Commit b3072f73 authored by Jarunan Panyasantisuk's avatar Jarunan Panyasantisuk
Browse files

add postprocessing script and update setup script

parent 8449c170
>sp|Q07955|SRSF1_HUMAN Serine/arginine-rich splicing factor 1 OS=Homo sapiens OX=9606 GN=SRSF1 PE=1 SV=2
MSGGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRGTGRGGGGGGGGGAPRGRYGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSPSYG
>6E3K_1|Chains A|Interferon gamma|Homo sapiens (9606)
GPGSQDPYVKEAENLKKYFNAGHSDVADNGTLFLGILKNWKEESDRKIMQSQIVSFYFKLFKNFKDDQSIQKSVETIKEDMNVKFFNSNKKKRDDFEKLTNYSVTDLNVQRKAIHELIQVMAELSPAAKTGKRKRSQAAAHHHHHHHH
>6E3K_2|Chains B|Interferon gamma|Homo sapiens (9606)
GPGSQDPYVKEAENLKKYFNAGHSDVADNGTLFLGILKNWKEESDRKIMQSQIVSFYFKLFKNFKDDQSIQKSVETIKEDMNVKFFNSNKKKRDDFEKLTNYSVTDLNVQRKAIHELIQVMAELSPAAKTGKRKRSQAAAHHHHHHHH
>6E3K_3|Chains C|Interferon gamma receptor 1|Homo sapiens (9606)
GSEMGTADLGPSSVPTPTNVTIESYNMNPIVYWEYQIMPQVPVFTVEVKNYGVKNSEWIDACINISHHYCNISDHVGDPSNSLWVRVKARVGQKESAYAKSEEFAVCRDGKIGPPKLDIRKEEKQIMIDIFHPSVFVNGDEQEVDYDPETICYIRVYNVYVRKNGSEIKYKILTQNEDDCDEIRCQLAIPVSSLNSQYCVSAEGVLNVWGVTTEKSKEVCITIFNSSIKGSAAAHHHHHHHH
>6E3K_4|Chains D|Interferon gamma receptor 1|Homo sapiens (9606)
GSEMGTADLGPSSVPTPTNVTIESYNMNPIVYWEYQIMPQVPVFTVEVKNYGVKNSEWIDACINISHHYCNISDHVGDPSNSLWVRVKARVGQKESAYAKSEEFAVCRDGKIGPPKLDIRKEEKQIMIDIFHPSVFVNGDEQEVDYDPETICYIRVYNVYVRKNGSEIKYKILTQNEDDCDEIRCQLAIPVSSLNSQYCVSAEGVLNVWGVTTEKSKEVCITIFNSSIKGSAAAHHHHHHHH
>6E3K_5|Chains E|Interferon gamma receptor 2|Homo sapiens (9606)
GSSQLPAPQHPKIRLYNAEQVLSWEPVALSNSTRPVVYQVQFKYTDSKWFTADIMSIGVNCTQITATECDFTAASPSAGFPMDFNVTLRLRAELGALHSAWVTMPWFQHYRNVTVGPPENIEVTPGEGSLIIRFSSPFDIADTSTAFFCYYVHYWEKGGIQQVKGPFRSNSISLDNLKPSRVYCLQVQAQLLWNKSNIFRVGHLSNISCYETMADASTELQQAAAHHHHHHHH
>6E3K_6|Chains F[auth I]|Interferon gamma receptor 2|Homo sapiens (9606)
GSSQLPAPQHPKIRLYNAEQVLSWEPVALSNSTRPVVYQVQFKYTDSKWFTADIMSIGVNCTQITATECDFTAASPSAGFPMDFNVTLRLRAELGALHSAWVTMPWFQHYRNVTVGPPENIEVTPGEGSLIIRFSSPFDIADTSTAFFCYYVHYWEKGGIQQVKGPFRSNSISLDNLKPSRVYCLQVQAQLLWNKSNIFRVGHLSNISCYETMADASTELQQAAAHHHHHHHH
>T1050 A7LXT1, Bacteroides Ovatus, 779 residues|
