Zhanglab forum

Hello

I have try to put the file in other fold but the same problem
(base) user@STATION-PCMC:/mnt/c/I-TASSER5.2$ sudo perl /mnt/c/I-TASSER5.2/I-TASSERmod/runI-TASSER.pl -libdir /home/user/ITLIB -seqname example -datadir /home/user/test

Your setting for running I-TASSER is:
-pkgdir = /mnt/c/I-TASSER5.2
-libdir = /home/user/ITLIB
-java_home = /usr
-seqname = example
-datadir = /home/user/test
-outdir = /home/user/test
-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 120 residues:
> example
MYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLA
LQDSGLEVNIVTDSQYALGIITQWIHNWKKRGWPVKNVDLVNQIIEQLIKKEKVYLAWVP

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 ................
FORTRAN STOP
30000 6379375 total lib str & residues
number of observations 26.22755 1133030.
pair done
3.1 do threading
start serial threading PPAS
/tmp/root/ITexample
/home/user/test/PPAS_example
hostname: STATION-PCMC
starting time: Tue Jun 6 05:09:25 CEST 2023
pwd: /tmp/root/ITexample
running zalign .....
ending time: Tue Jun 6 05:14:48 CEST 2023

start serial threading dPPAS
/tmp/root/ITexample
/home/user/test/dPPAS_example
hostname: STATION-PCMC
starting time: Tue Jun 6 05:14:49 CEST 2023
pwd: /tmp/root/ITexample
running zalign .....
ending time: Tue Jun 6 05:22:44 CEST 2023

start serial threading dPPAS2
/tmp/root/ITexample
/home/user/test/dPPAS2_example
hostname: STATION-PCMC
starting time: Tue Jun 6 05:22:45 CEST 2023
pwd: /tmp/root/ITexample
running zalign .....
ending time: Tue Jun 6 05:30:43 CEST 2023

start serial threading Env-PPAS
/tmp/root/ITexample
/home/user/test/Env-PPAS_example
hostname: STATION-PCMC
starting time: Tue Jun 6 05:30:45 CEST 2023
pwd: /tmp/root/ITexample
running zalign .....
ending time: Tue Jun 6 05:42:10 CEST 2023

start serial threading MUSTER
/tmp/root/ITexample
/home/user/test/MUSTER_example
Illegal division by zero at /home/user/test/MUSTER_example line 599.
hostname: STATION-PCMC
starting time: Tue Jun 6 05:42:11 CEST 2023
pwd: /tmp/root/ITexample
running Psi-blast .....
running zalign .....


start serial threading wPPAS
/tmp/root/ITexample
/home/user/test/wPPAS_example
java.io.FileNotFoundException: /home/user/ITLIB/dotProfiles/7b1bA.dotProfile (No such file or directory)
at java.base/java.io.FileInputStream.open0(Native Method)
at java.base/java.io.FileInputStream.open(FileInputStream.java:219)
at java.base/java.io.FileInputStream.<init>(FileInputStream.java:157)
at java.base/java.io.FileInputStream.<init>(FileInputStream.java:112)
at java.base/java.io.FileReader.<init>(FileReader.java:60)
at d.a(d.java)
at d.main(d.java)
Exception in thread "main" java.lang.NullPointerException
at d.a(d.java)
at d.main(d.java)
hostname: STATION-PCMC
starting time: Tue Jun 6 05:44:53 CEST 2023
pwd: /tmp/root/ITexample
running Psi-blast .....
ending time: Tue Jun 6 05:59:46 CEST 2023

start serial threading wdPPAS
/tmp/root/ITexample
/home/user/test/wdPPAS_example
Exception in thread "main" java.lang.NumberFormatException: For input string: "-NAN."
at java.base/jdk.internal.math.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:2054)
at java.base/jdk.internal.math.FloatingDecimal.parseFloat(FloatingDecimal.java:122)
at java.base/java.lang.Float.parseFloat(Float.java:455)
at java.base/java.lang.Float.valueOf(Float.java:419)
at c.a(c.java)
at c.main(c.java)
hostname: STATION-PCMC
starting time: Tue Jun 6 05:59:47 CEST 2023
pwd: /tmp/root/ITexample
running Psi-blast .....
ending time: Tue Jun 6 06:23:40 CEST 2023

start serial threading wMUSTER
/tmp/root/ITexample
/home/user/test/wMUSTER_example
Exception in thread "main" java.lang.NumberFormatException: For input string: "-NAN."
at java.base/jdk.internal.math.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:2054)
at java.base/jdk.internal.math.FloatingDecimal.parseFloat(FloatingDecimal.java:122)
at java.base/java.lang.Float.parseFloat(Float.java:455)
at java.base/java.lang.Float.valueOf(Float.java:419)
at e.a(e.java)
at e.main(e.java)
hostname: STATION-PCMC
starting time: Tue Jun 6 06:23:41 CEST 2023
pwd: /tmp/root/ITexample
running Psi-blast .....
running Psi-blast .....
==>1rilA 1goaA 21.2687428585168 19.2121968496078
1rilA 1goaA 26.67 35.83
score_flag=2
ending time: Tue Jun 6 06:53:52 CEST 2023

