Zhanglab forum

Hi,

When I run I-TASSER using the command line "$pkgdir/I-TASSERmod/runI-TASSER.pl -pkgdir /home/yourname/I-TASSER5.0 -libdir /home/yourname/ITLIB -seqname example -datadir /home/yourname/I-TASSER5.0/example -runstyle parallel -homoflag benchmark -idcut 0.3 -LBS true -EC true -GO true -java_home /usr", the output are as follows:

Your setting for running I-TASSER is:
-pkgdir = /home/ubuntu/test/I-TASSER5.1
-libdir = /home/ubuntu/test/I-TASSER5.1/template_library_directory
-java_home = /usr
-seqname = osm3
-datadir = /home/ubuntu/test
-outdir = /home/ubuntu/test
-runstyle = serial
-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 699 residues:
> osm3

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
2.4.2 running pair ................
FORTRAN STOP
30000 6368400 total lib str & residues
number of observations 18.32879 2.6866394E+07
pair done
3.1 do threading
start serial threading PPAS
/tmp/ubuntu/ITosm3
/home/ubuntu/test/osm3_XLMS/PPAS_osm3
Illegal division by zero at /home/ubuntu/test/osm3_XLMS/PPAS_osm3 line 354.
hostname: ubuntu-Precision-3660
starting time: Fri 27 Oct 2023 01:15:34 AM CST
pwd: /tmp/ubuntu/ITosm3
running zalign .....

start serial threading dPPAS
/tmp/ubuntu/ITosm3
/home/ubuntu/test/osm3_XLMS/dPPAS_osm3
Illegal division by zero at /home/ubuntu/test/osm3_XLMS/dPPAS_osm3 line 356.
hostname: ubuntu-Precision-3660
starting time: Fri 27 Oct 2023 01:15:37 AM CST
pwd: /tmp/ubuntu/ITosm3
running zalign .....

start serial threading dPPAS2
/tmp/ubuntu/ITosm3
/home/ubuntu/test/osm3_XLMS/dPPAS2_osm3
Illegal division by zero at /home/ubuntu/test/osm3_XLMS/dPPAS2_osm3 line 355.
hostname: ubuntu-Precision-3660
starting time: Fri 27 Oct 2023 01:15:45 AM CST
pwd: /tmp/ubuntu/ITosm3
running zalign .....

start serial threading Env-PPAS
/tmp/ubuntu/ITosm3
/home/ubuntu/test/osm3_XLMS/Env-PPAS_osm3
Illegal division by zero at /home/ubuntu/test/osm3_XLMS/Env-PPAS_osm3 line 352.
hostname: ubuntu-Precision-3660
starting time: Fri 27 Oct 2023 01:15:52 AM CST
pwd: /tmp/ubuntu/ITosm3
running zalign .....

start serial threading MUSTER
/tmp/ubuntu/ITosm3
/home/ubuntu/test/osm3_XLMS/MUSTER_osm3
Illegal division by zero at /home/ubuntu/test/osm3_XLMS/MUSTER_osm3 line 599.
hostname: ubuntu-Precision-3660
starting time: Fri 27 Oct 2023 01:16:00 AM CST
pwd: /tmp/ubuntu/ITosm3
running Psi-blast .....
running zalign .....
can not handle sec 1 99000


start serial threading wPPAS
/tmp/ubuntu/ITosm3
/home/ubuntu/test/osm3_XLMS/wPPAS_osm3
hostname: ubuntu-Precision-3660
starting time: Fri 27 Oct 2023 01:20:51 AM CST
pwd: /tmp/ubuntu/ITosm3
running Psi-blast .....
ending time: Fri 27 Oct 2023 01:48:09 AM CST

start serial threading wdPPAS
/tmp/ubuntu/ITosm3
/home/ubuntu/test/osm3_XLMS/wdPPAS_osm3
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: ubuntu-Precision-3660
starting time: Fri 27 Oct 2023 01:48:11 AM CST
pwd: /tmp/ubuntu/ITosm3
running Psi-blast .....
ending time: Fri 27 Oct 2023 02:19:38 AM CST

start serial threading wMUSTER
/tmp/ubuntu/ITosm3
/home/ubuntu/test/osm3_XLMS/wMUSTER_osm3
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: ubuntu-Precision-3660
starting time: Fri 27 Oct 2023 02:19:39 AM CST
pwd: /tmp/ubuntu/ITosm3
running Psi-blast .....
running Psi-blast .....
==>3zfcA 5mioC 22.2995959808701 21.4955599823275
3zfcA 5mioC 23.18 17.45
score_flag=1
ending time: Fri 27 Oct 2023 02:58:29 AM CST

only 3 threading programs have output, please check threading programs


I feel very confused with this error and I would really appreciate it if you can help me with it. Thank you very much and looking forward to your reply.

Weiye

Dear user,

Please see this viewtopic.php?f=3&t=721&p=1314&hilit=za ... 3bab#p1314

And try to download the zal* in my answer to see if the issue could be solved.

