Zhanglab forum

Hi!

I installed local I-TASSER, but when I used a short protein to test whether I-TASSER can work or not, I met this error which is shown under below. I thought it was due to MUSTER process, so I made some changes according to this solution. viewtopic.php?f=3&t=721&sid=9cb43186ffc ... 088f504d9d. But the problem was not fixed. Could you please give me some suggestions? Thank you very much!

Best wishes!

MCUI


[root@FHZX-19: i-tasser]$$itasser/I-TASSER5.2/I-TASSERmod/runI-TASSER.pl -libdir /$itasser/ITLIB -seqname seq.fasta -datadir /$itasser/test

Your setting for running I-TASSER is:
-pkgdir = /mnt/d/home/i-tasser/I-TASSER5.2
-libdir = /mnt/d/home/i-tasser/ITLIB
-java_home = /usr
-seqname = seq.fasta
-datadir = /mnt/d/home/i-tasser/test
-outdir = /mnt/d/home/i-tasser/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 19 residues:
> seq.fasta
MNSERSDVTLYQPFLDYAI
2.1 run Psi-blast
2.2 Secondary structure prediction was done before.
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 12.97329 14050.07
pair done
3.1 do threading
start serial threading PPAS
/tmp/root/ITseq.fasta
/mnt/d/home/i-tasser/test/PPAS_seq.fasta
hostname: FHZX-19
starting time: Fri Apr 21 17:13:04 CST 2023
pwd: /tmp/root/ITseq.fasta
running zalign .....
ending time: Fri Apr 21 17:17:22 CST 2023

start serial threading dPPAS
/tmp/root/ITseq.fasta
/mnt/d/home/i-tasser/test/dPPAS_seq.fasta
hostname: FHZX-19
starting time: Fri Apr 21 17:17:23 CST 2023
pwd: /tmp/root/ITseq.fasta
running zalign .....
ending time: Fri Apr 21 17:35:09 CST 2023

start serial threading dPPAS2
/tmp/root/ITseq.fasta
/mnt/d/home/i-tasser/test/dPPAS2_seq.fasta
hostname: FHZX-19
starting time: Fri Apr 21 17:35:11 CST 2023
pwd: /tmp/root/ITseq.fasta
running zalign .....
ending time: Fri Apr 21 17:39:53 CST 2023

start serial threading Env-PPAS
/tmp/root/ITseq.fasta
/mnt/d/home/i-tasser/test/Env-PPAS_seq.fasta
hostname: FHZX-19
starting time: Fri Apr 21 17:39:54 CST 2023
pwd: /tmp/root/ITseq.fasta
running zalign .....
ending time: Fri Apr 21 17:59:27 CST 2023

start serial threading MUSTER
/tmp/root/ITseq.fasta
/mnt/d/home/i-tasser/test/MUSTER_seq.fasta
[blastpgp] WARNING: [000.000] posPurgeMatches: Due to purging near identical sequences, only the query is used to construct the position-specific score matrix

hostname: FHZX-19
starting time: Fri Apr 21 17:59:28 CST 2023
pwd: /tmp/root/ITseq.fasta
running Psi-blast .....
running zalign .....
err 2 !! 3iz5a1 129 64 37960

==>3mjhD 2vmlC 7.54978786739518 4.10661456395812
3mjhD 2vmlC 31 21
score_flag=1
ending time: Fri Apr 21 18:34:51 CST 2023

start serial threading wPPAS
/tmp/root/ITseq.fasta
/mnt/d/home/i-tasser/test/wPPAS_seq.fasta
[blastpgp] WARNING: posPurgeMatches: Due to purging near identical sequences, only the query is used to construct the position-specific score matrix

Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: Index 66 out of bounds for length 66
at d.a(d.java)
at d.main(d.java)
hostname: FHZX-19
starting time: Fri Apr 21 18:34:53 CST 2023
pwd: /tmp/root/ITseq.fasta
running Psi-blast .....
ending time: Fri Apr 21 18:54:24 CST 2023

start serial threading wdPPAS
/tmp/root/ITseq.fasta
/mnt/d/home/i-tasser/test/wdPPAS_seq.fasta
[blastpgp] WARNING: posPurgeMatches: Due to purging near identical sequences, only the query is used to construct the position-specific score matrix

Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: Index 66 out of bounds for length 66
at c.a(c.java)
at c.main(c.java)
hostname: FHZX-19
starting time: Fri Apr 21 18:54:25 CST 2023
pwd: /tmp/root/ITseq.fasta
running Psi-blast .....
ending time: Fri Apr 21 19:21:08 CST 2023

start serial threading wMUSTER
/tmp/root/ITseq.fasta
/mnt/d/home/i-tasser/test/wMUSTER_seq.fasta
[blastpgp] WARNING: [000.000] posPurgeMatches: Due to purging near identical sequences, only the query is used to construct the position-specific score matrix

[blastpgp] WARNING: posPurgeMatches: Due to purging near identical sequences, only the query is used to construct the position-specific score matrix

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/home/i-tasser/test/wMUSTER_seq.fasta line 570.
hostname: FHZX-19
starting time: Fri Apr 21 19:21:10 CST 2023
pwd: /tmp/root/ITseq.fasta
running Psi-blast .....
running Psi-blast .....

3.2 make restraints
without init: /mnt/d/home/i-tasser/test/init.wMUSTER
type= easy, n_good=25, 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,

The problem threading seems to be on wMUSTER, which uses a Java program post to deal with MUSTER threading. We are now working to find the source code of those Java programs. Before that, you can remove wMUSTER from the threading list.

BTW, could you list the folder /mnt/d/home/i-tasser/test using "ls /mnt/d/home/i-tasser/test"? We want to check if all other files are ready.

Best
IT Team