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kalininalab / alphafold_non_docker

AlphaFold2 non-docker setup
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obsolete data #20

Closed AnjaliSetiya closed 2 years ago

AnjaliSetiya commented 2 years ago

File "/home/ngayatri/alphafold/alphafold/data/templates.py", line 137, in _parse_obsolete with open(obsolete_file_path) as f: IsADirectoryError: [Errno 21] Is a directory: '/home/ngayatri/mmcif_ob1/rsync.rcsb.org/pub/pdb/data/structures/obsolete/mmCIF' I have downloaded the data with wget command from this website rsync.rcsb.org/pub/pdb/data/structures/obsolete/mmCIF can you help me with error what exactly is it trying to find

sanjaysrikakulam commented 2 years ago

Hi @AnjaliSetiya

I guess you are not following the folder structure of AF2. Please make sure you have the following folder structure of your download/data directory.

$DOWNLOAD_DIR/                             # Total: ~ 2.2 TB (download: 438 GB)
    bfd/                                   # ~ 1.7 TB (download: 271.6 GB)
        # 6 files.
    mgnify/                                # ~ 64 GB (download: 32.9 GB)
        mgy_clusters_2018_12.fa
    params/                                # ~ 3.5 GB (download: 3.5 GB)
        # 5 CASP14 models,
        # 5 pTM models,
        # LICENSE,
        # = 11 files.
    pdb70/                                 # ~ 56 GB (download: 19.5 GB)
        # 9 files.
    pdb_mmcif/                             # ~ 206 GB (download: 46 GB)
        mmcif_files/
            # About 180,000 .cif files.
        obsolete.dat
    small_bfd/                             # ~ 17 GB (download: 9.6 GB)
        bfd-first_non_consensus_sequences.fasta
    uniclust30/                            # ~ 86 GB (download: 24.9 GB)
        uniclust30_2018_08/
            # 13 files.
    uniref90/                              # ~ 58 GB (download: 29.7 GB)
        uniref90.fasta

obsolete should be a file and not a directory. Please make sure you have the above download/data directory structure and use the bash script from this repo to run AF2.

AnjaliSetiya commented 2 years ago

Thank You