update to v2.3.2

alphafold/common/stereo_chemical_props.txt

+Bond			Residue		Mean		StdDev
+CA-CB			ALA		1.520		0.021
+N-CA			ALA		1.459		0.020
+CA-C			ALA		1.525		0.026
+C-O			ALA		1.229		0.019
+CA-CB			ARG		1.535		0.022
+CB-CG			ARG		1.521		0.027
+CG-CD			ARG		1.515		0.025
+CD-NE			ARG		1.460		0.017
+NE-CZ			ARG		1.326		0.013
+CZ-NH1			ARG		1.326		0.013
+CZ-NH2			ARG		1.326		0.013
+N-CA			ARG		1.459		0.020
+CA-C			ARG		1.525		0.026
+C-O			ARG		1.229		0.019
+CA-CB			ASN		1.527		0.026
+CB-CG			ASN		1.506		0.023
+CG-OD1			ASN		1.235		0.022
+CG-ND2			ASN		1.324		0.025
+N-CA			ASN		1.459		0.020
+CA-C			ASN		1.525		0.026
+C-O			ASN		1.229		0.019
+CA-CB			ASP		1.535		0.022
+CB-CG			ASP		1.513		0.021
+CG-OD1			ASP		1.249		0.023
+CG-OD2			ASP		1.249		0.023
+N-CA			ASP		1.459		0.020
+CA-C			ASP		1.525		0.026
+C-O			ASP		1.229		0.019
+CA-CB			CYS		1.526		0.013
+CB-SG			CYS		1.812		0.016
+N-CA			CYS		1.459		0.020
+CA-C			CYS		1.525		0.026
+C-O			CYS		1.229		0.019
+CA-CB			GLU		1.535		0.022
+CB-CG			GLU		1.517		0.019
+CG-CD			GLU		1.515		0.015
+CD-OE1			GLU		1.252		0.011
+CD-OE2			GLU		1.252		0.011
+N-CA			GLU		1.459		0.020
+CA-C			GLU		1.525		0.026
+C-O			GLU		1.229		0.019
+CA-CB			GLN		1.535		0.022
+CB-CG			GLN		1.521		0.027
+CG-CD			GLN		1.506		0.023
+CD-OE1			GLN		1.235		0.022
+CD-NE2			GLN		1.324		0.025
+N-CA			GLN		1.459		0.020
+CA-C			GLN		1.525		0.026
+C-O			GLN		1.229		0.019
+N-CA			GLY		1.456		0.015
+CA-C			GLY		1.514		0.016
+C-O			GLY		1.232		0.016
+CA-CB			HIS		1.535		0.022
+CB-CG			HIS		1.492		0.016
+CG-ND1			HIS		1.369		0.015
+CG-CD2			HIS		1.353		0.017
+ND1-CE1			HIS		1.343		0.025
+CD2-NE2			HIS		1.415		0.021
+CE1-NE2			HIS		1.322		0.023
+N-CA			HIS		1.459		0.020
+CA-C			HIS		1.525		0.026
+C-O			HIS		1.229		0.019
+CA-CB			ILE		1.544		0.023
+CB-CG1			ILE		1.536		0.028
+CB-CG2			ILE		1.524		0.031
+CG1-CD1			ILE		1.500		0.069
+N-CA			ILE		1.459		0.020
+CA-C			ILE		1.525		0.026
+C-O			ILE		1.229		0.019
+CA-CB			LEU		1.533		0.023
+CB-CG			LEU		1.521		0.029
+CG-CD1			LEU		1.514		0.037
+CG-CD2			LEU		1.514		0.037
+N-CA			LEU		1.459		0.020
+CA-C			LEU		1.525		0.026
+C-O			LEU		1.229		0.019
+CA-CB			LYS		1.535		0.022
+CB-CG			LYS		1.521		0.027
+CG-CD			LYS		1.520		0.034
+CD-CE			LYS		1.508		0.025
+CE-NZ			LYS		1.486		0.025
+N-CA			LYS		1.459		0.020
+CA-C			LYS		1.525		0.026
+C-O			LYS		1.229		0.019
+CA-CB			MET		1.535		0.022
+CB-CG			MET		1.509		0.032
