terry-r123
commented
2 years ago When I went to try to deal with the 6d2v in casp it was the same problem
python3 docker/run_docker.py --left_pdb_filepath project/test_data/6d2v_l_u.pdb --right_pdb_filepath project/test_data/6d2v_r_u.pdb --input_dataset_dir project/datasets/CASP_CAPRI --ckpt_name project/checkpoints/LitGINI-GeoTran-DilResNet.ckpt --hhsuite_db ~/Data/Databases/uniclust30/uniclust30_2018_08/uniclust30_2018_08
I0621 12:34:57.949921 140401309815360 run_docker.py:59] Mounting /home/ryc/pro/DeepInteract/project/test_data -> /mnt/input_pdbs
I0621 12:34:57.950060 140401309815360 run_docker.py:59] Mounting /home/ryc/pro/DeepInteract/project/test_data -> /mnt/input_pdbs
I0621 12:34:57.950130 140401309815360 run_docker.py:59] Mounting /home/ryc/pro/DeepInteract/project/datasets/CASP_CAPRI -> /mnt/Input
I0621 12:34:57.950197 140401309815360 run_docker.py:59] Mounting /home/ryc/pro/DeepInteract/project/checkpoints -> /mnt/checkpoints
I0621 12:34:57.950261 140401309815360 run_docker.py:59] Mounting /home/ryc/Data/Databases/uniclust30/uniclust30_2018_08 -> /mnt/hhsuite_db
I0621 12:35:00.932015 140401309815360 run_docker.py:135] DGL backend not selected or invalid. Assuming PyTorch for now.
I0621 12:35:00.932425 140401309815360 run_docker.py:135] Using backend: pytorch
I0621 12:35:00.936037 140401309815360 run_docker.py:135] I0621 12:35:00.935270 139901744678720 deepinteract_utils.py:1098] Seeding everything with random seed 42
I0621 12:35:00.936292 140401309815360 run_docker.py:135] Global seed set to 42
I0621 12:35:01.005911 140401309815360 run_docker.py:135] I0621 12:35:01.004549 139901744678720 deepinteract_utils.py:608] Making interim data set from raw data
I0621 12:35:01.029856 140401309815360 run_docker.py:135] I0621 12:35:01.029068 139901744678720 parse.py:43] 62 requested keys, 60 produced keys, 2 work keys
I0621 12:35:01.030803 140401309815360 run_docker.py:135] I0621 12:35:01.029560 139901744678720 parallel.py:46] Processing 2 inputs.
I0621 12:35:01.031013 140401309815360 run_docker.py:135] I0621 12:35:01.030477 139901744678720 parallel.py:62] Sequential Mode.
I0621 12:35:01.031196 140401309815360 run_docker.py:135] I0621 12:35:01.030538 139901744678720 parse.py:63] Reading /mnt/Input/raw/d2/6d2v_l_u.pdb
I0621 12:35:01.167531 140401309815360 run_docker.py:135] I0621 12:35:01.166552 139901744678720 parse.py:65] Writing /mnt/Input/raw/d2/6d2v_l_u.pdb to /mnt/Input/interim/parsed/d2/6d2v_l_u.pdb.pkl
I0621 12:35:01.171257 140401309815360 run_docker.py:135] I0621 12:35:01.170504 139901744678720 parse.py:67] Done writing /mnt/Input/raw/d2/6d2v_l_u.pdb to /mnt/Input/interim/parsed/d2/6d2v_l_u.pdb.pkl
I0621 12:35:01.171559 140401309815360 run_docker.py:135] I0621 12:35:01.170890 139901744678720 parse.py:63] Reading /mnt/Input/raw/d2/6d2v_r_u.pdb
I0621 12:35:01.255915 140401309815360 run_docker.py:135] I0621 12:35:01.254935 139901744678720 parse.py:65] Writing /mnt/Input/raw/d2/6d2v_r_u.pdb to /mnt/Input/interim/parsed/d2/6d2v_r_u.pdb.pkl
I0621 12:35:01.258986 140401309815360 run_docker.py:135] I0621 12:35:01.258208 139901744678720 parse.py:67] Done writing /mnt/Input/raw/d2/6d2v_r_u.pdb to /mnt/Input/interim/parsed/d2/6d2v_r_u.pdb.pkl
I0621 12:35:01.259291 140401309815360 run_docker.py:135] I0621 12:35:01.258671 139901744678720 complex.py:38] Getting filenames...