MASQSYLFKHLEVSDGLSNNSVNTIYKDRDGFMWFGTTTGLNRYDGYTFKIYQHAENEPGSLPDNYITDIVEMPDGRFWINTARGYVLFDKERDYFITDVTGFMKNLESWGVPEQVFVDREGNTWLSVAGEGCYRYKEGGKRLFFSYTEHSLPEYGVTQMAECSDGILLIYNTGLLVCLDRATLAIKWQSDEIKKYIPGGKTIELSLFVDRDNCIWAYSLMGIWAYDCGTKSWRTDLTGIWSSRPDVIIHAVAQDIEGRIWVGKDYDGIDVLEKETGKVTSLVAHDDNGRSLPHNTIYDLYADRDGVMWVGTYKKGVSYYSESIFKFNMYEWGDITCIEQADEDRLWLGTNDHGILLWNRSTGKAEPFWRDAEGQLPNPVVSMLKSKDGKLWVGTFNGGLYCMNGSQVRSYKEGTGNALASNNVWALVEDDKGRIWIASLGGGLQCLEPLSGTFETYTSNNSALLENNVTSLCWVDDNTLFFGTASQGVGTMDMRTREIKKIQGQSDSMKLSNDAVNHVYKDSRGLVWIATREGLNVYDTRRHMFLDLFPVVEAKGNFIAAITEDQERNMWVSTSRKVIRVTVASDGKGSYLFDSRAYNSEDGLQNCDFNQRSIKTLHNGIIAIGGLYGVNIFAPDHIRYNKMLPNVMFTGLSLFDEAVKVGQSYGGRVLIEKELNDVENVEFDYKQNIFSVSFASDNYNLPEKTQYMYKLEGFNNDWLTLPVGVHNVTFTNLAPGKYVLRVKAINSDGYVGIKEATLGIVVNPPFKLAAALQHHHHHH
#!/usr/bin/bash
#BSUB -n 12
#BSUB -n 04:00
#BSUB -n 24:00
#BSUB -R "rusage[mem=10000, scratch=10000]"
#BSUB -R "rusage[ngpus_excl_p=1] select[gpu_mtotal0>=10240]"
#BSUB -R "span[hosts=1]"
#BSUB -J alphafold
source /cluster/apps/local/env2lmod.sh
module load gcc/6.3.0 openmpi/4.0.2 alphafold/2.1.1
module load gcc/6.3.0 openmpi/4.0.2 alphafold/2.2.0
source /cluster/apps/nss/alphafold/venv_alphafold/bin/activate
# Define paths to databases and out put directory
......@@ -15,22 +15,29 @@ DATA_DIR=/cluster/project/alphafold
OUTPUT_DIR=${TMPDIR}/output
# Activate unified memory
export TF_FORCE_UNIFIED_MEMORY=0
export XLA_PYTHON_CLIENT_MEM_FRACTION=1.0
export TF_FORCE_UNIFIED_MEMORY=1
export XLA_PYTHON_CLIENT_MEM_FRACTION=2.0
python /cluster/apps/nss/alphafold/alphafold-2.1.1/run_alphafold.py \
# If use_gpu_relax is enabled, enable CUDA multi-process service. Uncomment the line below
#nvidia-cuda-mps-control -d
python /cluster/apps/nss/alphafold/alphafold-2.2.0/run_alphafold.py \
--data_dir=$DATA_DIR \
--output_dir=$OUTPUT_DIR \
--max_template_date="2022-02-21" \
--max_template_date="2022-04-04" \
--bfd_database_path=$DATA_DIR/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \
--uniref90_database_path=$DATA_DIR/uniref90/uniref90.fasta \
--uniclust30_database_path=$DATA_DIR/uniclust30/uniclust30_2018_08/uniclust30_2018_08 \
--mgnify_database_path=$DATA_DIR/mgnify/mgy_clusters_2018_12.fa \
--template_mmcif_dir=$DATA_DIR/pdb_mmcif/mmcif_files \
--obsolete_pdbs_path=$DATA_DIR/pdb_mmcif/obsolete.dat \
--pdb70_database_path=$DATA_DIR/pdb70/pdb70 \
--fasta_paths=/cluster/home/ruedsimo/alphafold/alphafold_on_euler/SRSF1.fasta
--use_gpu_relax=0 \
