xide/I_TASSER/I-TASSER4.3/example/dPPAS_seq
At line 273 of file ppa1.f
Fortran runtime error: No such file or directory
Illegal division by zero at /groups/alquraishi/Protein-DNA/Xide/I_TASSER/I-TASSER4.3/example/dPPAS_seq line 356.
hostname: clarinet001-219
starting time: Mon Aug 24 14:57:56 EDT 2015
pwd: /tmp/xx40/ITseq
running zalign .....
start serial threading dPPAS2
/tmp/xx40/ITseq
/groups/alquraishi/Protein-DNA/Xide/I_TASSER/I-TASSER4.3/example/dPPAS2_seq
At line 273 of file ppa1.f
Fortran runtime error: No such file or directory
Illegal division by zero at /groups/alquraishi/Protein-DNA/Xide/I_TASSER/I-TASSER4.3/example/dPPAS2_seq line 355.
hostname: clarinet001-219
starting time: Mon Aug 24 14:58:00 EDT 2015
pwd: /tmp/xx40/ITseq
running zalign .....
start serial threading Env-PPAS
/tmp/xx40/ITseq
/groups/alquraishi/Protein-DNA/Xide/I_TASSER/I-TASSER4.3/example/Env-PPAS_seq
At line 284 of file zal3.f
Fortran runtime error: No such file or directory
Illegal division by zero at /groups/alquraishi/Protein-DNA/Xide/I_TASSER/I-TASSER4.3/example/Env-PPAS_seq line 352.
hostname: clarinet001-219
starting time: Mon Aug 24 14:58:05 EDT 2015
pwd: /tmp/xx40/ITseq
running zalign .....
start serial threading MUSTER
/tmp/xx40/ITseq
/groups/alquraishi/Protein-DNA/Xide/I_TASSER/I-TASSER4.3/example/MUSTER_seq
can't open model file /groups/alquraishi/Protein-DNA/Xide/I_TASSER/I-TASSER4.3/ITLIB/summary/modelpsi_0.005_1.dat
can't open model file /groups/alquraishi/Protein-DNA/Xide/I_TASSER/I-TASSER4.3/ITLIB/summary/modelphi_0.005_1.dat
At line 522 of file zal33.f
Fortran runtime error: End of file
Illegal division by zero at /groups/alquraishi/Protein-DNA/Xide/I_TASSER/I-TASSER4.3/example/MUSTER_seq line 599.
hostname: clarinet001-219
starting time: Mon Aug 24 14:58:10 EDT 2015
pwd: /tmp/xx40/ITseq
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
start serial threading wPPAS
/tmp/xx40/ITseq
/groups/alquraishi/Protein-DNA/Xide/I_TASSER/I-TASSER4.3/example/wPPAS_seq
Exception in thread "main" java.io.FileNotFoundException: /groups/alquraishi/Protein-DNA/Xide/I_TASSER/I-TASSER4.3/ITLIB/summary/AAA.seq (No such file or directory)
at java.io.FileInputStream.open(Native Method)
at java.io.FileInputStream.(FileInputStream.java:120)
at java.io.FileInputStream.(FileInputStream.java:79)
at java.io.FileReader.(FileReader.java:41)
at d.a(d.java)
at d.main(d.java)
Illegal division by zero at /groups/alquraishi/Protein-DNA/Xide/I_TASSER/I-TASSER4.3/example/wPPAS_seq line 340.
hostname: clarinet001-219
starting time: Mon Aug 24 15:01:39 EDT 2015
pwd: /tmp/xx40/ITseq
running Psi-blast .....
start serial threading wdPPAS
/tmp/xx40/ITseq
/groups/alquraishi/Protein-DNA/Xide/I_TASSER/I-TASSER4.3/example/wdPPAS_seq
Exception in thread "main" java.io.FileNotFoundException: /groups/alquraishi/Protein-DNA/Xide/I_TASSER/I-TASSER4.3/ITLIB/summary/AAA.seq (No such file or directory)
at java.io.FileInputStream.open(Native Method)
at java.io.FileInputStream.(FileInputStream.java:120)
at java.io.FileInputStream.(FileInputStream.java:79)
at java.io.FileReader.(FileReader.java:41)
at c.a(c.java)
at c.main(c.java)
Illegal division by zero at /groups/alquraishi/Protein-DNA/Xide/I_TASSER/I-TASSER4.3/example/wdPPAS_seq line 348.
hostname: clarinet001-219
starting time: Mon Aug 24 15:10:22 EDT 2015
pwd: /tmp/xx40/ITseq
running Psi-blast .....
start serial threading wMUSTER
/tmp/xx40/ITseq
/groups/alquraishi/Protein-DNA/Xide/I_TASSER/I-TASSER4.3/example/wMUSTER_seq
can't open model file /groups/alquraishi/Protein-DNA/Xide/I_TASSER/I-TASSER4.3/ITLIB/summary/modelpsi_0.005_1.dat
can't open model file /groups/alquraishi/Protein-DNA/Xide/I_TASSER/I-TASSER4.3/ITLIB/summary/modelphi_0.005_1.dat
Exception in thread "main" java.io.FileNotFoundException: /groups/alquraishi/Protein-DNA/Xide/I_TASSER/I-TASSER4.3/ITLIB/summary/AAA.seq (No such file or directory)
at java.io.FileInputStream.open(Native Method)
at java.io.FileInputStream.(FileInputStream.java:120)
at java.io.FileInputStream.(FileInputStream.java:79)
at java.io.FileReader.(FileReader.java:41)
at e.a(e.java)
at e.main(e.java)
Illegal division by zero at /groups/alquraishi/Protein-DNA/Xide/I_TASSER/I-TASSER4.3/example/wMUSTER_seq line 570.
hostname: clarinet001-219
starting time: Mon Aug 24 15:19:18 EDT 2015
pwd: /tmp/xx40/ITseq
running Psi-blast .....
running Psi-blast .....
only 0 threading programs have output, please check threading programs
Could anyone point me to where is the problem and how to correct it? Thank you very much!
Sincerely,
Xide