SpeedPPI

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How to determine the memory requirement?

3

I am running SpeedPPI on GPU nodes. But some of the jobs would run out of memory even with 250GB memory. The error says `RESOURCE_EXHAUSTED: Out of memory while trying...

Rohit-Satyam

SpeedPPI terminates with error: Cannot reshape a tensor with 2024432 elements to shape [4363,471,1] (2054973 elements)

1

Hi @patrickbryant1 I am trying to run SpeedPPI for two fasta files. Fasta1 contains a single protein, whereas fasta2 contain 2000 proteins sequences. So I decided to use some.vs.some script....

Rohit-Satyam

pip can't find "tf-nightly==2.16.0.dev20231211"

2

It looks like pip can't find "tf-nightly==2.16.0.dev20231211" (from speed_ppi.yml) ``` Pip subprocess error: ERROR: Could not find a version that satisfies the requirement tf-nightly==2.16.0.dev20231211 (from versions: 2.16.0.dev20231219, 2.16.0.dev20231220, 2.16.0.dev20231221, 2.16.0.dev20231222,...

ChristopherBottomsOMRF

error when creating the environment

4

hi again! i was able to run it to predict 3 proteins-protein interactions for my project and it worked, thanks!! but then i wanted to do it again with more...

theammn

protein ordering changes the pdockQ score

1

Hi, Thanks a lot for developing this great tool. I am trying to run interaction analysis on two proteins. bash predict_single.sh A.fasta B.fasta gives pdockQ score of 0.5 bash predict_single.sh...

akdess

SCOPData is no longer provided in the most recent versions of Bio.Data, but PDBData provides the same function.

ChristopherBottomsOMRF

jax_config.define_bool_state('flax_' + name, default, help) AttributeError: 'Config' object has no attribute 'define_bool_state'

5

I get this runtime error while running all vs all. I assume that I'm using the wrong version of Jax or something? ``` create_ppi_all_vs_all.sh broken_1RWY.fa $HHBLITS 0.5 outdir Writing fastas...

ChristopherBottomsOMRF