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