I0621 12:35:01.261862 140401309815360 run_docker.py:135] I0621 12:35:01.261171 139901744678720 complex.py:40] Getting complexes...
I0621 12:35:01.275393 140401309815360 run_docker.py:135] I0621 12:35:01.274663 139901744678720 pair.py:79] 31 requested keys, 30 produced keys, 1 work keys
I0621 12:35:01.275643 140401309815360 run_docker.py:135] I0621 12:35:01.274730 139901744678720 parallel.py:46] Processing 1 inputs.
I0621 12:35:01.275848 140401309815360 run_docker.py:135] I0621 12:35:01.274770 139901744678720 parallel.py:62] Sequential Mode.
I0621 12:35:01.276017 140401309815360 run_docker.py:135] I0621 12:35:01.274824 139901744678720 pair.py:97] Working on 6d2v
I0621 12:35:01.280996 140401309815360 run_docker.py:135] I0621 12:35:01.280404 139901744678720 pair.py:102] For complex 6d2v found 1 pairs out of 2 chains
I0621 12:35:02.040871 140401309815360 run_docker.py:135] I0621 12:35:02.039833 139901744678720 deepinteract_utils.py:689] Generating PSAIA features from PDB files in /mnt/Input/interim/parsed
I0621 12:35:02.044532 140401309815360 run_docker.py:135] I0621 12:35:02.043665 139901744678720 conservation.py:361] 2 PDB files to process with PSAIA
I0621 12:35:02.044819 140401309815360 run_docker.py:135] I0621 12:35:02.043990 139901744678720 parallel.py:46] Processing 1 inputs.
I0621 12:35:02.045027 140401309815360 run_docker.py:135] I0621 12:35:02.044081 139901744678720 parallel.py:62] Sequential Mode.
I0621 12:35:02.045209 140401309815360 run_docker.py:135] I0621 12:35:02.044131 139901744678720 conservation.py:43] PSAIA'ing /mnt/Input/interim/external_feats/PSAIA/INPUT/pdb_list.fls
I0621 12:35:02.461821 140401309815360 run_docker.py:135] I0621 12:35:02.460934 139901744678720 conservation.py:200] For generating protrusion indices, spent 00.42 PSAIA'ing, 00.00 writing, and 00.42 overall.
I0621 12:35:02.462200 140401309815360 run_docker.py:135] I0621 12:35:02.461326 139901744678720 deepinteract_utils.py:706] Generating profile HMM features from PDB files in /mnt/Input/interim/parsed
I0621 12:35:02.466627 140401309815360 run_docker.py:135] I0621 12:35:02.465923 139901744678720 conservation.py:458] 62 requested keys, 60 produced keys, 2 work filenames
I0621 12:35:02.466909 140401309815360 run_docker.py:135] I0621 12:35:02.466000 139901744678720 conservation.py:464] 2 work filenames
I0621 12:35:02.467137 140401309815360 run_docker.py:135] I0621 12:35:02.466323 139901744678720 parallel.py:46] Processing 2 inputs.
I0621 12:35:02.467322 140401309815360 run_docker.py:135] I0621 12:35:02.466411 139901744678720 parallel.py:62] Sequential Mode.
I0621 12:35:02.519334 140401309815360 run_docker.py:135] I0621 12:35:02.518395 139901744678720 conservation.py:152] HHblits'ing /mnt/Input/interim/external_feats/d2/work/6d2v_r_u.pdb-0-B.fa
I0621 12:37:49.408494 140401309815360 run_docker.py:135] I0621 12:37:49.407436 139901744678720 conservation.py:238] For 1 profile HMMs generated from 6d2v_r_u.pdb, spent 166.94 blitsing, 00.00 writing, and 166.94 overall.
I0621 12:37:49.474091 140401309815360 run_docker.py:135] I0621 12:37:49.473318 139901744678720 conservation.py:152] HHblits'ing /mnt/Input/interim/external_feats/d2/work/6d2v_l_u.pdb-0-A.fa
I0621 12:39:17.033113 140401309815360 run_docker.py:135] I0621 12:39:17.032159 139901744678720 conservation.py:238] For 1 profile HMMs generated from 6d2v_l_u.pdb, spent 87.62 blitsing, 00.00 writing, and 87.62 overall.