+CG-SD			MET		1.807		0.026
+SD-CE			MET		1.774		0.056
+N-CA			MET		1.459		0.020
+CA-C			MET		1.525		0.026
+C-O			MET		1.229		0.019
+CA-CB			PHE		1.535		0.022
+CB-CG			PHE		1.509		0.017
+CG-CD1			PHE		1.383		0.015
+CG-CD2			PHE		1.383		0.015
+CD1-CE1			PHE		1.388		0.020
+CD2-CE2			PHE		1.388		0.020
+CE1-CZ			PHE		1.369		0.019
+CE2-CZ			PHE		1.369		0.019
+N-CA			PHE		1.459		0.020
+CA-C			PHE		1.525		0.026
+C-O			PHE		1.229		0.019
+CA-CB			PRO		1.531		0.020
+CB-CG			PRO		1.495		0.050
+CG-CD			PRO		1.502		0.033
+CD-N			PRO		1.474		0.014
+N-CA			PRO		1.468		0.017
+CA-C			PRO		1.524		0.020
+C-O			PRO		1.228		0.020
+CA-CB			SER		1.525		0.015
+CB-OG			SER		1.418		0.013
+N-CA			SER		1.459		0.020
+CA-C			SER		1.525		0.026
+C-O			SER		1.229		0.019
+CA-CB			THR		1.529		0.026
+CB-OG1			THR		1.428		0.020
+CB-CG2			THR		1.519		0.033
+N-CA			THR		1.459		0.020
+CA-C			THR		1.525		0.026
+C-O			THR		1.229		0.019
+CA-CB			TRP		1.535		0.022
+CB-CG			TRP		1.498		0.018
+CG-CD1			TRP		1.363		0.014
+CG-CD2			TRP		1.432		0.017
+CD1-NE1			TRP		1.375		0.017
+NE1-CE2			TRP		1.371		0.013
+CD2-CE2			TRP		1.409		0.012
+CD2-CE3			TRP		1.399		0.015
+CE2-CZ2			TRP		1.393		0.017
+CE3-CZ3			TRP		1.380		0.017
+CZ2-CH2			TRP		1.369		0.019
+CZ3-CH2			TRP		1.396		0.016
+N-CA			TRP		1.459		0.020
+CA-C			TRP		1.525		0.026
+C-O			TRP		1.229		0.019
+CA-CB			TYR		1.535		0.022
+CB-CG			TYR		1.512		0.015
+CG-CD1			TYR		1.387		0.013
+CG-CD2			TYR		1.387		0.013
+CD1-CE1			TYR		1.389		0.015
+CD2-CE2			TYR		1.389		0.015
+CE1-CZ			TYR		1.381		0.013
+CE2-CZ			TYR		1.381		0.013
+CZ-OH			TYR		1.374		0.017
+N-CA			TYR		1.459		0.020
+CA-C			TYR		1.525		0.026
+C-O			TYR		1.229		0.019
+CA-CB			VAL		1.543		0.021
+CB-CG1			VAL		1.524		0.021
+CB-CG2			VAL		1.524		0.021
+N-CA			VAL		1.459		0.020
+CA-C			VAL		1.525		0.026
+C-O			VAL		1.229		0.019
+-
+
+Angle			Residue		Mean		StdDev
+N-CA-CB			ALA		110.1		1.4
+CB-CA-C			ALA		110.1		1.5
+N-CA-C			ALA		111.0		2.7
+CA-C-O			ALA		120.1		2.1
+N-CA-CB			ARG		110.6		1.8
+CB-CA-C			ARG		110.4		2.0
+CA-CB-CG		ARG		113.4		2.2
+CB-CG-CD		ARG		111.6		2.6
+CG-CD-NE		ARG		111.8		2.1
+CD-NE-CZ		ARG		123.6		1.4
+NE-CZ-NH1		ARG		120.3		0.5
+NE-CZ-NH2		ARG		120.3		0.5
+NH1-CZ-NH2		ARG		119.4		1.1
+N-CA-C			ARG		111.0		2.7
+CA-C-O			ARG		120.1		2.1
+N-CA-CB			ASN		110.6		1.8
+CB-CA-C			ASN		110.4		2.0
+CA-CB-CG		ASN		113.4		2.2
+CB-CG-ND2		ASN		116.7		2.4
