Errors in threading programs in standalone C-I-TASSER-1.0

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francisco977
Posts: 2
Joined: Thu Jul 01, 2021 5:26 pm

Errors in threading programs in standalone C-I-TASSER-1.0

Post by francisco977 »

Hello,

I downloaded the standalone version of C-I-TASSER and the required libraries, and I am trying to run the model prediction (runI-TASSER.pl) on the test sequence included in the package. Unfortunately I am getting errors with some of the threading programs, where CEthreader, mCEthreader, eCEthreader, wPPAS, wdPPAS and wMUSTER are producing output but PPAS, dPPAS, dPPAS2, Env-PPAS and MUSTER are not, and they show an error related to some missing files.

I paste some of the stdout here, since I'm having trouble attaching a text file:

```

Code: Select all

Your setting for running I-TASSER is:
-pkgdir    = /ibex/scratch/projects/c2102/mutation_classifier/programs/cITASSER/C-I-TASSER-1.0
-libdir    = /ibex/scratch/projects/c2102/mutation_classifier/programs/cITASSER/C-I-TASSER-1.0/ITLIB2
-java_home = /usr
-python2   = /usr/bin/python2
-python3   = /ibex/scratch/projects/c2102/mutation_classifier/env_pytorchcuda/bin/python3
-seqname   = example3
-datadir   = /ibex/scratch/projects/c2102/mutation_classifier/programs/cITASSER/C-I-TASSER-1.0/example3
-outdir    = /ibex/scratch/projects/c2102/mutation_classifier/programs/cITASSER/C-I-TASSER-1.0/example3
-runstyle  = serial
-homoflag  = real
-idcut     = 1
-cit       = true
-ntemp     = 20
-nmodel    = 5
-light     = false
-hours     = 50
-LBS       = false
-EC        = false
-GO        = false

1. make seq.txt and rmsinp
Your protein contains 143 residues:
> example3
MYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLA
LQDSGLEVNIVTDSQYALGIITQWIHNWKKRGWPVKNVDLVNQIIEQLIKKEKVYLAWVP
AHKGIGGNEQVDKLVSAGIRKVL

...
...
...

start serial threading eCEthreader
/tmp/guzmanfj/CITexample3
/ibex/scratch/projects/c2102/mutation_classifier/programs/cITASSER/C-I-TASSER-1.0/example3/CITeCEthreader_example3
WARNING: MSA seq looks too diverse (Neff=11.1>11). Better check it with an alignment viewer for non-homologous segments. Also consider building the MSA with hhblits using the - option to limit MSA diversity.
hostname: gpu609-09
starting time: Thu  1 Jul 16:49:14 +03 2021
pwd: /tmp/guzmanfj/CITexample3
run psipred...
do initial threading by HHD...
$ cp initial.a3m /tmp/XCfLIlff8V/4lQkEUqiey.in.a3m
Filtering alignment to diversity 7 ...
$ /ibex/scratch/projects/c2102/mutation_classifier/programs/cITASSER/C-I-TASSER-1.0/contact/DeepMSA/bin/hhfilter -v 1 -neff 7 -i /tmp/XCfLIlff8V/4lQkEUqiey.in.a3m -o /tmp/XCfLIlff8V/4lQkEUqiey.in.a3m
hhlib=/ibex/scratch/projects/c2102/mutation_classifier/programs/cITASSER/C-I-TASSER-1.0/contact/DeepMSA
$ /ibex/scratch/projects/c2102/mutation_classifier/programs/cITASSER/C-I-TASSER-1.0/contact/DeepMSA/scripts/reformat.pl -v 1 -r -noss a3m psi /tmp/XCfLIlff8V/4lQkEUqiey.in.a3m /tmp/XCfLIlff8V/4lQkEUqiey.in.psi
Predicting secondary structure with PSIPRED ... $ /ibex/scratch/projects/c2102/mutation_classifier/programs/cITASSER/C-I-TASSER-1.0/contact/DeepMSA/bin/blastpgp -b 1 -j 1 -h 0.001 -d /ibex/scratch/projects/c2102/mutation_classifier/programs/cITASSER/C-I-TASSER-1.0/contact/DeepMSA/data/do_not_delete -i /tmp/XCfLIlff8V/4lQkEUqiey.sq -B /tmp/XCfLIlff8V/4lQkEUqiey.in.psi -C /tmp/XCfLIlff8V/4lQkEUqiey.chk 1> /tmp/XCfLIlff8V/4lQkEUqiey.blalog 2> /tmp/XCfLIlff8V/4lQkEUqiey.blalog
$ echo 4lQkEUqiey.chk > /tmp/XCfLIlff8V/4lQkEUqiey.pn