I0621 12:39:17.033506 140401309815360 run_docker.py:135] I0621 12:39:17.032451 139901744678720 deepinteract_utils.py:722] Starting postprocessing for all unprocessed pairs in /mnt/Input/interim/pairs
I0621 12:39:17.033727 140401309815360 run_docker.py:135] I0621 12:39:17.032506 139901744678720 deepinteract_utils.py:729] Looking for all pairs in /mnt/Input/interim/pairs
I0621 12:39:17.036458 140401309815360 run_docker.py:135] I0621 12:39:17.035934 139901744678720 deepinteract_utils.py:743] Found 1 work pair(s) in /mnt/Input/interim/pairs
I0621 12:39:17.036752 140401309815360 run_docker.py:135] I0621 12:39:17.036222 139901744678720 parallel.py:46] Processing 1 inputs.
I0621 12:39:17.036959 140401309815360 run_docker.py:135] I0621 12:39:17.036313 139901744678720 parallel.py:62] Sequential Mode.
I0621 12:39:17.818867 140401309815360 run_docker.py:135] sphere_mange_arete: inconcistence
I0621 12:39:30.032725 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'H' for Atom (name=HA2) with given element ''
I0621 12:39:30.033130 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:30.033359 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'H' for Atom (name=HA3) with given element ''
I0621 12:39:30.033550 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:30.033724 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'H' for Atom (name=H) with given element ''
I0621 12:39:30.033896 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:30.034178 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'C' for Atom (name=CD) with given element ''
I0621 12:39:30.034348 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:30.034514 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'O' for Atom (name=OE1) with given element ''
I0621 12:39:30.034679 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:30.034842 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'C' for Atom (name=CA) with given element ''
I0621 12:39:30.035007 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:30.035169 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'C' for Atom (name=C) with given element ''
I0621 12:39:30.035333 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:30.035496 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'N' for Atom (name=N) with given element ''
I0621 12:39:30.035658 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:30.035860 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'O' for Atom (name=O) with given element ''
I0621 12:39:30.036026 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:30.036188 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'C' for Atom (name=CB) with given element ''
I0621 12:39:30.036351 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:30.036514 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'C' for Atom (name=CG) with given element ''
I0621 12:39:30.036676 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:30.036838 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'H' for Atom (name=HA) with given element ''
I0621 12:39:30.037000 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:30.037161 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'H' for Atom (name=HB2) with given element ''
I0621 12:39:30.037324 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:30.037485 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'H' for Atom (name=HB3) with given element ''
I0621 12:39:30.037646 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:30.037807 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'H' for Atom (name=HG2) with given element ''
I0621 12:39:30.037969 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:30.038134 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'H' for Atom (name=HG3) with given element ''
I0621 12:39:30.038298 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:30.038460 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'H' for Atom (name=HE) with given element ''
I0621 12:39:30.038623 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:30.038783 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'O' for Atom (name=OD2) with given element ''
I0621 12:39:30.038945 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:30.039104 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'C' for Atom (name=CD1) with given element ''
I0621 12:39:30.039266 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:30.039426 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'C' for Atom (name=CD2) with given element ''
I0621 12:39:30.039587 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:30.039760 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'N' for Atom (name=NE1) with given element ''
I0621 12:39:30.039926 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:30.040086 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'C' for Atom (name=CE2) with given element ''
I0621 12:39:30.040247 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:30.040407 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'C' for Atom (name=CE3) with given element ''
I0621 12:39:30.040569 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:30.040728 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'C' for Atom (name=CZ2) with given element ''
I0621 12:39:30.040890 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:30.041053 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'H' for Atom (name=HD1) with given element ''
I0621 12:39:30.041217 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:30.041379 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'H' for Atom (name=HE1) with given element ''
I0621 12:39:30.041543 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:30.041704 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'H' for Atom (name=HE3) with given element ''
I0621 12:39:30.041868 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:30.042028 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'H' for Atom (name=HZ2) with given element ''