+CB-CG-OD1		ASN		121.6		2.0
+ND2-CG-OD1		ASN		121.9		2.3
+N-CA-C			ASN		111.0		2.7
+CA-C-O			ASN		120.1		2.1
+N-CA-CB			ASP		110.6		1.8
+CB-CA-C			ASP		110.4		2.0
+CA-CB-CG		ASP		113.4		2.2
+CB-CG-OD1		ASP		118.3		0.9
+CB-CG-OD2		ASP		118.3		0.9
+OD1-CG-OD2		ASP		123.3		1.9
+N-CA-C			ASP		111.0		2.7
+CA-C-O			ASP		120.1		2.1
+N-CA-CB			CYS		110.8		1.5
+CB-CA-C			CYS		111.5		1.2
+CA-CB-SG		CYS		114.2		1.1
+N-CA-C			CYS		111.0		2.7
+CA-C-O			CYS		120.1		2.1
+N-CA-CB			GLU		110.6		1.8
+CB-CA-C			GLU		110.4		2.0
+CA-CB-CG		GLU		113.4		2.2
+CB-CG-CD		GLU		114.2		2.7
+CG-CD-OE1		GLU		118.3		2.0
+CG-CD-OE2		GLU		118.3		2.0
+OE1-CD-OE2		GLU		123.3		1.2
+N-CA-C			GLU		111.0		2.7
+CA-C-O			GLU		120.1		2.1
+N-CA-CB			GLN		110.6		1.8
+CB-CA-C			GLN		110.4		2.0
+CA-CB-CG		GLN		113.4		2.2
+CB-CG-CD		GLN		111.6		2.6
+CG-CD-OE1		GLN		121.6		2.0
+CG-CD-NE2		GLN		116.7		2.4
+OE1-CD-NE2		GLN		121.9		2.3
+N-CA-C			GLN		111.0		2.7
+CA-C-O			GLN		120.1		2.1
+N-CA-C			GLY		113.1		2.5
+CA-C-O			GLY		120.6		1.8
+N-CA-CB			HIS		110.6		1.8
+CB-CA-C			HIS		110.4		2.0
+CA-CB-CG		HIS		113.6		1.7
+CB-CG-ND1		HIS		123.2		2.5
+CB-CG-CD2		HIS		130.8		3.1
+CG-ND1-CE1		HIS		108.2		1.4
+ND1-CE1-NE2		HIS		109.9		2.2
+CE1-NE2-CD2		HIS		106.6		2.5
+NE2-CD2-CG		HIS		109.2		1.9
+CD2-CG-ND1		HIS		106.0		1.4
+N-CA-C			HIS		111.0		2.7
+CA-C-O			HIS		120.1		2.1
+N-CA-CB			ILE		110.8		2.3
+CB-CA-C			ILE		111.6		2.0
+CA-CB-CG1		ILE		111.0		1.9
+CB-CG1-CD1		ILE		113.9		2.8
+CA-CB-CG2		ILE		110.9		2.0
+CG1-CB-CG2		ILE		111.4		2.2
+N-CA-C			ILE		111.0		2.7
+CA-C-O			ILE		120.1		2.1
+N-CA-CB			LEU		110.4		2.0
+CB-CA-C			LEU		110.2		1.9
+CA-CB-CG		LEU		115.3		2.3
+CB-CG-CD1		LEU		111.0		1.7
+CB-CG-CD2		LEU		111.0		1.7
+CD1-CG-CD2		LEU		110.5		3.0
+N-CA-C			LEU		111.0		2.7
+CA-C-O			LEU		120.1		2.1
+N-CA-CB			LYS		110.6		1.8
+CB-CA-C			LYS		110.4		2.0
+CA-CB-CG		LYS		113.4		2.2
+CB-CG-CD		LYS		111.6		2.6
+CG-CD-CE		LYS		111.9		3.0
+CD-CE-NZ		LYS		111.7		2.3
+N-CA-C			LYS		111.0		2.7
+CA-C-O			LYS		120.1		2.1
+N-CA-CB			MET		110.6		1.8
+CB-CA-C			MET		110.4		2.0
+CA-CB-CG		MET		113.3		1.7
+CB-CG-SD		MET		112.4		3.0
+CG-SD-CE		MET		100.2		1.6
+N-CA-C			MET		111.0		2.7
+CA-C-O			MET		120.1		2.1
+N-CA-CB			PHE		110.6		1.8
+CB-CA-C			PHE		110.4		2.0
+CA-CB-CG		PHE		113.9		2.4
+CB-CG-CD1		PHE		120.8		0.7
+CB-CG-CD2		PHE		120.8		0.7
+CD1-CG-CD2		PHE		118.3		1.3
+CG-CD1-CE1		PHE		120.8		1.1
+CG-CD2-CE2		PHE		120.8		1.1
