CITASSER errors

[Asystole]

I cannot resolve the following errors:
1. error without MSA file generate!
I have updated all library files and still cannot resolve.
2. error: /home/michael/C-I-TASSER-1.0/example/MSA/protein.aln does not exist!

INPUT:

Code: Select all

michael@michaelvm:~/ITLIB$ /home/michael/C-I-TASSER-1.0/I-TASSERmod/runI-TASSER.pl -pkgdir /home/michael/C-I-TASSER-1.0 -libdir /home/michael/ITLIB -seqname Tins26 -datadir /home/michael/C-I-TASSER-1.0/example

OUTPUT:
Your setting for running I-TASSER is:
-pkgdir = /home/michael/C-I-TASSER-1.0
-libdir = /home/michael/ITLIB
-java_home = /usr
-python2 = /nfs/amino-library/anaconda/bin/python
-python3 = /nfs/amino-home/zhng/local_library/anaconda3/bin/python3
-seqname = Tins26
-datadir = /home/michael/C-I-TASSER-1.0/example
-outdir = /home/michael/C-I-TASSER-1.0/example
-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:
> Tins26
MYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLA
LQDSGLEVNIVTDSQYALGIITQWIHNWKKRGWPVKNVDLVNQIIEQLIKKEKVYLAWVP
AHKGIGGNEQVDKLVSAGIRKVL
2.0 run DeepMSA
--------- /home/michael/C-I-TASSER-1.0/example/CITTins26_MSA
hostname: michaelvm
starting time: Sat 21 Aug 2021 06:29:00 PM EDT
pwd: /tmp/michael/CITTins26
error: without MSA file generate!
2.1 run Psi-blast
2.2 Secondary structure prediction was done before.
2.3 Predict solvent accessibility...
2.4 run pairmod
2.4.1 Use all templates
2.4.2 running pair ................
FORTRAN STOP
30000 6379375 total lib str & residues
number of observations 27.03459 1658491.
pair done
3.0 do contact prediction
run restriplet for contact prediction...
hostname: michaelvm
starting time: Sat 21 Aug 2021 06:47:31 PM EDT
pwd: /tmp/michael/CITTins26
error: /home/michael/C-I-TASSER-1.0/example/MSA/protein.aln does not exist!


- I have copied COACH and COFACTOR folders and placed them in the ITLIB directory to see if this helps - it does not.
- I downloaded the BioLIP files via the download_all_sets.pl from within the ITLIB directory which creates several new folders and they are all placed into ITLIB directory.
- I have renamed the metaclust, uniref90, and uniclust30 folders per instructions.
- Created the metaclust.fasta.ssi and uniref90.fasta.ssi files per instructions.

[jlspzw]

Hi

Thank you for using our package

could you first show the "ls" results of /home/michael/ITLIB

and the files in metaclust, uniref90, uniclust etc

It seems you also didn't install your own python2 and python3m where python3 is used for deep-learning predictors,

you can check the readme about this part

#######

In addition, your system needs to have Java, python2,
python3 (which supports pytorch 0.3.0) installed.

"$pkgdir/I-TASSERmod/runI-TASSER.pl -pkgdir /home/yourname/C-I-TASSER-1.0 -libdir /home/yourname/ITLIB -seqname example -datadir /home/yourname/C-I-TASSER-1.0/example -runstyle parallel -homoflag benchmark -idcut 0.3 -LBS true -EC true -GO true -java_home /usr -python2 /usr/bin/python2 -python3 /usr/bin/python3 -cit true"

-python2 path to python 2, for example /bin/python
-python3 path to python 3 for contact prediction, need to support pytorch 0.3.0, for example /bin/python3


#######

you need chane those path to yours
-python2 = /nfs/amino-library/anaconda/bin/python
-python3 = /nfs/amino-home/zhng/local_library/anaconda3/bin/python3

Let me know if you have any question.

Best
IT team

[Asystole]

Thank you for the reply. When I designated a python2 and python3 location I was getting the same error, thus I used the simple examply string.

michael@michaelvm:~$ whereis python2
python2: /usr/bin/python2.7 /usr/bin/python2 /usr/lib/python2.7 /etc/python2.7 /usr/local/lib/python2.7 /usr/share/man/man1/python2.1.gz

michael@michaelvm:~$ whereis python3
python3: /usr/bin/python3.8 /usr/bin/python3 /usr/lib/python3.9 /usr/lib/python3.8 /usr/lib/python3 /etc/python3.8 /etc/python3 /usr/local/lib/python3.8 /usr/include/python3.8 /usr/share/python3 /usr/share/man/man1/python3.1.gz

michael@michaelvm:~$whereis java
java: /usr/bin/java /usr/share/java /usr/share/man/man1/java.1.gz
#HOWEVER, if

