bzip2: Can't open input file rep*.tra: No such file or directory.

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Ffakher
Posts: 18
Joined: Sat May 20, 2023 7:44 am

Re: bzip2: Can't open input file rep*.tra: No such file or directory.

Post by Ffakher »

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
Attachments
test.rar
(650.3 KiB) Downloaded 510 times
jlspzw
Posts: 240
Joined: Tue May 04, 2021 5:04 pm

Re: bzip2: Can't open input file rep*.tra: No such file or directory.

Post by jlspzw »

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
Ffakher
Posts: 18
Joined: Sat May 20, 2023 7:44 am

Re: bzip2: Can't open input file rep*.tra: No such file or directory.

Post by Ffakher »

(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$
jlspzw
Posts: 240
Joined: Tue May 04, 2021 5:04 pm

Re: bzip2: Can't open input file rep*.tra: No such file or directory.

Post by jlspzw »

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
Ffakher
Posts: 18
Joined: Sat May 20, 2023 7:44 am

Re: bzip2: Can't open input file rep*.tra: No such file or directory.

Post by Ffakher »

Thank you for your help

Please find in attache the folder compressed in two rar file
Attachments
MUSTER_example.part01.rar
(900 KiB) Downloaded 551 times
Ffakher
Posts: 18
Joined: Sat May 20, 2023 7:44 am

Re: bzip2: Can't open input file rep*.tra: No such file or directory.

Post by Ffakher »

the second part
Ffakher
Posts: 18
Joined: Sat May 20, 2023 7:44 am

Re: bzip2: Can't open input file rep*.tra: No such file or directory.

Post by Ffakher »

the second part
Attachments
MUSTER_example.part02.rar
(636.62 KiB) Downloaded 544 times
Ffakher
Posts: 18
Joined: Sat May 20, 2023 7:44 am

Re: bzip2: Can't open input file rep*.tra: No such file or directory.

Post by Ffakher »

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$
jlspzw
Posts: 240
Joined: Tue May 04, 2021 5:04 pm

Re: bzip2: Can't open input file rep*.tra: No such file or directory.

Post by jlspzw »

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
Ffakher
Posts: 18
Joined: Sat May 20, 2023 7:44 am

Re: bzip2: Can't open input file rep*.tra: No such file or directory.

Post by Ffakher »

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
Attachments
capture 4.jpg
capture 4.jpg (117.89 KiB) Viewed 17364 times
Capture 3.jpg
Capture 3.jpg (15.85 KiB) Viewed 17364 times
capture 2.jpg
capture 2.jpg (29.16 KiB) Viewed 17364 times
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