+CD1-CE1-CZ		PHE		120.1		1.2
+CD2-CE2-CZ		PHE		120.1		1.2
+CE1-CZ-CE2		PHE		120.0		1.8
+N-CA-C			PHE		111.0		2.7
+CA-C-O			PHE		120.1		2.1
+N-CA-CB			PRO		103.3		1.2
+CB-CA-C			PRO		111.7		2.1
+CA-CB-CG		PRO		104.8		1.9
+CB-CG-CD		PRO		106.5		3.9
+CG-CD-N			PRO		103.2		1.5
+CA-N-CD			PRO		111.7		1.4
+N-CA-C			PRO		112.1		2.6
+CA-C-O			PRO		120.2		2.4
+N-CA-CB			SER		110.5		1.5
+CB-CA-C			SER		110.1		1.9
+CA-CB-OG		SER		111.2		2.7
+N-CA-C			SER		111.0		2.7
+CA-C-O			SER		120.1		2.1
+N-CA-CB			THR		110.3		1.9
+CB-CA-C			THR		111.6		2.7
+CA-CB-OG1		THR		109.0		2.1
+CA-CB-CG2		THR		112.4		1.4
+OG1-CB-CG2		THR		110.0		2.3
+N-CA-C			THR		111.0		2.7
+CA-C-O			THR		120.1		2.1
+N-CA-CB			TRP		110.6		1.8
+CB-CA-C			TRP		110.4		2.0
+CA-CB-CG		TRP		113.7		1.9
+CB-CG-CD1		TRP		127.0		1.3
+CB-CG-CD2		TRP		126.6		1.3
+CD1-CG-CD2		TRP		106.3		0.8
+CG-CD1-NE1		TRP		110.1		1.0
+CD1-NE1-CE2		TRP		109.0		0.9
+NE1-CE2-CD2		TRP		107.3		1.0
+CE2-CD2-CG		TRP		107.3		0.8
+CG-CD2-CE3		TRP		133.9		0.9
+NE1-CE2-CZ2		TRP		130.4		1.1
+CE3-CD2-CE2		TRP		118.7		1.2
+CD2-CE2-CZ2		TRP		122.3		1.2
+CE2-CZ2-CH2		TRP		117.4		1.0
+CZ2-CH2-CZ3		TRP		121.6		1.2
+CH2-CZ3-CE3		TRP		121.2		1.1
+CZ3-CE3-CD2		TRP		118.8		1.3
+N-CA-C			TRP		111.0		2.7
+CA-C-O			TRP		120.1		2.1
+N-CA-CB			TYR		110.6		1.8
+CB-CA-C			TYR		110.4		2.0
+CA-CB-CG		TYR		113.4		1.9
+CB-CG-CD1		TYR		121.0		0.6
+CB-CG-CD2		TYR		121.0		0.6
+CD1-CG-CD2		TYR		117.9		1.1
+CG-CD1-CE1		TYR		121.3		0.8
+CG-CD2-CE2		TYR		121.3		0.8
+CD1-CE1-CZ		TYR		119.8		0.9
+CD2-CE2-CZ		TYR		119.8		0.9
+CE1-CZ-CE2		TYR		119.8		1.6
+CE1-CZ-OH		TYR		120.1		2.7
+CE2-CZ-OH		TYR		120.1		2.7
+N-CA-C			TYR		111.0		2.7
+CA-C-O			TYR		120.1		2.1
+N-CA-CB			VAL		111.5		2.2
+CB-CA-C			VAL		111.4		1.9
+CA-CB-CG1		VAL		110.9		1.5
+CA-CB-CG2		VAL		110.9		1.5
+CG1-CB-CG2		VAL		110.9		1.6
+N-CA-C			VAL		111.0		2.7
+CA-C-O			VAL		120.1		2.1
+-
+
+Non-bonded distance     Minimum Dist    Tolerance
+C-C                     3.4             1.5
+C-N                     3.25            1.5
+C-S                     3.5             1.5
+C-O                     3.22            1.5
+N-N                     3.1             1.5
+N-S                     3.35            1.5
+N-O                     3.07            1.5
+O-S                     3.32            1.5
+O-O                     3.04            1.5
+S-S                     2.03            1.0
+-

