This test case fails with both '-light true' and '-light false'. Runstyle is always serial.
Command used is at the bottom of the message below
I've attached the seq.fasta for reference.
Below is the standard output:
Your setting for running I-TASSER is:
-pkgdir = /data/projects/myproject/I-TASSER5.0
-libdir = /data/projects/myproject/ITLIB
-java_home = /usr/local/easybuild/software/Java/1.8.0_71/
-seqname = seq.fasta
-datadir = /home/myname/jobs/homo_sapiens_250_heavy_singlethreaded/results/00/myprotein
-outdir = /home/myname/jobs/homo_sapiens_250_heavy_singlethreaded/results/00/myprotein
-runstyle = serial
-homoflag = real
-idcut = 1
-ntemp = 20
-nmodel = 1
-light = false
-hours = 50
-LBS = true
-EC = true
-GO = true
1. make seq.txt and rmsinp
Your protein contains 549 residues:
> seq.fasta
GGAVAIPSWGKFWLAVLNVYSWEGLNTLFPEMWLFPDWAPAHPSTLWCHCRQVYLPMSYC
YAVRLSAAEDPLVQSLRQELYVEDFASIDWLAQRNNVAPDELYTPHSWLLRVVYALLNLY
EHHHSAHLRQRAVQKLYEHIVADDRFTKSISIGPISKTINMLVRWYVDGPASTAFQEHVS
RIPDYLWMGLDGMKMQGTNGSQIWDTAFAIQALLEAGGHHRPEFSSCLQKAHEFLRLSQV
PDNPPDYQKYYRQMRKGGFSFSTLDCGWIVSDCTAEALKAVLLLQEKCPHVTEHIPRERL
CDAVAVLLNMRNPDGGFATYETKRGGHLLELLNPSEVFGDIMIDYTYVECTSAVMQALKY
FHKRFPEHRAAEIRETLTQGLEFCRRQQRADGSWEGSWGVCFTYGTWFGLEAFACMGQTY
RDGTACAEVSRACDFLLSRQMADGGWGEDFESCEERRYLQSAQSQIHNTCWAMMGLMAVR
HPDIEAQERGVRCLLEKQLPNGDWPQENIAGVFNKSCAISYTSYRNIFPIWALGRFSQLY
PERALAGHP
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 18.74265 1.6947162E+07
pair done
3.1 do threading
start serial threading PPAS
/tmp/myname/ITseq.fasta
/home/myname/jobs/homo_sapiens_250_heavy_singlethreaded/results/00/myprotein/PPAS_seq.fasta
hostname: myhost
starting time: Thu Oct 20 23:14:04 AEDT 2016
pwd: /tmp/myname/ITseq.fasta
running zalign .....
ending time: Thu Oct 20 23:25:56 AEDT 2016
start serial threading dPPAS
/tmp/myname/ITseq.fasta
/home/myname/jobs/homo_sapiens_250_heavy_singlethreaded/results/00/myprotein/dPPAS_seq.fasta
hostname: myhost
starting time: Thu Oct 20 23:25:57 AEDT 2016
pwd: /tmp/myname/ITseq.fasta
running zalign .....
ending time: Thu Oct 20 23:49:10 AEDT 2016
start serial threading dPPAS2
/tmp/myname/ITseq.fasta
/home/myname/jobs/homo_sapiens_250_heavy_singlethreaded/results/00/myprotein/dPPAS2_seq.fasta
hostname: myhost
starting time: Thu Oct 20 23:49:11 AEDT 2016
pwd: /tmp/myname/ITseq.fasta
running zalign .....
ending time: Fri Oct 21 00:11:47 AEDT 2016
start serial threading Env-PPAS
/tmp/myname/ITseq.fasta
/home/myname/jobs/homo_sapiens_250_heavy_singlethreaded/results/00/myprotein/Env-PPAS_seq.fasta
hostname: myhost
starting time: Fri Oct 21 00:11:49 AEDT 2016
pwd: /tmp/myname/ITseq.fasta
running zalign .....
ending time: Fri Oct 21 00:38:49 AEDT 2016
start serial threading MUSTER
/tmp/myname/ITseq.fasta
/home/myname/jobs/homo_sapiens_250_heavy_singlethreaded/results/00/myprotein/MUSTER_seq.fasta
hostname: myhost
starting time: Fri Oct 21 00:38:50 AEDT 2016
pwd: /tmp/myname/ITseq.fasta
running Psi-blast .....
running zalign .....