3.2 make restraints
without init: /home/user/test/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
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 2 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 3 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 4 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 5 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 6 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 7 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 8 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 9 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 10 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 11 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 12 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 13 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 14 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
5.1 do clustering
No. of trajectory files: 0

Dear user,

Thank you for the update,

please go to /mnt/c/I-TASSER5.1/example folder (your former test). There should be a script named 'examplesim_1A'. Please directly run (./examplesim_1A) this script to see what the output message is.

Best
IT Team

(base) user@STATION-PCMC:/mnt/c/I-TASSER5.2/example$ ./examplesim_1A
hostname: STATION-PCMC
starting time: Thu Jun 8 01:00:04 CEST 2023
pwd: /mnt/c/I-TASSER5.2/example
mkdir: cannot create directory ‘/tmp/root/examplesim_1A’: Permission denied
cp: '/mnt/c/I-TASSER5.2/example/seq.dat' and './seq.dat' are the same file
cp: '/mnt/c/I-TASSER5.2/example/rmsinp' and './rmsinp' are the same file
cp: '/mnt/c/I-TASSER5.2/example/comb.dat' and './comb.dat' are the same file
cp: '/mnt/c/I-TASSER5.2/example/combCA.dat' and './combCA.dat' are the same file
cp: '/mnt/c/I-TASSER5.2/example/comb8CA.dat' and './comb8CA.dat' are the same file
cp: '/mnt/c/I-TASSER5.2/example/dist.dat' and './dist.dat' are the same file
cp: '/mnt/c/I-TASSER5.2/example/distL.dat' and './distL.dat' are the same file
cp: '/mnt/c/I-TASSER5.2/example/exp.dat' and './exp.dat' are the same file
cp: '/mnt/c/I-TASSER5.2/example/init.dat' and './init.dat' are the same file
cp: '/mnt/c/I-TASSER5.2/example/par.dat' and './par.dat' are the same file
cp: '/mnt/c/I-TASSER5.2/example/pair1.dat' and './pair1.dat' are the same file
cp: '/mnt/c/I-TASSER5.2/example/pair3.dat' and './pair3.dat' are the same file
hostname: STATION-PCMC
starting time: Thu Jun 8 01:00:04 CEST 2023
pwd: /mnt/c/I-TASSER5.2/example
bzip2: Can't open input file rep*.tra: No such file or directory.
ending time: Thu Jun 8 01:00:04 CEST 2023

(base) user@STATION-PCMC:/mnt/c/I-TASSER5.2/example$ sudo ./examplesim_1A
hostname: STATION-PCMC
starting time: Thu Jun 8 01:00:10 CEST 2023
pwd: /mnt/c/I-TASSER5.2/example
hostname: STATION-PCMC
starting time: Thu Jun 8 01:00:10 CEST 2023
pwd: /tmp/root/examplesim_1A
bzip2: Can't open input file rep*.tra: No such file or directory.
ending time: Thu Jun 8 01:00:10 CEST 2023
(base) user@STATION-PCMC:/mnt/c/I-TASSER5.2/example$

Dear user,

Can you check the files in /tmp/root/examplesim_1A, you can send me the files in /tmp/root/examplesim_1A.

Best
IT Team

Thank you for your help

Please find in attache the folder compressed in two rar file

the second part

the second part

Hello

***** for gfortran *****
(base) user@STATION-PCMC:~$ gfortran --version
GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
Copyright (C) 2019 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.


***** for the version 5.1 *****
(base) user@STATION-PCMC:~$ cd /mnt/c/I-TASSER5.1/example
(base) user@STATION-PCMC:/mnt/c/I-TASSER5.1/example$ sudo ./examplesim_1A
[sudo] password for user:
hostname: STATION-PCMC
starting time: Fri Jun 9 18:41:49 CEST 2023
pwd: /mnt/c/I-TASSER5.1/example
hostname: STATION-PCMC
starting time: Fri Jun 9 18:41:49 CEST 2023
pwd: /tmp/root/examplesim_1A
bzip2: Can't open input file rep*.tra: No such file or directory.
ending time: Fri Jun 9 18:41:49 CEST 2023
(base) user@STATION-PCMC:/mnt/c/I-TASSER5.1/example$



