Remove extra files

ec2-testing.txt

-python3 run_pretrained_openfold.py \
-    target.fasta \
-    data/pdb_mmcif/mmcif_files/ \
-    --uniref90_database_path data/uniref90/uniref90.fasta \
-    --mgnify_database_path data/mgnify/mgy_clusters_2018_12.fa \
-    --pdb70_database_path data/pdb70/pdb70 \
-    --uniclust30_database_path data/uniclust30/uniclust30_2018_08/uniclust30_2018_08 \
-    --output_dir ./ \
-    --bfd_database_path data/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \
-    --model_device cuda:1 \
-    --jackhmmer_binary_path lib/conda/envs/openfold_venv/bin/jackhmmer \
-    --hhblits_binary_path lib/conda/envs/openfold_venv/bin/hhblits \
-    --hhsearch_binary_path lib/conda/envs/openfold_venv/bin/hhsearch \
-    --kalign_binary_path lib/conda/envs/openfold_venv/bin/kalign
-
-docker run \
---gpus all \
--v $PWD/:/data \
--v /mnt/alphafold_database/:/database \
--ti openfold:latest \
-python3 /opt/openfold/run_pretrained_openfold.py \
-/data/input.fasta \
-/database/pdb_mmcif/mmcif_files/ \
---uniref90_database_path /database/uniref90/uniref90.fasta \
---mgnify_database_path /database/mgnify/mgy_clusters_2018_12.fa \
---pdb70_database_path /database/pdb70/pdb70 \
---uniclust30_database_path /database/uniclust30/uniclust30_2018_08/uniclust30_2018_08 \
---output_dir /data \
---bfd_database_path /database/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \
---model_device cuda:0 \
---jackhmmer_binary_path /opt/conda/bin/jackhmmer \
---hhblits_binary_path /opt/conda/bin/hhblits \
---hhsearch_binary_path /opt/conda/bin/hhsearch \
---kalign_binary_path /opt/conda/bin/kalign \
---param_path /database/params/params_model_1.npz
-
-# T1083
-docker run \
---rm \
---gpus all \
--v /home/ec2-user/data:/data \
--v /fsx/:/database/ \
--e CUDA_VISIBLE_DEVICES=0 \
-617302ff1b5a \
-python3 /opt/openfold/run_pretrained_openfold.py \
-/data/T1083/input.fasta \
-/database/pdb_mmcif/mmcif_files/ \
---use_precomputed_alignments /data \
---output_dir /data/T1083 \
---model_device cuda:0 \
---param_path /database/params/params_model_1.npz
-
-# T1070
-docker run \
---rm \
---gpus all \
--v /home/ec2-user/data:/data \
--v /fsx/:/database/ \
--e CUDA_VISIBLE_DEVICES=0 \
-617302ff1b5a \
-python3 /opt/openfold/run_pretrained_openfold.py \
-/data/T1070/input.fasta \
-/database/pdb_mmcif/mmcif_files/ \
---use_precomputed_alignments /data \
---output_dir /data/T1070 \
---model_device cuda:0 \
---param_path /database/params/params_model_1.npz
-
-# Notes: The current implementation of OpenFold assumes that the sequences 
-# in the input FASTA file are each in a single line. Sequences that span multiple
-# lines are interpreted as sequence IDs and cause errors.
-# https://github.com/aqlaboratory/openfold/issues/89
-
-# Also, it seems like it's not possible to run the MSA step with the reduced DB at this time
-
-### MMseqs 2 
-python3 scripts/precompute_alignments_mmseqs.py \
-    /home/ubuntu/data/T1082/input.fasta \
-    /fsx/mmseqs_dbs \
-    uniref30_2103_db \
-    /home/ubuntu/data/T1082 \
-    /home/ubuntu/openfold/mmseqs/bin/mmseqs \
-    --hhsearch_binary_path home/ubuntu/openfold/lib/conda/envs/openfold_venv/bin/hhsearch \
-    --pdb70 pdb70 \
-    --env_db colabfold_envdb_202108_db
-
-bash scripts/colabfold_search.sh \
-    /home/ubuntu/openfold/mmseqs/bin/mmseqs \
-    /home/ubuntu/data/T1080/input.fasta \
-    /fsx/mmseqs_dbs \
-    /home/ubuntu/data/T1080/output \
-    uniref30_2103_db \
-    "" \
-    colabfold_envdb_202108_db \ 
-    1 0 1 1 0
-
-#Note seems to take a fair amount of time to finish (30 minutes - not faster than hhblits). 
-Need to retry using memory recommendations from https://colabfold.mmseqs.com/
-e.g. 768 GiB RAM. A x2gd.12xlarge looks to be the most cost-effective instance for this ($4/hr), or else
-a r5.24xlarge if we need an AMD ($6/hr)
-
-
-sudo wget -P /tmp "https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh" \
-    && sudo bash /tmp/Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda \
-    && sudo rm /tmp/Miniconda3-latest-Linux-x86_64.sh
-
-
-220614
-
-docker run \
---gpus all \
--v /home/ec2-user/data:/data \
--v /fsx/:/database/ \
--ti openfold:latest \
-python3 /opt/openfold/run_pretrained_openfold.py \
-/data/fasta_dir \
-/database/pdb_mmcif/mmcif_files/ \
---use_precomputed_alignments /data/alignments/ \
---output_dir /data \
---model_device cuda:0 \
---jax_param_path /database/params/params_model_1.npz
-
-python3 /opt/openfold/run_pretrained_openfold.py \
-/data/fasta_dir \
-/database/pdb_mmcif/mmcif_files/ \
---use_precomputed_alignments /data/alignments/ \
---output_dir /data \
---model_device cuda:0 \
---jax_param_path /database/params/params_model_1.npz
-
-
-docker run \
---gpus all \
--v /home/ec2-user/data:/data \
--v /fsx/:/database/ \
--ti openfold:latest \
-python3 /opt/openfold/run_pretrained_openfold.py \
-/data/fasta_dir \
-/database/pdb_mmcif/mmcif_files/ \
---uniref90_database_path /database/uniref90/uniref90.fasta \
---mgnify_database_path /database/mgnify/mgy_clusters_2018_12.fa \
---pdb70_database_path /database/pdb70/pdb70 \
---uniclust30_database_path /database/uniclust30/uniclust30_2018_08/uniclust30_2018_08 \
---output_dir /data \
---model_device cuda:0 \
---jackhmmer_binary_path /opt/conda/bin/jackhmmer \
---hhblits_binary_path /opt/conda/bin/hhblits \
---hhsearch_binary_path /opt/conda/bin/hhsearch \
---kalign_binary_path /opt/conda/bin/kalign \
---jax_param_path /database/params/params_model_1.npz
-
-
-
-docker run --gpus all -v /home/ec2-user/data:/data -v /fsx/:/database/ -ti openfold:latest bash run_batch_job.sh \
-    s3://sagemaker-us-east-2-032243382548/openfold_testing/T1084.fasta \
-    /data/fasta_dir \
-    "python3 /opt/openfold/run_pretrained_openfold.py \
-    /data/fasta_dir \
-    /database/pdb_mmcif/mmcif_files/ \
-    --uniref90_database_path /database/uniref90/uniref90.fasta \
-    --mgnify_database_path /database/mgnify/mgy_clusters_2018_12.fa \
-    --pdb70_database_path /database/pdb70/pdb70 \
-    --uniclust30_database_path /database/uniclust30/uniclust30_2018_08/uniclust30_2018_08 \
-    --output_dir /data \
-    --model_device cuda:0 \
-    --jackhmmer_binary_path /opt/mamba/bin/jackhmmer \
-    --hhblits_binary_path /opt/mamba/bin/hhblits \
-    --hhsearch_binary_path /opt/mamba/bin/hhsearch \
-    --kalign_binary_path /opt/mamba/bin/kalign \
-    --jax_param_path /database/params/params_model_1.npz" \
-    /data \
-    s3://sagemaker-us-east-2-032243382548/openfold_testing/
\ No newline at end of file

