Search found 17 matches

by rpearson_7
Thu Apr 20, 2023 6:46 pm
Forum: Main Forum
Topic: C-I-Tasser Standalone Installation Help Request
Replies: 10
Views: 25734

Re: C-I-Tasser Standalone Installation Help Request

Is it possible for you to provide the correct versions to use for the python dependencies required for the standalone version? Also, what are the settings that the server runs in the bash script? I am interested in this for I-Tasser and C-I-Tasser. for example: perl runI-TASSER.pl -pkgdir ./C-I-TASS...
by rpearson_7
Thu Apr 20, 2023 6:40 pm
Forum: Main Forum
Topic: Locally Installed C-I-Tasser and I-Tasser fails for certain proteins
Replies: 12
Views: 38328

Re: Locally Installed C-I-Tasser and I-Tasser fails for certain proteins

Okay, I made some more progress. First, let's recap what I am doing and some quick problems and solutions I found so far. I am using the standalone C-I-Tasser program on an HPC (linux with CentOS and SLURM job manager). I downloaded the libraries a long time ago and have just recently started using ...
by rpearson_7
Mon Apr 17, 2023 11:39 pm
Forum: Main Forum
Topic: Locally Installed C-I-Tasser and I-Tasser fails for certain proteins
Replies: 12
Views: 38328

Re: Locally Installed C-I-Tasser and I-Tasser fails for certain proteins

Well, this is not looking good so far... I am now getting the following error in err_CITwMUSTER_Q9KL03.fasta slurmstepd: error: couldn't chdir to `/tmp/rpearson/CITQ9KL03.fasta': No such file or directory: going to /tmp instead Exception in thread "main" java.lang.NumberFormatException: Fo...
by rpearson_7
Mon Apr 17, 2023 9:16 pm
Forum: Main Forum
Topic: Locally Installed C-I-Tasser and I-Tasser fails for certain proteins
Replies: 12
Views: 38328

Re: Locally Installed C-I-Tasser and I-Tasser fails for certain proteins

I am still experiencing problems. It appears now that only 6 threading programs yield output. 3.1 do threading start parallel threading CEthreader start parallel threading mCEthreader start parallel threading eCEthreader start parallel threading PPAS start parallel threading dPPAS start parallel thr...
by rpearson_7
Fri Apr 14, 2023 5:43 pm
Forum: Main Forum
Topic: Locally Installed C-I-Tasser and I-Tasser fails for certain proteins
Replies: 12
Views: 38328

Re: Locally Installed C-I-Tasser and I-Tasser fails for certain proteins

Got some data back... Everything failed during the threading portion. I have it set to run in parallel and I received the following error message: (base) [rpearson@spartan01 P0DMV8]$ cat err_CITMUSTER_P0DMV8.fasta slurmstepd: error: couldn't chdir to `/tmp/rpearson/CITP0DMV8.fasta': No such file or ...
by rpearson_7
Thu Apr 13, 2023 7:14 pm
Forum: Main Forum
Topic: Locally Installed C-I-Tasser and I-Tasser fails for certain proteins
Replies: 12
Views: 38328

Re: Locally Installed C-I-Tasser and I-Tasser fails for certain proteins

I just re-downloaded the DEP directory from the following website: https://seq2fun.dcmb.med.umich.edu//C-I-TASSER/download.html I then extracted the files using the following command: tar -xvjf DEP.tar.bz2 I checked the file I was looking for existed and it did. I copied that file to the DEP directo...
by rpearson_7
Wed Apr 12, 2023 7:49 pm
Forum: Main Forum
Topic: Locally Installed C-I-Tasser and I-Tasser fails for certain proteins
Replies: 12
Views: 38328

Re: Locally Installed C-I-Tasser and I-Tasser fails for certain proteins

Here is an update: I went into runITasser.pl and (since I am using the parallel flag) I increased the wall time to 144:00:00 and the memory to 100000mb from 72:00:00 and 10000mb respectively. I did the same to the runCEThreader.pl script. I have yet to see how this impacts the runs... My hypothesis ...
by rpearson_7
Wed Apr 12, 2023 12:58 am
Forum: Main Forum
Topic: C-I-Tasser Standalone Installation Help Request
Replies: 10
Views: 25734

Re: C-I-Tasser Standalone Installation Help Request

Thank you for your reply. I was looking to troubleshoot some of the standalone version problems I occasionally face. I am using a HPC server that uses SLURM. Do I need to adjust anything when I am running in parallel still or has this issue been resolved? I am looking here: https://zhanggroup.org/bb...
by rpearson_7
Wed Apr 12, 2023 12:41 am
Forum: Main Forum
Topic: Locally Installed C-I-Tasser and I-Tasser fails for certain proteins
Replies: 12
Views: 38328

Re: Locally Installed C-I-Tasser and I-Tasser fails for certain proteins

Oh, I also have a few more general questions. Question 1) What is the difference between "real" and "benchmark"? Question 2) I am trying to create an ensemble of protein conformations for both C-I-Tasser and I-Tasser so having 0 or 1 model does not help much. Is there something i...
by rpearson_7
Wed Apr 12, 2023 12:22 am
Forum: Main Forum
Topic: Locally Installed C-I-Tasser and I-Tasser fails for certain proteins
Replies: 12
Views: 38328

Re: Locally Installed C-I-Tasser and I-Tasser fails for certain proteins

Thanks! I decided to re-run some of the queries to see if that helped. For some, it did. For others, re-running did not solve the problem. For the proteins that still have issues producing any models I am noticing a trend. Here is the example output: Your setting for running I-TASSER is: -pkgdir = /...