alphafold/relax/amber_minimize.py

@@ -27,10 +27,19 @@ from alphafold.relax import utils
 import ml_collections
 import numpy as np
 import jax
-from simtk import openmm
-from simtk import unit
-from simtk.openmm import app as openmm_app
-from simtk.openmm.app.internal.pdbstructure import PdbStructure
+try:
+  # openmm >= 7.6
+  import openmm
+  from openmm import unit
+  from openmm import app as openmm_app
+  from openmm.app.internal.pdbstructure import PdbStructure
+except ImportError:
+  # openmm < 7.6
+  from simtk import openmm
+  from simtk import unit
+  from simtk.openmm import app as openmm_app
+  from simtk.openmm.app.internal.pdbstructure import PdbStructure
+
 
 
 ENERGY = unit.kilocalories_per_mole
@@ -92,7 +101,7 @@ def _openmm_minimize(
     _add_restraints(system, pdb, stiffness, restraint_set, exclude_residues)
 
   integrator = openmm.LangevinIntegrator(0, 0.01, 0.0)
-  platform = openmm.Platform.getPlatformByName("CUDA" if use_gpu else "CPU")
+  platform = openmm.Platform.getPlatformByName("HIP" if use_gpu else "CPU")
   simulation = openmm_app.Simulation(
       pdb.topology, system, integrator, platform)
   simulation.context.setPositions(pdb.positions)

requirements.txt

@@ -3,11 +3,11 @@ biopython==1.79
 chex==0.0.7
 dm-haiku==0.0.9
 dm-tree==0.1.6
-docker==5.0.0
+# docker==5.0.0
 immutabledict==2.0.0
-jax==0.3.25
+# jax==0.3.25
 ml-collections==0.1.0
 numpy==1.21.6
 pandas==1.3.4
 scipy==1.7.0
-tensorflow-cpu==2.11.0
+# tensorflow-cpu==2.11.0

run_alphafold.py

@@ -60,6 +60,7 @@ flags.DEFINE_list(
     'basename is used to name the output directories for each prediction.')
 