Code: Select all

-java_home /usr/bin/java

is defined, I get the error:
Error: /usr/bin/java/bin/java does not exist.
Use /usr/bin/java instead.
#Changing line to

Code: Select all

 -java_home /usr

eliminates error.

michael@michaelvm:~$ java --version
openjdk 14.0.2 2020-07-14
OpenJDK Runtime Environment (build 14.0.2+12-Ubuntu-120.04)
OpenJDK 64-Bit Server VM (build 14.0.2+12-Ubuntu-120.04, mixed mode, sharing)

#When I add the paths back to the input line (below) I get the same errors:

michael@michaelvm:~/ITLIB$ ls
abs CNT dotProfiles log PSSpred src
Bfactor COACH download_all_sets.pl map receptor stride
bin COFACTOR download_lib.pl metaclust receptor1 summary
BioLiP common Enzyme MTX receptor_nr uniclust30
blast contact GO nr receptor_nr1 uniref90
BPOCKET data ligand PDB ResQ weekly.html
CE DEP ligand_nr PSSM SIG

michael@michaelvm:~/ITLIB/metaclust$ ls
metaclust_2017_05.fasta metaclust.fasta
metaclust_2017_05.fasta.ssi metaclust.fasta.ssi

michael@michaelvm:~/ITLIB/uniclust30$ ls
uniclust30_2017_04_a3m_db uniclust30_2017_04_hhm_db.index
uniclust30_2017_04_a3m_db.index uniclust30_2017_04_hhm.ffdata
uniclust30_2017_04_a3m.ffdata uniclust30_2017_04_hhm.ffindex
uniclust30_2017_04_a3m.ffindex uniclust30_2017_04_md5sum
uniclust30_2017_04_consensus.fasta uniclust30_2017_04_seed.fasta
uniclust30_2017_04.cs219 uniclust30_2017_04.tsv
uniclust30_2017_04_cs219.ffdata uniclust30_2017_10_consensus.fasta
uniclust30_2017_04_cs219.ffindex uniclust30_2017_10_md5sum
uniclust30_2017_04.cs219.sizes uniclust30_2017_10_seed.fasta
uniclust30_2017_04_hhm_db uniclust30_2017_10.tsv

michael@michaelvm:~/ITLIB/uniref90$ ls
uniref90.fasta uniref90.fasta.ssi

#I reinstalled python2 and python3 --> restart.
# Now have a new additional error:
michael@michaelvm:~$ /home/michael/C-I-TASSER-1.0/I-TASSERmod/runI-TASSER.pl -pkgdir /home/michael/C-I-TASSER-1.0 -libdir /home/michael/ITLIB -seqname Tins26 -datadir /home/michael/C-I-TASSER-1.0/example -outdir /home/michael/C-I-TASSER-1.0/output -homoflag benchmark -idcut 0.3 -LBS true -EC true -GO true -java_home /usr -python2 /usr/bin/python2 -python3 /usr/bin/python3

Your setting for running I-TASSER is:
-pkgdir = /home/michael/C-I-TASSER-1.0
-libdir = /home/michael/ITLIB
-java_home = /usr
-python2 = /usr/bin/python2
-python3 = /usr/bin/python3
-seqname = Tins26
-datadir = /home/michael/C-I-TASSER-1.0/example
-outdir = /home/michael/C-I-TASSER-1.0/output
-runstyle = serial
-homoflag = benchmark
-idcut = 0.3
-cit = true
-ntemp = 20
-nmodel = 5
-light = false
-hours = 50
-LBS = true
-EC = true
-GO = true

1. make seq.txt and rmsinp
Your protein contains 143 residues:
> Tins26
MYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLA
LQDSGLEVNIVTDSQYALGIITQWIHNWKKRGWPVKNVDLVNQIIEQLIKKEKVYLAWVP
AHKGIGGNEQVDKLVSAGIRKVL
2.0 run DeepMSA
--------- /home/michael/C-I-TASSER-1.0/example/CITTins26_MSA
hostname: michaelvm
starting time: Wed 25 Aug 2021 12:40:40 AM EDT
pwd: /tmp/michael/CITTins26
Traceback (most recent call last):
File "/home/michael/C-I-TASSER-1.0/contact/DeepMSA/scripts/build_MSA.py", line 66, in <module>
import numpy
ImportError: No module named numpy
error: without MSA file generate!

[jlspzw]

Based on your current message, you need install module numpy to your python2, also please make sure you install pytorch in your python3, I suggest you install anaconda2 and anaconda3 python, those python package include most of the useful module, except pytorch you need install by yourself

[elonmaski]

Yes, you can use the standalone package of https://zhanggroup.org/C-I-TASSER/, or you can put your sequence to FUpred server to predicted the domains first, then put each individual domain to C-I-TASSER server, then use DEMO server assembles the domains, all the servers and standalone package can be found in our home page.