May I know how to execute run_multimer_jobs.py with CPU about alphapulldown HOT 8 CLOSED

Hi @herman-einstein

Really sorry this error occurred. It seems that msa_mask feature of one of your proteins is correct and this error has nothing to do with GPU or CPU. Could you let us know how you created the pickles in the create_individual_features.py```? I wonder if it's also related to mmseqs2``` mode. Thank you.

Yours
Dingquan

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I successfully created the pickles by running the following command

export HHLIB=/home/anaconda3/envs/AlphaPulldown
export HMMER=/home/Analysis/alphafold_analysis/hmmer-3.4
create_individual_features.py --fasta_paths=/home/Analysis/alphafold_analysis/output/alphapulldown/baits.fasta --data_dir=/home/Analysis/alphafold_analysis/alphafold_database --output_dir=/home/Analysis/alphafold_analysis/output/alphapulldown/output --skip_existing=False --use_mmseqs2=True --max_template_date=$(date +"%Y-%m-%d") --seq_index=1

However, it stopped at line 191 like the following. I do not know whether it is completed or not.

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In addition, I came across this error while running alpha-analysis.sif to calculate the pi score. Is it because I only have one pull-down group? And it assumes more than one pull-down group for pi score calculation?

from alphapulldown.

In addition, I came across this error while running alpha-analysis.sif to calculate the pi score. Is it because I only have one pull-down group? And it assumes more than one pull-down group for pi score calculation?

Hi @herman-einstein ,

According to your screenshot, it should be caused by mounting a wrong directory. You should in this case mount one level above.

Yours
Dingquan

from alphapulldown.

In addition, I came across this error while running alpha-analysis.sif to calculate the pi score. Is it because I only have one pull-down group? And it assumes more than one pull-down group for pi score calculation?

Hi @herman-einstein ,

According to your screenshot, it should be caused by mounting a wrong directory. You should in this case mount one level above.

Yours Dingquan

Hi, @dingquanyu

Thank you for your quick reply,

I tried mounting the directory one level above. However, there is the same issue.

This is the command I ran:

"singularity exec --no-home --bind /home/Desktop/pulldown/pull2:/mnt /media/data/alpha-analysis_jax_0.4.sif run_get_good_pae.sh --output_dir=/mnt --cutoff=10"

from alphapulldown.

In addition, I came across this error while running alpha-analysis.sif to calculate the pi score. Is it because I only have one pull-down group? And it assumes more than one pull-down group for pi score calculation?

Hi @herman-einstein ,
According to your screenshot, it should be caused by mounting a wrong directory. You should in this case mount one level above.
Yours Dingquan

Hi, @dingquanyu

Thank you for your quick reply,

I tried mounting the directory one level above. However, there is the same issue.

This is the command I ran:

"singularity exec --no-home --bind /home/Desktop/pulldown/pull2:/mnt /media/data/alpha-analysis_jax_0.4.sif run_get_good_pae.sh --output_dir=/mnt --cutoff=10"

Hi @herman-einstein ,

Sorry this still persisted. I suspected that this model quality wasn't good enough to pass the cutoff. Could you change the cutoff to 100 and run again?

Yours
Dingquan

from alphapulldown.

In addition, I came across this error while running alpha-analysis.sif to calculate the pi score. Is it because I only have one pull-down group? And it assumes more than one pull-down group for pi score calculation?

Hi @herman-einstein ,
According to your screenshot, it should be caused by mounting a wrong directory. You should in this case mount one level above.
Yours Dingquan

Hi, @dingquanyu
Thank you for your quick reply,
I tried mounting the directory one level above. However, there is the same issue.

This is the command I ran:
"singularity exec --no-home --bind /home/Desktop/pulldown/pull2:/mnt /media/data/alpha-analysis_jax_0.4.sif run_get_good_pae.sh --output_dir=/mnt --cutoff=10"

Hi @herman-einstein ,

Sorry this still persisted. I suspected that this model quality wasn't good enough to pass the cutoff. Could you change the cutoff to 100 and run again?

Yours Dingquan

It works!!!! very much appreciate your help!

May I know what the cutoff means in this calculation?

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Hi @herman-einstein ,

Glad it worked for you! cutoff is to check if any residues has a PAE value below the specified cutoff in the PAE plot between 2 or more chains. For the details about what PAE means, please refer to AlphaFold Multimer paper. In short, the lower the value, the more strict the selection.

Yours
Dingquan

from alphapulldown.