 flags.DEFINE_string('data_dir', None, 'Path to directory of supporting data.')
+flags.DEFINE_string('model_names', None, 'Names of models to use.')
 flags.DEFINE_string('output_dir', None, 'Path to a directory that will '
                     'store the results.')
 flags.DEFINE_string('jackhmmer_binary_path', shutil.which('jackhmmer'),
@@ -408,7 +409,8 @@ def main(argv):
     data_pipeline = monomer_data_pipeline
 
   model_runners = {}
-  model_names = config.MODEL_PRESETS[FLAGS.model_preset]
+  # model_names = config.MODEL_PRESETS[FLAGS.model_preset]
+  model_names = FLAGS.model_names
   for model_name in model_names:
     model_config = config.model_config(model_name)
     if run_multimer_system:
@@ -457,6 +459,7 @@ if __name__ == '__main__':
       'fasta_paths',
       'output_dir',
       'data_dir',
+      'model_names',
       'uniref90_database_path',
       'mgnify_database_path',
       'template_mmcif_dir',

run_monomer.sh

+ download_dir=/data/alphafold2 
+ python3 run_alphafold.py \
+ --fasta_paths=monomer.fasta \
+ --output_dir=./ \
+ --use_precomputed_msas=false \
+ --data_dir=$download_dir  \
+ --model_names="model_1" \
+ --uniref90_database_path=$download_dir/uniref90/uniref90.fasta \
+ --mgnify_database_path=$download_dir/mgnify/mgy_clusters_2022_05.fa \
+ --bfd_database_path=$download_dir/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \
+ --uniref30_database_path=$download_dir/uniref30/UniRef30_2021_03 \
+ --pdb70_database_path=$download_dir/pdb70/pdb70 \
+ --template_mmcif_dir=$download_dir/pdb_mmcif/mmcif_files \
+ --obsolete_pdbs_path=$download_dir/pdb_mmcif/obsolete.dat \
+ --max_template_date=2020-05-14 \
+ --model_preset=monomer \
+ --db_preset=full_dbs \
+ --models_to_relax=best \
+ --use_gpu_relax=false 
+
+ 
+ 
+ 
+

run_multimer.sh

+download_dir=/data/alphafold2 
+python3 run_alphafold.py \
+ --fasta_paths=multimer.fasta \
+ --output_dir=./ \
+ --num_multimer_predictions_per_model=1 \
+ --use_precomputed_msas=false \
+ --data_dir=$download_dir  \
+ --model_names="model_1_multimer_v3" \
+ --uniref90_database_path=$download_dir/uniref90/uniref90.fasta \
+ --mgnify_database_path=$download_dir/mgnify/mgy_clusters_2022_05.fa \
+ --bfd_database_path=$download_dir/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \
+ --uniref30_database_path=$download_dir/uniref30/UniRef30_2021_03 \
+ --uniprot_database_path=$download_dir/uniprot/uniprot.fasta \
+ --pdb_seqres_database_path=$download_dir/pdb_seqres/pdb_seqres.txt \
+ --template_mmcif_dir=$download_dir/pdb_mmcif/mmcif_files \
+ --obsolete_pdbs_path=$download_dir/pdb_mmcif/obsolete.dat \
+ --max_template_date=2020-05-14 \
+ --model_preset=multimer \
+ --db_preset=full_dbs \
+ --models_to_relax=best \
+ --use_gpu_relax=false 
+

scripts/download_mgnify.sh

@@ -38,6 +38,6 @@ BASENAME=$(basename "${SOURCE_URL}")
 
 mkdir --parents "${ROOT_DIR}"
 aria2c "${SOURCE_URL}" --dir="${ROOT_DIR}"
-pushd "${ROOT_DIR}"
+# pushd "${ROOT_DIR}"
 gunzip "${ROOT_DIR}/${BASENAME}"
-popd
+# popd

