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failed in hhblit #6

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Fazziekey opened this issue Aug 26, 2022 · 0 comments
Open

failed in hhblit #6

Fazziekey opened this issue Aug 26, 2022 · 0 comments

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@Fazziekey
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Fazziekey commented Aug 26, 2022

image

ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions. The detected shape was (5,) + inhomogeneous part.

  • inference.sh

python inference.py /data/scratch/alphafold/alphafold//pdb_mmcif/mmcif_files/
--fasta_paths target.fasta
--model_preset multimer
--output_dir ./tmp/
--param_dir /data/scratch/alphafold/alphafold//params/
--gpu_nums 1
--cpus 12
--use_fastfold_optimize
--uniref90_database_path /data/scratch/alphafold/alphafold//uniref90/uniref90.fasta
--mgnify_database_path /data/scratch/alphafold/alphafold//mgnify/mgy_clusters_2018_12.fa
--pdb70_database_path /data/scratch/alphafold/alphafold//pdb70/pdb70
--uniclust30_database_path /data/scratch/alphafold/alphafold//uniclust30/uniclust30_2018_08/uniclust30_2018_08
--pdb_seqres_database_path /home/lcmql/data/pdb_seqres.txt
--bfd_database_path /data/scratch/alphafold/alphafold/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt
--jackhmmer_binary_path which jackhmmer
--hhblits_binary_path which hhblits
--hhsearch_binary_path which hhsearch
--hmmsearch_binary_path which hmmsearch
--kalign_binary_path which kalign
--hmmbuild_binary_path which hmmbuild
--model_name model_1_multimer,model_2_multimer,model_3_multimer,model_4_multimer,model_5_multimer

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