Hi
I am trying to run runI-TASSER.pl on a cluster that uses SGE for job submission. I edited runI-TASSER.pl as directed in README.txt.
line 871
$bsub=`qsub -e $errfile -o $outfile -l $walltime -N $tag $jobname`;
changed to
$bsub=`qsub -cwd -S /usr/bin/perl -e $errfile -o $outfile -N $tag $jobname`;
line 1719
$bsub=`qsub $datadir/$tagnames{$i}`;
changed to
$bsub=`qsub -cwd -S /usr/bin/perl $datadir/$tagnames{$i}`;
I get the following error message:
Your setting for running I-TASSER is:
-pkgdir = /mnt/du-synology/v1shr1/scratch/ma40512/apps/I-TASSER5.1
-libdir = /mnt/du-synology/v1shr1/scratch/ma40512/apps/ITLIB
-java_home = /usr
-seqname = seq.fasta
-datadir = /mnt/shared/scratch/ma40512/protein_structure/R3a
-outdir = /mnt/shared/scratch/ma40512/protein_structure/R3a
-runstyle = parallel
-homoflag = benchmark
-idcut = 0.3
-ntemp = 20
-nmodel = 5
-light = false
-hours = 50
-LBS = true
-EC = true
-GO = true
1. make seq.txt and rmsinp
Your protein contains 1282 residues:
> seq.fasta
MEIGLAVGGAFLSSALNVLFDRLAPHGDLLNMFQKHKDHVKLLKKLEDILLGLQIVLSDA
ENKQASNRHVSQWFNKLQNAVDGAENLIEQVNYEALRLKVEGQHQNLAETSNQQVSDLNL
etc.
2.1 run Psi-blast
2.2 Predict secondary structure with PSSpred...
2.3 Predict solvent accessibility...
2.4 run pairmod
2.4.1 removing homology templates based on benchmark and 0.3
submit threading jobs first and run pair during threading
3.1 do threading
start parallel threading PPAS
qsub: Unknown option
qsub: Unknown option
start parallel threading dPPAS
qsub: Unknown option
qsub: Unknown option
start parallel threading dPPAS2
qsub: Unknown option
qsub: Unknown option
start parallel threading Env-PPAS
qsub: Unknown option
qsub: Unknown option
start parallel threading MUSTER
qsub: Unknown option
qsub: Unknown option
start parallel threading wPPAS
qsub: Unknown option
qsub: Unknown option
start parallel threading wdPPAS
qsub: Unknown option
qsub: Unknown option
start parallel threading wMUSTER
qsub: Unknown option
qsub: Unknown option
running pair now ................
FORTRAN STOP
30000 6379375 total lib str & residues
number of observations 36.28819 1.7892150E+08
pair done
only 0 threading programs have output, please check threading programs.
Here is the shell script I submitted using qsub
#!/bin/bash
#$ -cwd
#$ -V
#$ -j yes
#$ -pe smp 16
pkgdir=/mnt/shared/scratch/synology/ma40512/apps/I-TASSER5.1
datadir=/mnt/shared/scratch/ma40512/protein_structure/R3a
libdir=/mnt/shared/scratch/synology/ma40512/apps
$pkgdir/I-TASSERmod/runI-TASSER_SGE.pl -pkgdir $pkgdir -libdir $libdir/ITLIB -seqname seq.fasta -datadir $datadir -runstyle parallel -homoflag benchmark -idcut 0.3 -LBS true -EC true -GO true -java_home /usr
Any advice would be appreciated as I am not a computational biologist.
thanks
Miles