I-TASSER Illegal division by zero during MUSTER

[jimgene]

Hi,

When executing to
printf `./zalign 7.01 0.55 0.66 1.6 -0.99 0.31 0.19 0 1.0 0.39 0.19`;
in MUSTERmod

it gives an empty result file,
-rw-r--r-- 1 root root 0 Jan 29 16:06 rst.dat

with no error message given.

And I have checked all the files in in.dd, they all exist.

I wonder what could be the problem?

Thank you.
Jim

[jimgene]

It seems like ./zalign crashed with Segmentation fault. Even run the example fasta you provided it still crashes.

[jlspzw]

Dear user,

Could you check how many lines are in your $ITlib/PDB/list file? You can use "more $ITlib/PDB/list" see the first line. Here $ITlib is your I-TASSER library path.

BTW, is that package I-TASSER? C-I-TASSER or D-I-TASSER?

Thank you.

Best
IT Team

[jimgene]

"more $ITlib/PDB/list" gives 96666, and "ls $ITlib/PDB/ | wc -l" gives 98431.

When running "./zalign 7.01 0.55 0.66 1.6 -0.99 0.31 0.19 0 1.0 0.39 0.19" in centos instead of ubuntu, it outputs:
=====
At line 522 of file zal33.f
Fortran runtime error: End of file
=====

And MUSTERmod is in D-I-TASSER/I-TASSER.

Thank you for your time,
Jim

[jlspzw]

Dear user,

Please download the attached zip file for MUSTER and MUSTER-related programs.

1. unzip the zip files. you will get zal1 zal2 zal3 zal33, add permission by "chmod a+x zal1 zal2 zal3 zal33"
2. go to your I-TASSER/D-I-TASSER programs path,
cd bin/MUSTER/bin, backup zal33 by "mv zal33_old", and put the downloaded zal33 into this folder.
3. go to bin/zalign in D-I-TASSER/I-TASSSER package, backup zal1 zal2 zal3 by "mv zal1 zal1_old; mv zal2 zal2_old; mv zal3 zal3_old;"
and put the downloaded zal1 zal2 zal3 into this folder.

Please check if there are still any issues.

Best
IT Team

[jimgene]

Thank you! With the substitudes, MUSTER finishes except an abnormal message:
======
running zalign .....
#2 residue inconsistent ! /nfs/ITLIB/DEP/6lnwA.dep 129 495
======

However another critical issue comes out in "4.1 run simulation" while executing I-TASSERmod/dcasdpo4v2.1. The stdout gives:
======
4.1 run simulation
Congradulations! All your input files are correct. You can run TASSER simulations now!

run 5 serial simulations
run simulation job 1 / 5
...

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0 0x46239D in _gfortrani_backtrace
#1 0x44F1A0 in _gfortrani_backtrace_handler
#2 0x4A9CFF in gsignal
#3 0x40A75E in eshort_
#4 0x4172CA in move2_
#5 0x446B86 in MAIN__ at dcasdpo4v2.1.f:?
======

I have no clue since every file in tmp workdir seems non empty.

Much appreciated,
Jim

[jlspzw]

Hi Jim,

Could you send me the input and output files you get for this case. I will check what's the issue.

You can either attach to this forum or send it to me by email (zhengwei@umich.edu)

BTW, for the DEP issue, please check if re-downloading the ITlib helps.

Best
IT Team

[jimgene]

Hi,

https://drive.google.com/file/d/1EK1eQ7 ... share_link

extract with: tar -xvf dit-debug.tar

The contained dit-debug/ folder contains files created during I-TASSERmod/simulationmod.
And you can directly execute ./cas_DIT7e9p_1A once you have entered the dit-debug folder.

Thank you,
Jim

[jlspzw]

Dear Jim,

We seem to find the issue of your case. Please find the attached updated main D-I-TASSER program.

You can unzip the file and put the binary file dcasdpo4v2.1 to $pkgdir/I-TASSERmod/ (replace the old one), then re-run the main I-TASSER program,

If you want to try to debug testing with the file you send to me, put the binary file in that folder and, rename it as cas_DIT7e9p_1A, then run it.

Please let us know if you again find any issues.

Best
IT Team

[khainhienluu]

Dear IT team,

I have ran into this same problem, and after changing to the new zal files, only MUSTER was able to finished. PPAS, dPPAS, dPPAS2, and Env-PPAS still got 'Illegal division by zero' with empty rst,dat files in the /tmp.
I've made changes to the perl script, increasing the limit of residues to run my prediction (4563 res), could this be the cause of the problem? Because predicting smaller sequence still works fine.

Best regards,
Khai Nhien