$ echo 4lQkEUqiey.sq  > /tmp/XCfLIlff8V/4lQkEUqiey.sn

$ /ibex/scratch/projects/c2102/mutation_classifier/programs/cITASSER/C-I-TASSER-1.0/contact/DeepMSA/bin/makemat -P /tmp/XCfLIlff8V/4lQkEUqiey
$ /ibex/scratch/projects/c2102/mutation_classifier/programs/cITASSER/C-I-TASSER-1.0/contact/DeepMSA/bin/psipred /tmp/XCfLIlff8V/4lQkEUqiey.mtx /ibex/scratch/projects/c2102/mutation_classifier/programs/cITASSER/C-I-TASSER-1.0/contact/DeepMSA/data/weights.dat /ibex/scratch/projects/c2102/mutation_classifier/programs/cITASSER/C-I-TASSER-1.0/contact/DeepMSA/data/weights.dat2 /ibex/scratch/projects/c2102/mutation_classifier/programs/cITASSER/C-I-TASSER-1.0/contact/DeepMSA/data/weights.dat3 > /tmp/XCfLIlff8V/4lQkEUqiey.ss
$ /ibex/scratch/projects/c2102/mutation_classifier/programs/cITASSER/C-I-TASSER-1.0/contact/DeepMSA/bin/psipass2 /ibex/scratch/projects/c2102/mutation_classifier/programs/cITASSER/C-I-TASSER-1.0/contact/DeepMSA/data/weights_p2.dat 1 0.98 1.09 /tmp/XCfLIlff8V/4lQkEUqiey.ss2 /tmp/XCfLIlff8V/4lQkEUqiey.ss > /tmp/XCfLIlff8V/4lQkEUqiey.horiz
done 
hhlib=/ibex/scratch/projects/c2102/mutation_classifier/programs/cITASSER/C-I-TASSER-1.0/contact/DeepMSA
initial.a3m is in A2M, A3M or FASTA format
Read initial.a3m with 24300 sequences
Alignment in initial.a3m contains 143 match states
1560 out of 24298 sequences passed filter (up to 3518ef850osition-dependent max pairwise sequence identity)
Effective number of sequences exp(entropy) = 11.1
Writing HMM to initial.hhm
Done
.................................................. 1000 HMMs searched
.................................................. 2000 HMMs searched
...
.................................................. 83000 HMMs searched
.................................................. 84000 HMMs searched
..........................Realigning 20000 query-template alignments with maximum accuracy (MAC) algorithm ...
.run CEthreader...
 _____ _____ _____               _ 
|     |     |     |___ ___ ___ _| |
|   --|   --| | | | . |  _| -_| . |
|_____|_____|_|_|_|  _|_| |___|___|
                  |_|              

using CPU (1 thread(s))

Reweighted 20853 sequences with threshold 0.8 to Beff=14420.8 weight mean=0.691544, min=0.00806452, max=1

Will optimize 9020869 32-bit variables

iter    eval    f(x)            ║x║             ║g║             step
1       1       4.17263e+06     23442.5         3.2436609e+10   4.79e-06
2       1       4.077e+06       23442.5         2.353844e+10    3.47e-06
...
61      1       2.17173e+06     50013.7         4.7958867e+08   1.2e-05
62      2       2.16912e+06     50207.4         4.5074618e+08   7.01e-06

Done with status code 0 - Success!

Final fx = 2166684.750000

Writing raw output to /tmp/guzmanfj/CITeCEthreader_example3/deepmsa.contact.raw
xnorm = 119.446
Output can be found in /tmp/guzmanfj/CITeCEthreader_example3/deepmsa.contact.del
cuda is ready? : True
/tmp/guzmanfj/CITeCEthreader_example3/deepmsa_protein.aln
143

done.re-align and re-rank the top 4000 templates...
ending time: Thu  1 Jul 18:47:54 +03 2021

start serial threading PPAS
/tmp/guzmanfj/CITexample3
/ibex/scratch/projects/c2102/mutation_classifier/programs/cITASSER/C-I-TASSER-1.0/example3/CITPPAS_example3
open: No such file or directory
apparent state: unit 30 named /ibex/scratch/projects/c2102/mutation_classifier/programs/cITASSER/C-I-TASSER-1.0/ITLIB2/summary/AAA
last format: list io
lately reading sequential formatted external IO