scripts/download_pdb_mmcif.sh

@@ -45,9 +45,24 @@ echo "  * rsync.ebi.ac.uk::pub/databases/pdb/data/structures/divided/mmCIF/ (Eur
 echo "  * ftp.pdbj.org::ftp_data/structures/divided/mmCIF/ (Asia)"
 echo "or see https://www.wwpdb.org/ftp/pdb-ftp-sites for more download options."
 mkdir --parents "${RAW_DIR}"
-rsync --recursive --links --perms --times --compress --info=progress2 --delete --port=33444 \
-  rsync.rcsb.org::ftp_data/structures/divided/mmCIF/ \
-  "${RAW_DIR}"
+# rsync --recursive --links --perms --times --compress --info=progress2 --delete --port=33444 \
+#   rsync.rcsb.org::ftp_data/structures/divided/mmCIF/ \
+#   "${RAW_DIR}"
+
+# (Asia)
+rsync -rlpt -v -z --info=progress2 --delete \
+    ftp.pdbj.org::ftp_data/structures/divided/mmCIF/ \
+    "${RAW_DIR}"
+
+# (Europe)
+# rsync -rlpt -v -z --info=progress2 --delete \
+#   rsync.ebi.ac.uk::pub/databases/pdb/data/structures/divided/mmCIF/ \
+#   "${RAW_DIR}"
+
+# fast
+# rsync --recursive --links --perms --times --compress --info=progress2 --delete \
+# data.pdbj.org::ftp_data/structures/divided/mmCIF/ "${RAW_DIR}"
+
 
 echo "Unzipping all mmCIF files..."
 find "${RAW_DIR}/" -type f -iname "*.gz" -exec gunzip {} +

scripts/download_small_bfd.sh

@@ -36,6 +36,6 @@ BASENAME=$(basename "${SOURCE_URL}")
 
 mkdir --parents "${ROOT_DIR}"
 aria2c "${SOURCE_URL}" --dir="${ROOT_DIR}"
-pushd "${ROOT_DIR}"
+# pushd "${ROOT_DIR}"
 gunzip "${ROOT_DIR}/${BASENAME}"
-popd
+# popd

scripts/download_uniprot.sh

@@ -44,7 +44,7 @@ SPROT_UNZIPPED_BASENAME="${SPROT_BASENAME%.gz}"
 mkdir --parents "${ROOT_DIR}"
 aria2c "${TREMBL_SOURCE_URL}" --dir="${ROOT_DIR}"
 aria2c "${SPROT_SOURCE_URL}" --dir="${ROOT_DIR}"
-pushd "${ROOT_DIR}"
+# pushd "${ROOT_DIR}"
 gunzip "${ROOT_DIR}/${TREMBL_BASENAME}"
 gunzip "${ROOT_DIR}/${SPROT_BASENAME}"
 
@@ -52,4 +52,4 @@ gunzip "${ROOT_DIR}/${SPROT_BASENAME}"
 cat "${ROOT_DIR}/${SPROT_UNZIPPED_BASENAME}" >> "${ROOT_DIR}/${TREMBL_UNZIPPED_BASENAME}"
 mv "${ROOT_DIR}/${TREMBL_UNZIPPED_BASENAME}" "${ROOT_DIR}/uniprot.fasta"
 rm "${ROOT_DIR}/${SPROT_UNZIPPED_BASENAME}"
-popd
+# popd

scripts/download_uniref90.sh

@@ -36,6 +36,6 @@ BASENAME=$(basename "${SOURCE_URL}")
 
 mkdir --parents "${ROOT_DIR}"
 aria2c "${SOURCE_URL}" --dir="${ROOT_DIR}"
-pushd "${ROOT_DIR}"
+# pushd "${ROOT_DIR}"
 gunzip "${ROOT_DIR}/${BASENAME}"
-popd
+# popd