Best
IT Team

Hi,
Thanks for the quick reply! I tried the method in your answer and the out put changed to:

ubuntu@ubuntu-Precision-3660:~/test/I-TASSER5.1/bin/MUSTER/bin$ /home/ubuntu/test/I-TASSER5.1/I-TASSERmod/runI-TASSER.pl -libdir /home/ubuntu/test/I-TASSER5.1/template_library_directory -seqname osm3 -datadir /home/ubuntu/test/osm3_XLMS/seq.fasta -homoflag benchmark -idcut 0.3 -LBS true -EC true -GO true -java_home /usr -restraint1 /home/ubuntu/test/osm3_XLMS/input_all_cutoff_35_Intramolecular.txt -restraint4 /home/ubuntu/test/osm3_XLMS/osm3_ranked_0_monomer.pdb

Your setting for running I-TASSER is:
-pkgdir = /home/ubuntu/test/I-TASSER5.1
-libdir = /home/ubuntu/test/I-TASSER5.1/template_library_directory
-java_home = /usr
-seqname = osm3
-datadir = /home/ubuntu/test/osm3_XLMS
-outdir = /home/ubuntu/test/osm3_XLMS
-runstyle = serial
-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 699 residues:
> osm3
sequence
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
start serial threading PPAS
/tmp/ubuntu/ITosm3
/home/ubuntu/test/osm3_XLMS/PPAS_osm3
hostname: ubuntu-Precision-3660
starting time: Sat 28 Oct 2023 06:03:28 PM CST
pwd: /tmp/ubuntu/ITosm3
running zalign .....
ending time: Sat 28 Oct 2023 06:09:21 PM CST

start serial threading dPPAS
/tmp/ubuntu/ITosm3
/home/ubuntu/test/osm3_XLMS/dPPAS_osm3
hostname: ubuntu-Precision-3660
starting time: Sat 28 Oct 2023 06:09:22 PM CST
pwd: /tmp/ubuntu/ITosm3
running zalign .....
ending time: Sat 28 Oct 2023 06:14:39 PM CST

start serial threading dPPAS2
/tmp/ubuntu/ITosm3
/home/ubuntu/test/osm3_XLMS/dPPAS2_osm3
hostname: ubuntu-Precision-3660
starting time: Sat 28 Oct 2023 06:14:40 PM CST
pwd: /tmp/ubuntu/ITosm3
running zalign .....
ending time: Sat 28 Oct 2023 06:19:55 PM CST

start serial threading Env-PPAS
/tmp/ubuntu/ITosm3
/home/ubuntu/test/osm3_XLMS/Env-PPAS_osm3
hostname: ubuntu-Precision-3660
starting time: Sat 28 Oct 2023 06:19:57 PM CST
pwd: /tmp/ubuntu/ITosm3
running zalign .....
ending time: Sat 28 Oct 2023 06:29:05 PM CST

start serial threading MUSTER
/tmp/ubuntu/ITosm3
/home/ubuntu/test/osm3_XLMS/MUSTER_osm3
hostname: ubuntu-Precision-3660
starting time: Sat 28 Oct 2023 06:29:06 PM CST
pwd: /tmp/ubuntu/ITosm3
running Psi-blast .....
running zalign .....
#2 residue inconsistent ! /home/ubuntu/test/I-TASSER5.1/template_library_directory/DEP/6lnwA.dep 129 495

==>3zfcA 5mioC 16.8093227572644 16.5007768958656
3zfcA 5mioC 23 17
score_flag=1
ending time: Sat 28 Oct 2023 06:40:35 PM CST

/home/ubuntu/test/osm3_XLMS/init.wPPAS exists
/home/ubuntu/test/osm3_XLMS/init.wdPPAS exists
/home/ubuntu/test/osm3_XLMS/init.wMUSTER exists
can not open /home/ubuntu/test/osm3_XLMS//home/ubuntu/test/osm3_XLMS/input_all_cutoff_35_Intramolecular.txt at /home/ubuntu/test/I-TASSER5.1/I-TASSERmod/runI-TASSER.pl line 995.

Does that mean I need to remove init.wPPAS, init.wdPPAS exists, init.wdPPAS exists which were out put in the last run?
Besides, what should I do with the error about the restraint, "can not open /home/ubuntu/test/osm3_XLMS//home/ubuntu/test/osm3_XLMS/input_all_cutoff_35_Intramolecular.txt at /home/ubuntu/test/I-TASSER5.1/I-TASSERmod/runI-TASSER.pl line 995"?

Looking forward for hearing from you and thanks a lot for your kind help!
Weiye

Dear user,

You can keep the existing init.xxx if they are not making any trouble.

For your restraints, please put it to $datadir, and when you pass the parameters, I think you should just give the restraints name, like osm3_ranked_0_monomer.pdb directly without the path.

you can see your issue file path /home/ubuntu/test/osm3_XLMS//home/ubuntu/test/osm3_XLMS/input_all_cutoff_35_Intramolecular.txt,
it contains two times of /home/ubuntu/test/osm3_XLMS/.

Best
IT Team