I0621 12:39:30.042189 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:30.042351 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'H' for Atom (name=HZ3) with given element ''
I0621 12:39:30.042512 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:30.042673 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'H' for Atom (name=HZ1) with given element ''
I0621 12:39:30.042838 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:30.043000 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'C' for Atom (name=CE) with given element ''
I0621 12:39:30.043164 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:30.043326 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'H' for Atom (name=HD2) with given element ''
I0621 12:39:30.043487 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:30.043648 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'H' for Atom (name=HD3) with given element ''
I0621 12:39:30.043853 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:30.044018 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'H' for Atom (name=HE2) with given element ''
I0621 12:39:30.044178 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:30.044340 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'N' for Atom (name=NE) with given element ''
I0621 12:39:30.044503 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:30.044667 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'H' for Atom (name=HH21) with given element ''
I0621 12:39:30.044830 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:30.044990 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'H' for Atom (name=HH22) with given element ''
I0621 12:39:30.045150 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:30.045310 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/vectors.py:357: RuntimeWarning: invalid value encountered in double_scalars
I0621 12:39:30.045472 140401309815360 run_docker.py:135] c = (self other) / (n1 n2)
I0621 12:39:30.045633 140401309815360 run_docker.py:135] /app/DeepInteract/project/utils/dips_plus_utils.py:78: RuntimeWarning: invalid value encountered in true_divide
I0621 12:39:30.045795 140401309815360 run_docker.py:135] v = dv / n[:, np.newaxis]
I0621 12:39:30.045954 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'C' for Atom (name=CD) with given element ''
I0621 12:39:30.046115 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:30.046276 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'O' for Atom (name=OE1) with given element ''
I0621 12:39:30.046439 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:30.046631 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'O' for Atom (name=OE2) with given element ''
I0621 12:39:30.046795 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:30.046956 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'H' for Atom (name=HG2) with given element ''
I0621 12:39:30.047118 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:30.047278 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'H' for Atom (name=HG3) with given element ''
I0621 12:39:30.047440 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:30.047604 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'N' for Atom (name=NE) with given element ''
I0621 12:39:30.047809 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:41.832217 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'H' for Atom (name=HE) with given element ''
I0621 12:39:41.832617 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:41.832842 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'C' for Atom (name=CG) with given element ''
I0621 12:39:41.833028 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:41.833205 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'C' for Atom (name=CD2) with given element ''
I0621 12:39:41.833375 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:41.833542 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'N' for Atom (name=NE1) with given element ''
I0621 12:39:41.833707 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:41.833868 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'C' for Atom (name=CE2) with given element ''
I0621 12:39:41.834034 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:41.834198 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'C' for Atom (name=CE3) with given element ''
I0621 12:39:41.834363 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:41.834527 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'C' for Atom (name=CZ2) with given element ''
I0621 12:39:41.834693 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:41.834855 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'C' for Atom (name=CZ3) with given element ''
I0621 12:39:41.835098 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:41.835262 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'C' for Atom (name=CH2) with given element ''
I0621 12:39:41.835422 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:41.835580 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'H' for Atom (name=HD1) with given element ''
I0621 12:39:41.835739 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:41.835947 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'H' for Atom (name=HE1) with given element ''
I0621 12:39:41.836111 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:41.836276 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'H' for Atom (name=HE3) with given element ''
I0621 12:39:41.836437 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:41.836598 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'H' for Atom (name=HZ2) with given element ''
I0621 12:39:41.836760 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:41.836920 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'H' for Atom (name=HZ3) with given element ''
I0621 12:39:41.837083 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:41.837242 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'H' for Atom (name=HH2) with given element ''