run_batch_job.sh

-#!/bin/bash
-
-################
-# Example CMD
-./run_batch_job.sh \
-    s3://sagemaker-us-east-2-032243382548/openfold_testing/T1084.fasta \
-    /data/fasta_dir \
-    "python3 /opt/openfold/run_pretrained_openfold.py \
-    /data/fasta_dir \
-    /database/pdb_mmcif/mmcif_files/ \
-    --uniref90_database_path /database/uniref90/uniref90.fasta \
-    --mgnify_database_path /database/mgnify/mgy_clusters_2018_12.fa \
-    --pdb70_database_path /database/pdb70/pdb70 \
-    --uniclust30_database_path /database/uniclust30/uniclust30_2018_08/uniclust30_2018_08 \
-    --output_dir /data \
-    --model_device cuda:0 \
-    --jackhmmer_binary_path /opt/conda/bin/jackhmmer \
-    --hhblits_binary_path /opt/conda/bin/hhblits \
-    --hhsearch_binary_path /opt/conda/bin/hhsearch \
-    --kalign_binary_path /opt/conda/bin/kalign \
-    --jax_param_path /database/params/params_model_1.npz" \
-    /data \
-    s3://sagemaker-us-east-2-032243382548/openfold_testing/
-
-input_source=$1
-input_destination=$2
-script=$3
-output_source=$4
-output_destination=$5
-
-aws s3 cp $input_source $input_destination
-$script
-a2s s3 cp $output_source $output_destination
\ No newline at end of file