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