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Use the module name alphafold to discover versions available and to load the application.
Loading the particular alphafold module version will appropriate set the following environment variables: ALPHADB and ALPHABIN and set the associated singularity module version.
Running Alphafold
Alphafold has been built via a docker image, but has been converted to a Singularity image, so must be run using Singularity.
Loading the alphafold will set the following environment variables: ALPHADB and ALPHABIN and set the associated singularity module version.
The current databases/files can be viewed here: /pfs/tc1/udata/alphafold/data/
An example of calling Alphafold:
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Flag Help
As versions of alphafold update, available options will change. On loading the alphafold module, a full list of flags can be found by running:
| Code Block |
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singularity run -B .:/etc --nv $ALPHABIN/alphafold220.sif \ --use_gpu_relax=<False|True> \
--data_dir=$ALPHADB \
--bfd_database_path=$ALPHADB/bfd/bfd_help
singularity run -B .:/etc $ALPHABIN/alphafold220.sif --helpfull |
Data Files and Examples
Version | Data Tree | Example |
|---|
2.3.0 | | Code Block |
|---|
├── bfd
│ ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt |
|
...
_a3m.ffdata
│ ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_a3m.ffindex
│ ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_cs219.ffdata
│ ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_cs219.ffindex
│ ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_hhm.ffdata
│ └── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_hhm.ffindex
├── mgnify
│ └── mgy_clusters_2022_05.fa
├── params
│ ├── LICENSE
│ ├── params_model_1_multimer_v3.npz
│ ├── params_model_1.npz
│ ├── params_model_1_ptm.npz
│ ├── params_model_2_multimer_v3.npz
│ ├── params_model_2.npz
│ ├── params_model_2_ptm.npz
│ ├── params_model_3_multimer_v3.npz
│ ├── params_model_3.npz
│ ├── params_model_3_ptm.npz
│ ├── params_model_4_multimer_v3.npz
│ ├── params_model_4.npz
│ ├── params_model_4_ptm.npz
│ ├── params_model_5_multimer_v3.npz
│ ├── params_model_5.npz
│ └── params_model_5_ptm.npz
├── pdb70
│ ├── md5sum
│ ├── pdb70_a3m.ffdata
│ ├── pdb70_a3m.ffindex
│ ├── pdb70_clu.tsv
│ ├── pdb70_cs219.ffdata
│ ├── pdb70_cs219.ffindex
│ ├── pdb70_hhm.ffdata
│ ├── pdb70_hhm.ffindex
│ └── pdb_filter.dat
├── pdb_mmcif
│ ├── mmcif_files
│ └── obsolete.dat
├── pdb_seqres
│ └── pdb_seqres.txt
├── uniprot
│ └── uniprot.fasta
├── uniref30
│ ├── UniRef30_2021_03_a3m.ffdata
│ ├── UniRef30_2021_03_a3m.ffindex
│ ├── UniRef30_2021_03_cs219.ffdata
│ ├── UniRef30_2021_03_cs219.ffindex
│ ├── UniRef30_2021_03_hhm.ffdata
│ ├── UniRef30_2021_03_hhm.ffindex
│ └── UniRef30_2021_03.md5sums
└── uniref90
└── uniref90.fasta
10 directories, 43 files |
| | Code Block |
|---|
singularity run -B .:/etc --nv $ALPHABIN/alphafold.sif \
--fasta_paths=T1050.fasta \
--output_dir=./<output_folder> \
--model_preset=monomer \
--db_preset=full_dbs \
