Hello,
I've just tried to run I-TASSER (for the first time!) on a server using a batch queueing system. After running for a short time (~30 mins) the job was no longer running and it had produced only two files, AtSUMO.csh.o50375 and AtSUMO.csh.e50375 (AtSUMO.csh being the script I used to run the job). The .o(...) file had the following contents:
Warning: no access to tty (Bad file descriptor).
Thus no job control in this shell.
Your setting for I-TASSER is:
-pkgdir = /biol/programs/I-TASSER4.0
-libdir = /biol/programs/I-TASSER4.0/ITLIB
-java_home = /usr
-seqname = AtSUMO1
-datadir = .
-usrname = co631
-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 93 residues:
> AtSUMO1
MSANQEEDKKPGDGGAHINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVDMNSIAF
LFDGRRLRAEQTPDELDMEDGDEIDAMLHQTGG
2.1 run Psi-blast
2.2 Predict secondary structure with PSSpred...
2.3 Predict solvent accessibility...
2.4 run pairmod
2.4.1 Use all templates
2.4.2 running pair ................
30000 6379375 total lib str & residues
number of observations 12.92597 335390.1
pair done
3.1 do threading
start serial threading PPAS
/tmp/co631/ITAtSUMO1
./PPAS_AtSUMO1
hostname: biolar113
starting time: Fri Aug 1 18:25:14 BST 2014
pwd: /tmp/co631/ITAtSUMO1
running Psi-blast .....
start serial threading dPPAS
/tmp/co631/ITAtSUMO1
./dPPAS_AtSUMO1
hostname: biolar113
starting time: Fri Aug 1 18:25:14 BST 2014
pwd: /tmp/co631/ITAtSUMO1
running Psi-blast .....
start serial threading dPPAS2
/tmp/co631/ITAtSUMO1
./dPPAS2_AtSUMO1
hostname: biolar113
starting time: Fri Aug 1 18:25:14 BST 2014
pwd: /tmp/co631/ITAtSUMO1
running Psi-blast .....
start serial threading Env-PPAS
/tmp/co631/ITAtSUMO1
./Env-PPAS_AtSUMO1
hostname: biolar113
starting time: Fri Aug 1 18:25:14 BST 2014
pwd: /tmp/co631/ITAtSUMO1
running Psi-blast .....
start serial threading MUSTER
/tmp/co631/ITAtSUMO1
./MUSTER_AtSUMO1
hostname: biolar113
starting time: Fri Aug 1 18:25:14 BST 2014
pwd: /tmp/co631/ITAtSUMO1
running Psi-blast .....
start serial threading wPPAS
/tmp/co631/ITAtSUMO1
./wPPAS_AtSUMO1
hostname: biolar113
starting time: Fri Aug 1 18:25:28 BST 2014
pwd: /tmp/co631/ITAtSUMO1
running Psi-blast .....
running Psi-blast .....
start serial threading wdPPAS
/tmp/co631/ITAtSUMO1
./wdPPAS_AtSUMO1
hostname: biolar113
starting time: Fri Aug 1 18:25:28 BST 2014
pwd: /tmp/co631/ITAtSUMO1
running Psi-blast .....
running Psi-blast .....
start serial threading wMUSTER
/tmp/co631/ITAtSUMO1
./wMUSTER_AtSUMO1
hostname: biolar113
starting time: Fri Aug 1 18:25:28 BST 2014
pwd: /tmp/co631/ITAtSUMO1
error: without ./seq.fasta && ./seq.txt
only 0 threading programs have output, please check threading programs
Can anyone suggest why this hasn't worked? I'm afraid I don't have much experience of UNIX or batch queueing.
Many thanks,
Callum.