Hi,
let me start by stating I am not a programmer, so my software/script related troubleshooting skills are limited.
I am currently in the process of establishing the C-I-TASSER suite (v1.0) on a freshly set-up local machine and ironed out a fair amount of errors and deprecated behavior warnings I got returned while running the example sequence that comes with the install files (mostly missing software/package dependencies or related to the requirement of particular versions of such).
I finally got stuck in step 3.1 though (running the 11 threading programs). Here all threading programs seem to complete successfully with an output but the flavors of the CEthreader (CEthreader, mCEthreader, eCEthreader) do not.
The error for each is similar:
Error in /home/ihi/C-I-TASSER-1.0/contact/DeepMSA/bin/hhsearch: could not open file '/home/ihi/ITLIB/CE/pdb.hhm'
Illegal division by zero at /home/ihi/C-I-TASSER-1.0/example/CITCEthreader_example line 418.
Error in /home/ihi/C-I-TASSER-1.0/contact/DeepMSA/bin/hhsearch: could not open file '/home/ihi/ITLIB/CE/pdb.hhm'
Illegal division by zero at /home/ihi/C-I-TASSER-1.0/example/CITmCEthreader_example line 390.
Error in /home/ihi/C-I-TASSER-1.0/contact/DeepMSA/bin/hhsearch: could not open file '/home/ihi/ITLIB/CE/pdb.hhm'
Illegal division by zero at /home/ihi/C-I-TASSER-1.0/example/CITeCEthreader_example line 417.
FORTRAN STOP
only 8 threading programs have output, please check threading programs
The pdb.hhm file is indeed at the right path and I am somewhat at a loss why hhsearch cannot process it. It seems not corrupted and I can easily peak into that monster of a file with e.g. -head. Any idea what might be the issue or what specific information I could provide to get to the bottom of this?
Kind regards,
Robert
Dear user, Thank you for
Dear user,
Thank you for using the C-I-TASSER suite package,
let me first confirm, have you install the python, pytorch and set the location in the main script?
if not, you can follow the readme file to set them and retry.
if you run the full C-I-TASSER modeling by runITASSER.pl, you can check if there are protein.a3m in your $datadir/MSA and respre.dat in $datadir, and check if respre.dat has correct contact prediction (more than one line), this also can tell you whether you contact prediction correctly generated. since CEthreader need contact prediction, you need first confirm that.
you can run the hhsearch directly by $itpackage/contact/DeepMSA/bin/hhsearch -i $yoursequence -d /home/ihi/ITLIB/CE/pdb.hhm
see if the programs get any issue.
Best
Hi, thanks for your timely
Hi,
thanks for your timely reply and the I-TASSER/C-I-TASSER pipelines in general!
To the problem at hand:
I am indeed using the full pipeline script (runI-TASSER.pl) to run the $pkdir/example/seq.fasta and it completes all steps before step 3.1 to completion without any error report. I guess that answers the question of having installed python2, python3 and pytorch as well.
The files generated by the pipeline to this point include the respre.dat (198.5kB) as well as a protein.a3m (4.6MB) file.
When I run hhsearch directly, as per your instruction, I get the following error though:
$ ~/C-I-TASSER-1.0/contact/DeepMSA/bin/hhsearch -i ~/C-I-TASSER-1.0/example/seq.fasta -d ~/ITLIB/CE/pdb.hhm
Search results will be written to /home/ihi/C-I-TASSER-1.0/example/seq.hhr
/home/ihi/C-I-TASSER-1.0/example/seq.fasta is in A2M, A3M or FASTA format
Read /home/ihi/C-I-TASSER-1.0/example/seq.fasta with 1 sequences
Alignment in /home/ihi/C-I-TASSER-1.0/example/seq.fasta contains 143 match states
1 out of 1 sequences passed filter (90% max pairwise sequence identity)
Effective number of sequences exp(entropy) = 1.0
Error in /home/ihi/C-I-TASSER-1.0/contact/DeepMSA/bin/hhsearch: could not open file '/home/ihi/ITLIB/CE/pdb.hhm'
I gather this is the same problem as before.
I downloaded the CE library directly from 'https://zhanglab.ccmb.med.umich.edu/C-I-TASSER/library/CE.tar.bz2' and unpacked it as per the identical command used in the download_lib.pl. I am as well not aware of any alteration of the hhsearch binary that came with the C-I-TASSER files from 'https://zhanglab.ccmb.med.umich.edu/C-I-TASSER/standalone/C-I-TASSER-1.0.tar.bz2' nor is there to my knowledge a second installation of the hhsuite on that system.
Kind regards,
Robert