--bfd_database_path=$ALPHADB/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \
--pdb70_database_path=$ALPHADB/pdb70/pdb70 \
--uniref30_database_path=$ALPHADB/uniref30/UniRef30_2021_03 \
--max_template_date=2020-05-14 \
--use_gpu_relax=<False|True> \
--data_dir=$ALPHADB \
--uniref90_database_path=$ALPHADB/uniref90/uniref90.fasta \
--mgnify_database_path=$ALPHADB/mgnify/mgy_clusters_2022_05.fa \
--template_mmcif_dir=$ALPHADB/pdb_mmcif/mmcif_files \
--obsolete_pdbs_path=$ALPHADB/pdb_mmcif/obsolete.dat |
|
2.2.0 | | Code Block |
|---|
├── bfd
│ ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_a3m.ffdata
│ ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_a3m.ffindex
│ ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_cs219.ffdata
│ ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_cs219.ffindex
│ ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_hhm.ffdata
│ └── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_hhm.ffindex
├── mgnify
│ └── mgy_clusters_2018_12.fa
├── params
│ ├── LICENSE
│ ├── params_model_1_multimer_v2.npz
│ ├── params_model_1.npz
│ ├── params_model_1_ptm.npz
│ ├── params_model_2_multimer_v2.npz
│ ├── params_model_2.npz
│ ├── params_model_2_ptm.npz
│ ├── params_model_3_multimer_v2.npz
│ ├── params_model_3.npz
│ ├── params_model_3_ptm.npz
│ ├── params_model_4_multimer_v2.npz
│ ├── params_model_4.npz
│ ├── params_model_4_ptm.npz
│ ├── params_model_5_multimer_v2.npz
│ ├── params_model_5.npz
│ └── params_model_5_ptm.npz
├── pdb70
│ ├── md5sum
│ ├── pdb70_a3m.ffdata
│ ├── pdb70_a3m.ffindex
│ ├── pdb70_clu.tsv
│ ├── pdb70_cs219.ffdata
│ ├── pdb70_cs219.ffindex
│ ├── pdb70_hhm.ffdata
│ ├── pdb70_hhm.ffindex
│ └── pdb_filter.dat
├── pdb_mmcif
│ ├── mmcif_files
│ └── obsolete.dat
├── pdb_seqres
│ └── pdb_seqres.txt
├── small_bfd
│ └── bfd-first_non_consensus_sequences.fasta
├── uniclust30
│ └── uniclust30_2018_08
├── uniprot
│ └── uniprot.fasta
└── uniref90
└── uniref90.fasta
12 directories, 37 files |
| | Code Block |
|---|
singularity run -B .:/etc --nv $ALPHABIN/alphafold.sif \
--use_gpu_relax=<False|True> \
--data_dir=$ALPHADB \
--bfd_database_path=$ALPHADB/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \
--pdb70_database_path=$ALPHADB/pdb70/pdb70 \
--uniclust30_database_path=$ALPHADB/uniclust30/uniclust30_2018_08/uniclust30_2018_08 \
--uniref90_database_path=$ALPHADB/uniref90/uniref90.fasta \
--mgnify_database_path=$ALPHADB/mgnify/mgy_clusters_2018_12.fa \
--template_mmcif_dir=$ALPHADB/pdb_mmcif/mmcif_files \
--obsolete_pdbs_path=$ALPHADB/pdb_mmcif/obsolete.dat \
--max_template_date=2020-05-14 \
--output_dir=./<output_folder> \
--fasta_paths=T1050.fasta \
--model_preset=monomer |
|
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From our testing so far, all the above parameters needed to be set.
Flag Help
On loading the alphafold module, a full list of flags can be found by running:
| Code Block |
|---|
singularity run -B .:/etc $ALPHABIN/alphafold220.sif --help
singularity run -B .:/etc $ALPHABIN/alphafold220.sif --helpfull |
Our test file T1050.fasta looks like this.