==>1w6jA 1w6jA 16.5199680235665 21.2422757255165
1w6jA 1w6jA 100 100
score_flag=1
ending time: Fri Oct 21 01:08:13 AEDT 2016
start serial threading wPPAS
/tmp/myname/ITseq.fasta
/home/myname/jobs/homo_sapiens_250_heavy_singlethreaded/results/00/myprotein/wPPAS_seq.fasta
hostname: myhost
starting time: Fri Oct 21 01:08:14 AEDT 2016
pwd: /tmp/myname/ITseq.fasta
running Psi-blast .....
ending time: Fri Oct 21 01:43:40 AEDT 2016
start serial threading wdPPAS
/tmp/myname/ITseq.fasta
/home/myname/jobs/homo_sapiens_250_heavy_singlethreaded/results/00/myprotein/wdPPAS_seq.fasta
hostname: myhost
starting time: Fri Oct 21 01:43:41 AEDT 2016
pwd: /tmp/myname/ITseq.fasta
running Psi-blast .....
ending time: Fri Oct 21 02:26:40 AEDT 2016
start serial threading wMUSTER
/tmp/myname/ITseq.fasta
/home/myname/jobs/homo_sapiens_250_heavy_singlethreaded/results/00/myprotein/wMUSTER_seq.fasta
hostname: myhost
starting time: Fri Oct 21 02:26:41 AEDT 2016
pwd: /tmp/myname/ITseq.fasta
running Psi-blast .....
running Psi-blast .....
==>1w6jA 1w6jA 19.8630241935828 25.5227273137325
1w6jA 1w6jA 100.00 100.00
score_flag=1
ending time: Fri Oct 21 03:22:54 AEDT 2016
3.2 make restraints
MUSTER warning: GLY ne CYS for res=1, convert GLY to CYS
MUSTER warning: GLY ne CYS for res=1, convert GLY to CYS
MUSTER warning: GLY ne CYS for res=1, convert GLY to CYS
dPPAS warning: GLY ne CYS for res=1, convert GLY to CYS
dPPAS warning: GLY ne CYS for res=1, convert GLY to CYS
dPPAS warning: GLY ne CYS for res=1, convert GLY to CYS
dPPAS warning: GLY ne CYS for res=1, convert GLY to CYS
wdPPAS warning: GLY ne CYS for res=1, convert GLY to CYS
wdPPAS warning: GLY ne CYS for res=1, convert GLY to CYS
wdPPAS warning: GLY ne CYS for res=1, convert GLY to CYS
wdPPAS warning: GLY ne CYS for res=1, convert GLY to CYS
wMUSTER warning: GLY ne CYS for res=1, convert GLY to CYS
wMUSTER warning: GLY ne CYS for res=1, convert GLY to CYS
wMUSTER warning: GLY ne CYS for res=1, convert GLY to CYS
wMUSTER warning: GLY ne CYS for res=1, convert GLY to CYS
wPPAS warning: GLY ne CYS for res=1, convert GLY to CYS
wPPAS warning: GLY ne CYS for res=1, convert GLY to CYS
wPPAS warning: GLY ne CYS for res=1, convert GLY to CYS
wPPAS warning: GLY ne CYS for res=1, convert GLY to CYS
dPPAS2 warning: GLY ne CYS for res=1, convert GLY to CYS
dPPAS2 warning: GLY ne CYS for res=1, convert GLY to CYS
dPPAS2 warning: GLY ne CYS for res=1, convert GLY to CYS
dPPAS2 warning: GLY ne CYS for res=1, convert GLY to CYS
PPAS warning: GLY ne CYS for res=1, convert GLY to CYS
PPAS warning: GLY ne CYS for res=1, convert GLY to CYS
PPAS warning: GLY ne CYS for res=1, convert GLY to CYS
PPAS warning: GLY ne CYS for res=1, convert GLY to CYS
PPAS warning: GLY ne CYS for res=1, convert GLY to CYS
Env-PPAS warning: GLY ne CYS for res=1, convert GLY to CYS
Env-PPAS warning: GLY ne CYS for res=1, convert GLY to CYS
Env-PPAS warning: GLY ne CYS for res=1, convert GLY to CYS
Env-PPAS warning: GLY ne CYS for res=1, convert GLY to CYS
type= easy, n_good=40, M0= 8, M1_for_medm=1.6, n_sg= 8 role=SEQ
domain2=no
type=easy----n_temp_use_for_restraints=20
4.1 run simulation
1 CYS ne GLY !!!!!!
init.dat is wrong!!!!! 1 - 1w6jA CYS ne GLY MUSTER
init.dat is wrong!!!!! 2 - 1w6jA CYS ne GLY dPPAS
You have 3 errors in your input files. Please fix these problems before you run TASSER
There are problems with your input files
Please check before simulation
command: /home/myname/myproject/I-TASSER5.0/I-TASSERmod/runI-TASSER.pl -light false -runstyle serial -LBS true -EC true -GO true -nmodel 1 -pkgdir /home/myname/myproject/I-TASSER5.0/ -libdir /home/myname/myproject/ITLIB -seqname seq.fasta -datadir results/00/myprotein -java_home /usr/local/easybuild/software/Java/1.8.0_71/ -outdir results/00/myprotein