--fasta_paths=/cluster/work/sis/cdss/jarunanp/21_12_alphafold_benchmark/scripts/alphafold_on_euler/fastafiles/IFGSC_6mer.fasta \
--model_preset=multimer --pdb_seqres_database_path=$DATA_DIR/pdb_seqres/pdb_seqres.txt --uniprot_database_path=$DATA_DIR/uniprot/uniprot.fasta \
# Disable CUDA multi-process service
#echo quit | nvidia-cuda-mps-control
mkdir -p output/SRSF1
rsync -av $TMPDIR/output/SRSF1 ./output/SRSF1
mkdir -p output/IFGSC_6mer
rsync -av $TMPDIR/output/IFGSC_6mer ./output/IFGSC_6mer
......@@ -154,11 +154,11 @@ elif (( "$sum_aa" >= 3500 )); then
fi
echo -e " Estimate required resources: "
echo -e " Run time: " $RUNTIME
echo -e " Number of CPUs: " $NCPUS
echo -e " Total CPU memory: " $TOTAL_CPU_MEM_MB
echo -e " Number of GPUs: " $NGPUS
echo -e " Total GPU memory: " $TOTAL_GPU_MEM_MB
echo -e " Run time: " $RUNTIME
echo -e " Number of CPUs: " $NCPUS
echo -e " Total CPU memory: " $TOTAL_CPU_MEM_MB
echo -e " Number of GPUs: " $NGPUS
echo -e " Total GPU memory: " $TOTAL_GPU_MEM_MB
echo -e " Total scratch space: " $TOTAL_SCRATCH_MB
########################################
......@@ -188,9 +188,12 @@ OUTPUT_DIR=\${TMPDIR}/output
# Activate unified memory
export TF_FORCE_UNIFIED_MEMORY=$ENABLE_UNIFIED_MEMORY
export XLA_PYTHON_CLIENT_MEM_FRACTION=$MEM_FRACTION.0
export XLA_PYTHON_CLIENT_MEM_FRACTION=${MEM_FRACTION}.0
python /cluster/apps/nss/alphafold/alphafold-2.1.1/run_alphafold.py \\
# If use_gpu_relax is enabled, enable CUDA multi-process service. Uncomment the line below
#nvidia-cuda-mps-control -d
python /cluster/apps/nss/alphafold/alphafold-2.2.0/run_alphafold.py \\
--data_dir=\$DATA_DIR \\
--output_dir=\$OUTPUT_DIR \\
--max_template_date="$MAX_TEMPLATE_DATE" \\
......@@ -200,9 +203,13 @@ python /cluster/apps/nss/alphafold/alphafold-2.1.1/run_alphafold.py \\
--mgnify_database_path=\$DATA_DIR/mgnify/mgy_clusters_2018_12.fa \\
--template_mmcif_dir=\$DATA_DIR/pdb_mmcif/mmcif_files \\
--obsolete_pdbs_path=\$DATA_DIR/pdb_mmcif/obsolete.dat \\
--use_gpu_relax=0 \\
--fasta_paths=$FASTAFILE \\
$OPTIONS
# Disable CUDA multi-process service
#echo quit | nvidia-cuda-mps-control
mkdir -p output/$PROTEIN
rsync -av \$TMPDIR/output/$PROTEIN ./output/$PROTEIN
......
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