Re: bzip2: Can't open input file rep*.tra: No such file or directory.
Posted: Tue Jun 06, 2023 11:21 am
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
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