Fail to generate rep*.tra files

[Bowen]

Hi,

I have encountered an issue with I-TASSER standalone, which is basically the same as described in this older article: viewtopic.php?f=3&t=10&sid=9b1eef47915d ... b7bf248e58. I will be so grateful if anyone could offer me possible solutions.

In more details, I am using the latest I-TASSER5.1 in WSL-Ubuntu OS (Ubuntu 20.04.2 LTS (GNU/Linux 5.4.72-microsoft-standard-WSL2 x86_64)) on MobaXterm. The whole script of my job is attached subsequently.

Your setting for running I-TASSER is:
-pkgdir = /mnt/d/I/I-TASSER5.1
-libdir = /mnt/d/I/I-TASSER5.1/libdir
-java_home = /usr
-seqname = VIM-1
-datadir = /mnt/d/I/I-TASSER5.1/VIM-1
-outdir = /mnt/d/I/I-TASSER5.1/VIM-1
-runstyle = serial
-homoflag = real
-idcut = 1
-ntemp = 20
-nmodel = 5
-light = false
-hours = 50
-LBS = true
-EC = false
-GO = false

1. make seq.txt and rmsinp
Your protein contains 266 residues:
> VIM-1
MLKVISSLLVYMTASVMAVASPLAHSGEPSGEYPTVNEIPVGEVRLYQIADGVWSHIATQ
SFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRV
GGVDVLRAAGVATYASPSTRRLAEAEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHS
TDNLVVYVPSANVLYGGCAVHELSSTSAGNVADADLAEWPTSVERIQKHYPEAEVVIPGH
GLPGGLDLLQHTANVVKAHKNRSVAE
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/I-TASSER5.1/VIM-1/init.PPAS exists
/mnt/d/I/I-TASSER5.1/VIM-1/init.dPPAS exists
/mnt/d/I/I-TASSER5.1/VIM-1/init.dPPAS2 exists
/mnt/d/I/I-TASSER5.1/VIM-1/init.Env-PPAS exists
/mnt/d/I/I-TASSER5.1/VIM-1/init.MUSTER exists
/mnt/d/I/I-TASSER5.1/VIM-1/init.wPPAS exists
/mnt/d/I/I-TASSER5.1/VIM-1/init.wdPPAS exists
start serial threading wMUSTER
/tmp/bowen/ITVIM-1
/mnt/d/I/I-TASSER5.1/VIM-1/wMUSTER_VIM-1
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 101
at e.main(e.java)
Illegal division by zero at /mnt/d/I/I-TASSER5.1/VIM-1/wMUSTER_VIM-1 line 570.
hostname: LAPTOP-7JN2SDC4
starting time: Mon Sep 27 22:50:17 JST 2021
pwd: /tmp/bowen/ITVIM-1
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

[jlspzw]

Dear user,

It seems the wMUSTER threading failed, please re-try this step until you get the results. Based on the error message, it perhaps your java machine memory is too small,you can try increase it.

Best
Wei

[jlspzw]

BTW, it seems you use window subsystem, if I am correct, the java in the WSL system has some issue with the memory, you can try a native linux system instead of WSL if you don't know how to deal with the WSL issue.

[Bowen]

Dear Wei,

I tried to allocate more memory and processors to WSL as well as increase Java heap size but neither worked. I think I could only try to run I-TASSER on a native Linux machine. Anyway, thanks so much for your help!

Best wishes,
Bowen