Illegal division by zero at /ibex/scratch/projects/c2102/mutation_classifier/programs/cITASSER/C-I-TASSER-1.0/example3/CITPPAS_example3 line 354.
hostname: gpu609-09
starting time: Thu  1 Jul 18:47:57 +03 2021
pwd: /tmp/guzmanfj/CITexample3
running zalign .....

start serial threading dPPAS
/tmp/guzmanfj/CITexample3
/ibex/scratch/projects/c2102/mutation_classifier/programs/cITASSER/C-I-TASSER-1.0/example3/CITdPPAS_example3
At line 273 of file ppa1.f
Fortran runtime error: No such file or directory
Illegal division by zero at /ibex/scratch/projects/c2102/mutation_classifier/programs/cITASSER/C-I-TASSER-1.0/example3/CITdPPAS_example3 line 356.
hostname: gpu609-09
starting time: Thu  1 Jul 18:48:03 +03 2021
pwd: /tmp/guzmanfj/CITexample3
running zalign .....

start serial threading dPPAS2
/tmp/guzmanfj/CITexample3
/ibex/scratch/projects/c2102/mutation_classifier/programs/cITASSER/C-I-TASSER-1.0/example3/CITdPPAS2_example3
At line 273 of file ppa1.f
Fortran runtime error: No such file or directory
Illegal division by zero at /ibex/scratch/projects/c2102/mutation_classifier/programs/cITASSER/C-I-TASSER-1.0/example3/CITdPPAS2_example3 line 355.
hostname: gpu609-09
starting time: Thu  1 Jul 18:48:06 +03 2021
pwd: /tmp/guzmanfj/CITexample3
running zalign .....

start serial threading Env-PPAS
/tmp/guzmanfj/CITexample3
/ibex/scratch/projects/c2102/mutation_classifier/programs/cITASSER/C-I-TASSER-1.0/example3/CITEnv-PPAS_example3
At line 284 of file zal3.f
Fortran runtime error: No such file or directory
Illegal division by zero at /ibex/scratch/projects/c2102/mutation_classifier/programs/cITASSER/C-I-TASSER-1.0/example3/CITEnv-PPAS_example3 line 352.
hostname: gpu609-09
starting time: Thu  1 Jul 18:48:08 +03 2021
pwd: /tmp/guzmanfj/CITexample3
running zalign .....

start serial threading MUSTER
/tmp/guzmanfj/CITexample3
/ibex/scratch/projects/c2102/mutation_classifier/programs/cITASSER/C-I-TASSER-1.0/example3/CITMUSTER_example3
At line 354 of file zal33.f
Fortran runtime error: No such file or directory
Illegal division by zero at /ibex/scratch/projects/c2102/mutation_classifier/programs/cITASSER/C-I-TASSER-1.0/example3/CITMUSTER_example3 line 599.
hostname: gpu609-09
starting time: Thu  1 Jul 18:48:10 +03 2021
pwd: /tmp/guzmanfj/CITexample3
running Psi-blast .....
running zalign .....
./zalign 7.01 0.55 0.66 1.6 -0.99 0.31 0.19 0 1.0 0.39 0.19

start serial threading wPPAS
/tmp/guzmanfj/CITexample3
/ibex/scratch/projects/c2102/mutation_classifier/programs/cITASSER/C-I-TASSER-1.0/example3/CITwPPAS_example3
hostname: gpu609-09
starting time: Thu  1 Jul 18:50:37 +03 2021
pwd: /tmp/guzmanfj/CITexample3
running Psi-blast .....
ending time: Thu  1 Jul 20:16:25 +03 2021

start serial threading wdPPAS
/tmp/guzmanfj/CITexample3
/ibex/scratch/projects/c2102/mutation_classifier/programs/cITASSER/C-I-TASSER-1.0/example3/CITwdPPAS_example3
hostname: gpu609-09
starting time: Thu  1 Jul 20:16:27 +03 2021
pwd: /tmp/guzmanfj/CITexample3
running Psi-blast .....
ending time: Thu  1 Jul 21:57:24 +03 2021

start serial threading wMUSTER
/tmp/guzmanfj/CITexample3
/ibex/scratch/projects/c2102/mutation_classifier/programs/cITASSER/C-I-TASSER-1.0/example3/CITwMUSTER_example3
hostname: gpu609-09
starting time: Thu  1 Jul 21:57:26 +03 2021
pwd: /tmp/guzmanfj/CITexample3
running Psi-blast .....
running Psi-blast .....
==>1rilA 1goaA 26.1735605738703 20.1763750278109
 1rilA 1goaA 26.57 34.97
score_flag=2
ending time: Thu  1 Jul 23:24:25 +03 2021

only 6 threading programs have output, please check threading programs
```

