Guidance request for SPRINGDB error in PEPPI

[charaniiser]

Dear PEPPI team,
We are trying to run PEPPI with HHsuite 3.3.0. and I have installed all the dependencies but once the code starts running we are running into the following errors.
ERROR: In /opt/conda/conda-bld/hhsuite_1748404578192/work/src/ffindexdatabase.cpp:11: FFindexDatabase
ERROR: could not open file '/.../SPRINGDB/70negpos.db_cs219.ffdata'
It appears that the required 70negpos database file is missing in the installation. We would greatly appreciate your guidance on how to resolve this issue.

[XiZhang]

Hello! I have checked our webserver and only found the following files:

70negpos.db
70negpos.mono

Since Dr. Biao Zhang was the installer of this server, he may be in a better position to address your question.

Thank you for bringing this to our attention!

Best,
Xi

[zbiao]

Hello!

I did not encounter the above problem in my previous installation. According to my understanding of PEPPI, HHsuite in PEPPI uses txt format data, which may not be ffindex.

Thank you for bringing this to our attention!

Best,
Biao Zhang

[charaniiser]

Dear PEPPI Team,
Thank you for quick response, according to PEPPI's github page others are also facing the same issue. https://github.com/ewbell94/PEPPI/issues/3 . If your team can provide any installation guidance or otherwise to handle this error that would be wonderful. This tool is very vital to our work can you please provide us with the solution as soon as possible.
Best,
Sai Charan.

[zbiao]

Hi,Sai Charan.

According to GitHub, they encountered an issue when running makeHHR.pl. In my experience, this may be due to a problem with the following path. You can test whether the following method works. In PEPPI, the makeHHR.pl file has a path pointing to the following: my $uniprotdb="/nfs/amino-library/local/hhsuite/uniprot20_2016_02/uniprot20_2016_02"; #location of the Uniprot database for HHblits search

This path contains the following files: uniprot20_2016_02.cs219 uniprot20_2016_02_hhm_db.index
uniprot20_2016_02_a3m_db uniprot20_2016_02_cs219.ffdata uniprot20_2016_02_hhm.ffdata
uniprot20_2016_02_a3m_db.index uniprot20_2016_02_cs219.ffindex uniprot20_2016_02_hhm.ffindex
uniprot20_2016_02_a3m.ffdata uniprot20_2016_02.cs219.sizes
uniprot20_2016_02_a3m.ffindex uniprot20_2016_02_hhm_db

Check your path for any missing files. The files in this directory are crucial for the correct execution of makeHHR.pl.

Best，
Biao Zhang

[otiscavin]

Wenn du mir genauer sagen kannst, welche Dateien du im Ordner SPRINGDB sehen kannst und welche Inhalte die jeweiligen Dateien haben (z. B. .db, .mono), kann ich dir gezielter weiterhelfen. Sprunki

[bigbear]

Dear PEPPI Team,
Thank you for quick response, according to PEPPI's github page others are also facing the same issue. https://github.com/ewbell94/PEPPI/issues/3Friday Night Funkin . If your team can provide any installation guidance or otherwise to handle this error that would be wonderful. This tool is very vital to our work can you please provide us with the solution as soon as possible.
Best,
Sai Charan.

Dear PEPPI Team, others are also facing the same issue on GitHub, any installation guidance or solution would be greatly appreciated as this tool is vital to our work.