WARNING:root:Failed to run alignments for 6kal_A. Skipping

[chinmayraneQ]

Hey everyone,

I am trying to compute alignments for training of openfold. But I am getting stuck at the first step. I am running the following code python3 scripts/precompute_alignments.py /workspace/dataset/pdb_mmcif/mmcif_files/ /workspace/alignment_all_data/ --uniref90_database_path /workspace/dataset/uniref90/uniref90_fasta.fasta --mgnify_database_path /workspace/dataset/mgnify/mgy_clusters_2018_12.fa --pdb70_database_path /workspace/dataset/pdb70/pdb70 --uniclust30_database_path /workspace/dataset/uniclust30/uniclust30_2018_08 --bfd_database_path /workspace/dataset/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt --cpus_per_task 16 --jackhmmer_binary_path lib/conda/envs/openfold_venv/bin/jackhmmer --hhblits/ --bfd_database_path /workspace/dataset/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt --cpus_per_task 16 u --bfd_database_path /workspace/dataset/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt --cpus_per_task niclust30_2018_08 --bfd_database_path /workspace/dataset/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt --cpus_per_task 16 --jackhmmer_binary_path lib/conda/envs/openfold_venv/bin/jackhmmer --hhblits_binary_path lib/conda/envs/openfold_venv/bin/hhblits --hhs

which is from the instruction page. But not a single alignments are not getting computed. it gives me the following error

Started thread 0... fasta_path /tmp/tmpd8mmcd_8.fasta WARNING:root:Failed to run alignments for 6kal_A. Skipping... fasta_path /tmp/tmptcjo3lxo.fasta WARNING:root:Failed to run alignments for 1bjx_A. Skipping... fasta_path /tmp/tmpulf8j_mm.fasta WARNING:root:Failed to run alignments for 1abo_A. Skipping... fasta_path /tmp/tmpwr_tuxb2.fasta WARNING:root:Failed to run alignments for 1abo_C. Skipping...

after skipping it deletes all the folder. I checked all the directories and data. i even tried using the parsing function on a single file. it was able to parse the .cif file.

Looking at some of the issue, i can see that the alignments will consist of 4 files for each.cif files

Any suggestions

Thanks in advance