Thanks a lot for your help, and for your amazing work with this tool!

Best regards,
Francisco
jlspzw
Posts: 36
Joined: Tue May 04, 2021 5:04 pm

Re: Errors in threading programs in standalone C-I-TASSER-1.0

Post by jlspzw »

Dear user,

It may be caused by some uncomplete library file

could you do "ls /ibex/scratch/projects/c2102/mutation_classifier/programs/cITASSER/C-I-TASSER-1.0/ITLIB2" and "ls /ibex/scratch/projects/c2102/mutation_classifier/programs/cITASSER/C-I-TASSER-1.0/ITLIB2/summary" see if AAA.sec exist?

Best
ITteam
francisco977
Posts: 2
Joined: Thu Jul 01, 2021 5:26 pm

Re: Errors in threading programs in standalone C-I-TASSER-1.0

Post by francisco977 »

Hello, thank you for the reply. I did as you said and I found the file AAA.sec in the "ITLIB2/summary" directory. The outputs from the commands are the following:

Code: Select all

$ ll ITLIB2/
total 1313
drwxr-sr-x 2 guzmanfj ibex-c2102 292125 Jun  8  2016 Bfactor
drwxr-sr-x 3 guzmanfj ibex-c2102      4 Jun 13 16:11 BPOCKET
drwxr-sr-x 2 guzmanfj ibex-c2102  84420 Jan 15 00:56 CE
drwxr-sr-- 2 guzmanfj ibex-c2102  89747 May 30 13:04 CNT
drwxr-sr-- 2 guzmanfj ibex-c2102  89738 May 30 10:48 DEP
drwxr-sr-x 2 guzmanfj ibex-c2102  88789 Jun  1 21:59 dotProfiles
drwxr-sr-x 5 guzmanfj ibex-c2102   3658 Jan 18  2014 Enzyme
drwxr-sr-x 6 guzmanfj ibex-c2102  41036 Mar 18  2017 GO
drwxr-sr-x 2 guzmanfj ibex-c2102 228341 Jun 11 04:06 ligand
drwxr-sr-x 2 guzmanfj ibex-c2102     14 Aug 23  2014 map
drwxr-sr-x 2 guzmanfj ibex-c2102      5 Jun 19 21:17 metaclust
drwxr-sr-- 2 guzmanfj ibex-c2102  89746 May 30 10:51 MTX
drwxr-sr-x 2 guzmanfj ibex-c2102     30 Dec  5  2013 nr
drwxr-sr-- 2 guzmanfj ibex-c2102  89747 May 30 09:25 PDB
drwxr-sr-x 3 guzmanfj ibex-c2102      4 Jun 13 16:15 PSSM
drwxr-sr-x 2 guzmanfj ibex-c2102  58418 Jan 11  2012 receptor
drwxr-sr-- 2 guzmanfj ibex-c2102  89746 May 30 12:57 SIG
drwxr-sr-x 2 guzmanfj ibex-c2102  88788 Jun  1 16:21 stride
drwxr-sr-x 2 guzmanfj ibex-c2102     13 Jun 13 15:59 summary
drwxr-sr-x 2 guzmanfj ibex-c2102     13 Jun 19 20:34 uniclust30
drwxr-sr-x 2 guzmanfj ibex-c2102      4 Jun 20 09:07 uniref90