| Code Block |
|---|
>T1050 A7LXT1, Bacteroides Ovatus, 779 residues|
MASQSYLFKHLEVSDGLSNNSVNTIYKDRDGFMWFGTTTGLNRYDGYTFKIYQHAENEPGSLPDNYITDIVEMPDGRFWINTARGYVLFDKERDYFITDVTGFMKNLESWGVPEQVFVDREGNTWLSVAGEGCYRYKEGGKRLFFSYTEHSLPEYGVTQMAECSDGILLIYNTGLLVCLDRATLAIKWQSDEIKKYIPGGKTIELSLFVDRDNCIWAYSLMGIWAYDCGTKSWRTDLTGIWSSRPDVIIHAVAQDIEGRIWVGKDYDGIDVLEKETGKVTSLVAHDDNGRSLPHNTIYDLYADRDGVMWVGTYKKGVSYYSESIFKFNMYEWGDITCIEQADEDRLWLGTNDHGILLWNRSTGKAEPFWRDAEGQLPNPVVSMLKSKDGKLWVGTFNGGLYCMNGSQVRSYKEGTGNALASNNVWALVEDDKGRIWIASLGGGLQCLEPLSGTFETYTSNNSALLENNVTSLCWVDDNTLFFGTASQGVGTMDMRTREIKKIQGQSDSMKLSNDAVNHVYKDSRGLVWIATREGLNVYDTRRHMFLDLFPVVEAKGNFIAAITEDQERNMWVSTSRKVIRVTVASDGKGSYLFDSRAYNSEDGLQNCDFNQRSIKTLHNGIIAIGGLYGVNIFAPDHIRYNKMLPNVMFTGLSLFDEAVKVGQSYGGRVLIEKELNDVENVEFDYKQNIFSVSFASDNYNLPEKTQYMYKLEGFNNDWLTLPVGVHNVTFTNLAPGKYVLRVKAINSDGYVGIKEATLGIVVNPPFKLAAALQHHHHHH |
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Our test file T1050.fasta looks like this.
| Code Block |
|---|
>T1050 A7LXT1, Bacteroides Ovatus, 779 residues|
MASQSYLFKHLEVSDGLSNNSVNTIYKDRDGFMWFGTTTGLNRYDGYTFKIYQHAENEPGSLPDNYITDIVEMPDGRFWINTARGYVLFDKERDYFITDVTGFMKNLESWGVPEQVFVDREGNTWLSVAGEGCYRYKEGGKRLFFSYTEHSLPEYGVTQMAECSDGILLIYNTGLLVCLDRATLAIKWQSDEIKKYIPGGKTIELSLFVDRDNCIWAYSLMGIWAYDCGTKSWRTDLTGIWSSRPDVIIHAVAQDIEGRIWVGKDYDGIDVLEKETGKVTSLVAHDDNGRSLPHNTIYDLYADRDGVMWVGTYKKGVSYYSESIFKFNMYEWGDITCIEQADEDRLWLGTNDHGILLWNRSTGKAEPFWRDAEGQLPNPVVSMLKSKDGKLWVGTFNGGLYCMNGSQVRSYKEGTGNALASNNVWALVEDDKGRIWIASLGGGLQCLEPLSGTFETYTSNNSALLENNVTSLCWVDDNTLFFGTASQGVGTMDMRTREIKKIQGQSDSMKLSNDAVNHVYKDSRGLVWIATREGLNVYDTRRHMFLDLFPVVEAKGNFIAAITEDQERNMWVSTSRKVIRVTVASDGKGSYLFDSRAYNSEDGLQNCDFNQRSIKTLHNGIIAIGGLYGVNIFAPDHIRYNKMLPNVMFTGLSLFDEAVKVGQSYGGRVLIEKELNDVENVEFDYKQNIFSVSFASDNYNLPEKTQYMYKLEGFNNDWLTLPVGVHNVTFTNLAPGKYVLRVKAINSDGYVGIKEATLGIVVNPPFKLAAALQHHHHHH |
If you have alternative examples, please share.
TPU Warnings
TPUs are Google's specialized ASICs and are thus not available on our NVidia GPUs. The following form of warnings can be ignored:
| Code Block |
|---|
I0927 02:45:29.788146 47769932949376 tpu_client.py:54] Starting the local TPU driver.
I0927 02:45:29.829137 47769932949376 xla_bridge.py:212] Unable to initialize backend 'tpu_driver': Not found: Unable to find driver in registry given worker: local:// |
CPU Mode:
Slurm parameters and alphafold flag:
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