psipred terminated

[leodoned]

I'm trying to run "python -m rf2aa.run_inference --config-name protein" to test. But error comes.

Using the cif atom ordering for TRP.
./make_msa.sh examples/protein/7qxr.fasta 7qxr_job/A 4 64 pdb100_2021Mar03/pdb100_2021Mar03
Predicting: 100%|██████████████████████████████████████████████████████████████████████████| 1/1 [00:00<00:00, 1.18sequences/s]
Running PSIPRED
*** buffer overflow detected ***: psipred terminated
Running hhsearch

• 23:06:47.179 ERROR: In /opt/conda/conda-bld/hhsuite_1709621322429/work/src/hhalignment.cpp:223: Read:

• 23:06:47.179 ERROR: sequence ss_pred contains no residues.

I have checked the make_ss.stderr.
/spgpu01_data/Software/Rosettafold/RoseTTAFold-All-Atom/input_prep/make_ss.sh: line 21: 808151 Aborted (core dumped) psipred $ID.mtx $DATADIR/weights.dat $DATADIR/weights.dat2 $DATADIR/weights.dat3 > $ID.ss
Bad psipred pass1 file format!
rm: cannot remove '7qxr_job/A/t000_.msa0.a3m.csb.hhblits.ss2': No such file or directory

It seems that psipred doesn't work, I don't know why.

[GanQiao1990]

https://github.com/Sabryr/ProteinFolding/tree/master/RoseTTAFold/install

1. Acitvate conda/miniconda or load the module
2. export INSTALL_LOC=<YOUR_PATH>
3. conda env create -f RoseTTAFold-linux.yml --prefix=$INSTALL_LOC/RoseTTAFold
4. conda activate $INSTALL_LOC/RoseTTAFold
5. cd $INSTALL_LOC/RoseTTAFold
6. git clone git@github.com:RosettaCommons/RoseTTAFold.git
7. cd RoseTTAFold
8. ./install_dependencies.sh
9. wget https://files.ipd.uw.edu/pub/RoseTTAFold/weights.tar.gz
10. tar xfz weights.tar.gz
    10 rm weights.tar.gz
11. DATA_LOCATION=/itf-fi-ml/shared/databases/RoseTTAFold/
12. ln -s ${DATA_LOCATION}/pdb100_2021Mar03 pdb100_2021Mar03
13. ln -s ${DATA_LOCATION}/UniRef30_2020_06 UniRef30_2020_06
14. ln -s ${DATA_LOCATION}/bfd bfd
15. Make the python files executable
    for file in $(find -type f -name *.py); do echo $file; chmod +x $file; sed -i '1s/^/#!/usr/bin/env python\n/' $file; done;
16. Pyrosetta
    15.1. Get license
    15.2 Download pyrosetta-2021.24+release.16a09fe-cp37-cp37m-linux_x86_64.whl
    15.3 pip install pyrosetta-2021.24+release.16a09fe-cp37-cp37m-linux_x86_64.whl
17. Patch make_ss.sh
    Find the make_ss.sh and add BLASTMAT path below DATADIR.
    export BLASTMAT=$INSTALL_LOC/RoseTTAFold/RoseTTAFold/csblast-2.2.3/data
18. Remove all the place where conda activated in run_pyrosetta_ver.sh and manully acitivate conda env berfore executing.

[leodoned]

I think I figure it out
RosettaCommons/RoseTTAFold#13 (comment)
I followed the guide in this link, and it works

[leodoned]

It works! Great work!