ll ITLIB2/summary
total 2877861
-rwxr-xr-- 1 guzmanfj ibex-c2102  133484100 May 30 10:32 AAA.phi
-rwxr-xr-- 1 guzmanfj ibex-c2102  133484100 May 30 10:32 AAA.psi
-rwxr-xr-- 1 guzmanfj ibex-c2102   95718208 May 30 10:32 AAA.sa3
-rwxr-xr-- 1 guzmanfj ibex-c2102   20274304 May 30 11:00 AAA.sec
-rwxr-xr-- 1 guzmanfj ibex-c2102   20274304 May 30 11:00 AAA.seq
-rwxr-xr-x 1 guzmanfj ibex-c2102  535529646 Apr  2  2008 modelCA0
-rwxr-xr-x 1 guzmanfj ibex-c2102  708927349 Apr  2  2008 modelCA1
-rwxr-xr-x 1 guzmanfj ibex-c2102 1109402538 Apr  2  2008 modelCA2
-rwxr-xr-x 1 guzmanfj ibex-c2102   69160141 Oct 17  2007 modelphi_0.005_1.dat
-rwxr-xr-x 1 guzmanfj ibex-c2102  120643647 Oct 17  2007 modelpsi_0.005_1.dat
-rwxr-xr-x 1 guzmanfj ibex-c2102       8403 Apr  2  2008 par0
-rwxr-xr-x 1 guzmanfj ibex-c2102       8565 Apr  2  2008 par1
-rwxr-xr-x 1 guzmanfj ibex-c2102      10050 Apr  2  2008 par2

I don't know if this is related, but at first I was having issues downloading the libraries, so I used the script "download_lib_new.pl" shared by "xiaogenz" in the following forum thread: https://zhanglab.ccmb.med.umich.edu/for ... 586df761e1 , and later downloaded the uniclust30, uniref90, metaclust and CE libraries separately. However, upon further inspection of the script I found that the domain names for the download links differ between the "download_lib_new.pl" and "download_lib.pl" scripts: "http://zhanglab.ccmb.med.umich.edu" in "download_lib.pl" and "http://zhanglab.dcmb.med.umich.edu" in "download_lib_new.pl".

Other than that I couldn't find any irregularities. Thank you for your help!

Best regards,
Francisco
jlspzw
Posts: 36
Joined: Tue May 04, 2021 5:04 pm

Re: Errors in threading programs in standalone C-I-TASSER-1.0

Post by jlspzw »

Hi Francisco

I think I got the problem, in some old Fortran program, the library path are set at most 100 characters, thus you full AAA.sec path should be

/ibex/scratch/projects/c2102/mutation_classifier/programs/cITASSER/C-I-TASSER-1.0/ITLIB2/summary/AAA.sec, which over the limitation.

The simple solution is put ITLIB2 in a shallower path like /ibex/scratch/projects/c2102/ITLIB2, unfortunately some code are very old, I donot have all source code, thus I can not enlarge them in source code....

Best
Wei
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