Local MSAServer installation error: databases/pdb70_a3m.ffdata: no such file or directory

[serbulent-av]

Expected Behavior

With bash setup-and-start-local.sh the script should install all needed databases.

Current Behavior

However I'm getting open ~/databases/pdb70_a3m.ffdata: no such file or directory error.

Steps to Reproduce (for bugs)

Clone the repo and run bash setup-and-start-local.sh

ColabFold Output (for bugs)

2023/12/09 13:44:52 MMseqs2 worker
2023/12/09 13:44:52 MMseqs2 worker
2023/12/09 13:44:52 MMseqs2 worker
2023/12/09 13:44:52 MMseqs2 worker
2023/12/09 13:44:52 MMseqs2 worker
2023/12/09 13:44:52 MMseqs2 worker
2023/12/09 13:44:52 MMseqs2 worker
2023/12/09 13:44:52 MMseqs2 worker
2023/12/09 13:44:52 MMseqs2 worker
2023/12/09 13:44:52 MMseqs2 worker
2023/12/09 13:44:52 MMseqs2 worker
2023/12/09 13:44:52 MMseqs2 worker
2023/12/09 13:44:52 MMseqs2 worker
2023/12/09 13:44:52 MMseqs2 worker
2023/12/09 13:44:52 MMseqs2 worker
2023/12/09 13:44:52 MMseqs2 worker
2023/12/09 13:44:52 open ~/databases/pdb70_a3m.ffdata: no such file or directory

Context

It seems setup-databases.sh doesn't include any command to install pdb and pdb70 databases which satistifys config.json

Your Environment

debian11

[serbulent-av]

I tried two alternatives the first one is downloading and creating pdb70 as shown in setup-databases.sh but I still get the same error even the file is there.

The second approach is setting pdb to pdb100 in the config.json however still msg-server couldn't find the file.

user@mmseqs-server-cf:~/ColabFold/MsaServer$ ./msa-server -local -config config.json
2023/12/09 14:40:28 MMseqs2 worker
2023/12/09 14:40:28 MMseqs2 worker
2023/12/09 14:40:28 MMseqs2 worker
2023/12/09 14:40:28 MMseqs2 worker
2023/12/09 14:40:28 MMseqs2 worker
2023/12/09 14:40:28 MMseqs2 worker
2023/12/09 14:40:28 MMseqs2 worker
2023/12/09 14:40:28 MMseqs2 worker
2023/12/09 14:40:28 MMseqs2 worker
2023/12/09 14:40:28 MMseqs2 worker
2023/12/09 14:40:28 MMseqs2 worker
2023/12/09 14:40:28 MMseqs2 worker
2023/12/09 14:40:28 MMseqs2 worker
2023/12/09 14:40:28 MMseqs2 worker
2023/12/09 14:40:28 MMseqs2 worker
2023/12/09 14:40:28 MMseqs2 worker
2023/12/09 14:40:28 open ~/databases/pdb70_a3m.ffdata: no such file or directory

user@mmseqs-server-cf:~/ColabFold/MsaServer$ ./msa-server -local -config config.json
2023/12/09 14:38:39 MMseqs2 worker
2023/12/09 14:38:39 MMseqs2 worker
2023/12/09 14:38:39 MMseqs2 worker
2023/12/09 14:38:39 MMseqs2 worker
2023/12/09 14:38:39 MMseqs2 worker
2023/12/09 14:38:39 open ~/databases/pdb100_a3m.ffdata: no such file or directory
2023/12/09 14:38:39 MMseqs2 worker
2023/12/09 14:38:39 MMseqs2 worker
2023/12/09 14:38:39 MMseqs2 worker

user@mmseqs-server-cf:~/ColabFold/MsaServer$ ls ~/databases/
COLABDB_READY                         colabfold_envdb_202108_db_seq_h         pdb70_220313.fasta              uniref30_2302_db.idx
PDB100_READY                          colabfold_envdb_202108_db_seq_h.dbtype  pdb70_220313.idx                uniref30_2302_db.idx.dbtype
PDB_MMCIF_READY                       colabfold_envdb_202108_db_seq_h.index   pdb70_220313.idx.dbtype         uniref30_2302_db.idx.index
PDB_READY                             colabfold_envdb_202108_h.tsv            pdb70_220313.idx.index          uniref30_2302_db.idx_mapping
UNIREF30_READY                        colabfold_envdb_202108_seq.tsv          pdb70_220313.index              uniref30_2302_db.idx_taxonomy
colabfold_envdb_202108.tar.gz         pdb                                     pdb70_220313.lookup             uniref30_2302_db.index
colabfold_envdb_202108.tsv            pdb100_230517                           pdb70_220313.source             uniref30_2302_db_aln
colabfold_envdb_202108_aln.tsv        pdb100_230517.dbtype                    pdb70_220313_h                  uniref30_2302_db_aln.dbtype
colabfold_envdb_202108_db             pdb100_230517.fasta.gz                  pdb70_220313_h.dbtype           uniref30_2302_db_aln.index
colabfold_envdb_202108_db.dbtype      pdb100_230517.idx                       pdb70_220313_h.index            uniref30_2302_db_h
colabfold_envdb_202108_db.idx         pdb100_230517.idx.dbtype                pdb70_a3m.ffdata                uniref30_2302_db_h.dbtype
colabfold_envdb_202108_db.idx.dbtype  pdb100_230517.idx.index                 pdb70_a3m.ffindex               uniref30_2302_db_h.index
colabfold_envdb_202108_db.idx.index   pdb100_230517.index                     pdb70_from_mmcif_220313.tar.gz  uniref30_2302_db_mapping
colabfold_envdb_202108_db.index       pdb100_230517.lookup                    tmp1                            uniref30_2302_db_seq
colabfold_envdb_202108_db_aln         pdb100_230517.source                    tmp2                            uniref30_2302_db_seq.dbtype
colabfold_envdb_202108_db_aln.dbtype  pdb100_230517_h                         tmp3                            uniref30_2302_db_seq.index
colabfold_envdb_202108_db_aln.index   pdb100_230517_h.dbtype                  tmp4                            uniref30_2302_db_seq_h
colabfold_envdb_202108_db_h           pdb100_230517_h.index                   uniref30_2302.md5sum            uniref30_2302_db_seq_h.dbtype
colabfold_envdb_202108_db_h.dbtype    pdb100_a3m.ffdata                       uniref30_2302.tar.gz            uniref30_2302_db_seq_h.index
colabfold_envdb_202108_db_h.index     pdb100_a3m.ffindex                      uniref30_2302.tsv               uniref30_2302_db_taxonomy
colabfold_envdb_202108_db_seq         pdb100_foldseek_230517.tar.gz           uniref30_2302_aln.tsv           uniref30_2302_h.tsv
colabfold_envdb_202108_db_seq.dbtype  pdb70_220313                            uniref30_2302_db                uniref30_2302_seq.tsv
colabfold_envdb_202108_db_seq.index   pdb70_220313.dbtype                     uniref30_2302_db.dbtype

[serbulent-av]

After setting absolute path in the config.json file not found error disappeared however the pdb70 still should be manually installed or pdb100 should be set in the config.json. I am not sure which is the right path to choose.

[yank666]

me too