***** version 5.2*******

(base) user@STATION-PCMC:/mnt/c/I-TASSER5.2/example$ sudo ./examplesim_1A
hostname: STATION-PCMC
starting time: Fri Jun 9 18:45:30 CEST 2023
pwd: /mnt/c/I-TASSER5.2/example
hostname: STATION-PCMC
starting time: Fri Jun 9 18:45:30 CEST 2023
pwd: /tmp/root/examplesim_1A
bzip2: Can't open input file rep*.tra: No such file or directory.
ending time: Fri Jun 9 18:45:30 CEST 2023
(base) user@STATION-PCMC:/mnt/c/I-TASSER5.2/example$

Dear user,

After you run ./examplesim_1A, there should be a folder named examplesim_1A in /tmp/root/. It is simulation files, not the MUSTER program. If you can not find examplesim_1A, in /mnt/c/I-TASSER5.1/example/examplesim_1A script, there is a line in the last as '`rm -fr $work_dir`;' , please change it as

#`rm -fr $work_dir`; (add the # mark)

and re-run /mnt/c/I-TASSER5.1/example/examplesim_1A, you should get the /tmp/root/examplesim_1A let us check what it is in this folder.

Also, we suggest you use a normal account to run the program and do not use "root" (with sudo). It sometimes requires permission which may cause trouble.

Best
IT Team

Hello

1-I have reinstall I-TASSER5.2

2-I have verify gfortran :

(base) fakher@Calculateur:/mnt/d/I-TASSER5.2/example$ gfortran --version
GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
Copyright (C) 2019 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.


3-I have try again the sequence in example :

perl /mnt/d/I-TASSER5.2/I-TASSERmod/runI-TASSER.pl -libdir /mnt/d/I-TASSER5.2/libdir -seqname example -datadir /mnt/d//I-TASSER5.2/example

Your setting for running I-TASSER is:
-pkgdir = /mnt/d/I-TASSER5.2
-libdir = /mnt/d/I-TASSER5.2/libdir
-java_home = /usr
-seqname = example
-datadir = /mnt/d/I-TASSER5.2/example
-outdir = /mnt/d/I-TASSER5.2/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
/mnt/d/I-TASSER5.2/example/init.PPAS exists
/mnt/d/I-TASSER5.2/example/init.dPPAS exists
/mnt/d/I-TASSER5.2/example/init.dPPAS2 exists
/mnt/d/I-TASSER5.2/example/init.Env-PPAS exists
start serial threading MUSTER
/tmp/fakher/ITexample
/mnt/d/I-TASSER5.2/example/MUSTER_example
Illegal division by zero at /mnt/d/I-TASSER5.2/example/MUSTER_example line 599.
hostname: Calculateur
starting time: Sat Jun 10 15:20:19 WAT 2023
pwd: /tmp/fakher/ITexample
running Psi-blast .....
running zalign .....


/mnt/d/I-TASSER5.2/example/init.wPPAS exists
/mnt/d/I-TASSER5.2/example/init.wdPPAS exists
start serial threading wMUSTER
/tmp/fakher/ITexample
/mnt/d/I-TASSER5.2/example/wMUSTER_example
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: Index 101 out of bounds for length 101
at e.main(e.java)
Illegal division by zero at /mnt/d/I-TASSER5.2/example/wMUSTER_example line 570.
hostname: Calculateur
starting time: Sat Jun 10 15:30:02 WAT 2023
pwd: /tmp/fakher/ITexample
running Psi-blast .....
running Psi-blast .....

3.2 make restraints
4.1 run simulation
run 14 serial simulations
run simulation job 1 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 2 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 3 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 4 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 5 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 6 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 7 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 8 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 9 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 10 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 11 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 12 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 13 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 14 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
5.1 do clustering
No. of trajectory files: 0


*only these file are in my /temp/root when the program run : attached file (capture 2.jpg)

*after that there are only this : capture 3.jpg

*the file in example are figure 4.jpg

* I have add # as yout recommandation : capture 5.jpg

after that I have use :

(base) fakher@Calculateur:/mnt/d/I-TASSER5.2/example$ ./examplesim_1A
hostname: Calculateur
starting time: Sat Jun 10 16:12:22 WAT 2023
pwd: /mnt/d/I-TASSER5.2/example
hostname: Calculateur
starting time: Sat Jun 10 16:12:23 WAT 2023
pwd: /tmp/fakher/examplesim_1A
bzip2: Can't open input file rep*.tra: No such file or directory.
ending time: Sat Jun 10 16:12:23 WAT 2023
(base) fakher@Calculateur:/mnt/d/I-TASSER5.2/example$

these all step

My best