I0621 12:39:41.837404 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:41.837567 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'H' for Atom (name=HD2) with given element ''
I0621 12:39:41.837728 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:41.837892 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'H' for Atom (name=HD3) with given element ''
I0621 12:39:41.838057 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:41.838221 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'H' for Atom (name=HE2) with given element ''
I0621 12:39:41.838382 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:41.838543 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'N' for Atom (name=NZ) with given element ''
I0621 12:39:41.838704 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:41.838864 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'H' for Atom (name=HB2) with given element ''
I0621 12:39:41.839024 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:41.839185 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'H' for Atom (name=HB3) with given element ''
I0621 12:39:41.839348 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:41.839508 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'H' for Atom (name=HZ1) with given element ''
I0621 12:39:41.839670 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:41.839845 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'H' for Atom (name=HG) with given element ''
I0621 12:39:41.840006 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:41.840165 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'C' for Atom (name=CZ) with given element ''
I0621 12:39:41.840325 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:41.840486 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'N' for Atom (name=NH1) with given element ''
I0621 12:39:41.840647 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:41.840809 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'N' for Atom (name=NH2) with given element ''
I0621 12:39:41.840971 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:41.841133 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'H' for Atom (name=HH11) with given element ''
I0621 12:39:41.841294 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:41.841453 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'H' for Atom (name=HH12) with given element ''
I0621 12:39:41.841613 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:41.841772 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'H' for Atom (name=HH21) with given element ''
I0621 12:39:41.841933 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:41.842094 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/Atom.py:218: PDBConstructionWarning: Used element 'H' for Atom (name=HH22) with given element ''
I0621 12:39:41.842256 140401309815360 run_docker.py:135] warnings.warn(msg, PDBConstructionWarning)
I0621 12:39:41.842418 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/vectors.py:357: RuntimeWarning: invalid value encountered in double_scalars
I0621 12:39:41.842582 140401309815360 run_docker.py:135] c = (self other) / (n1 n2)
I0621 12:39:41.842744 140401309815360 run_docker.py:135] I0621 12:39:41.830886 139901744678720 dips_plus_utils.py:536] Normal vector missing for df0 residue -7 in chain A in file /mnt/Input/raw/d2/6d2v_l_u.pdb
I0621 12:39:41.865425 140401309815360 run_docker.py:135] I0621 12:39:41.864879 139901744678720 dips_plus_utils.py:536] Normal vector missing for df0 residue -2 in chain A in file /mnt/Input/raw/d2/6d2v_l_u.pdb
I0621 12:39:41.897109 140401309815360 run_docker.py:135] I0621 12:39:41.896541 139901744678720 dips_plus_utils.py:536] Normal vector missing for df0 residue 3 in chain A in file /mnt/Input/raw/d2/6d2v_l_u.pdb
I0621 12:39:41.942955 140401309815360 run_docker.py:135] I0621 12:39:41.942325 139901744678720 dips_plus_utils.py:536] Normal vector missing for df0 residue 10 in chain A in file /mnt/Input/raw/d2/6d2v_l_u.pdb
I0621 12:39:41.948890 140401309815360 run_docker.py:135] I0621 12:39:41.948352 139901744678720 dips_plus_utils.py:536] Normal vector missing for df0 residue 11 in chain A in file /mnt/Input/raw/d2/6d2v_l_u.pdb
I0621 12:39:41.961029 140401309815360 run_docker.py:135] I0621 12:39:41.960399 139901744678720 dips_plus_utils.py:536] Normal vector missing for df0 residue 13 in chain A in file /mnt/Input/raw/d2/6d2v_l_u.pdb
I0621 12:39:42.087909 140401309815360 run_docker.py:135] I0621 12:39:42.087159 139901744678720 dips_plus_utils.py:536] Normal vector missing for df0 residue 33 in chain A in file /mnt/Input/raw/d2/6d2v_l_u.pdb
I0621 12:39:42.107360 140401309815360 run_docker.py:135] I0621 12:39:42.106707 139901744678720 dips_plus_utils.py:536] Normal vector missing for df0 residue 36 in chain A in file /mnt/Input/raw/d2/6d2v_l_u.pdb
I0621 12:39:42.125646 140401309815360 run_docker.py:135] I0621 12:39:42.124898 139901744678720 dips_plus_utils.py:536] Normal vector missing for df0 residue 39 in chain A in file /mnt/Input/raw/d2/6d2v_l_u.pdb
I0621 12:39:42.183039 140401309815360 run_docker.py:135] I0621 12:39:42.182360 139901744678720 dips_plus_utils.py:536] Normal vector missing for df0 residue 48 in chain A in file /mnt/Input/raw/d2/6d2v_l_u.pdb
I0621 12:39:42.258430 140401309815360 run_docker.py:135] I0621 12:39:42.257756 139901744678720 dips_plus_utils.py:536] Normal vector missing for df0 residue 60 in chain A in file /mnt/Input/raw/d2/6d2v_l_u.pdb
I0621 12:39:42.294685 140401309815360 run_docker.py:135] I0621 12:39:42.294003 139901744678720 dips_plus_utils.py:536] Normal vector missing for df0 residue 66 in chain A in file /mnt/Input/raw/d2/6d2v_l_u.pdb
I0621 12:39:42.397612 140401309815360 run_docker.py:135] I0621 12:39:42.396705 139901744678720 dips_plus_utils.py:536] Normal vector missing for df0 residue 82 in chain A in file /mnt/Input/raw/d2/6d2v_l_u.pdb
I0621 12:39:42.415932 140401309815360 run_docker.py:135] I0621 12:39:42.415230 139901744678720 dips_plus_utils.py:536] Normal vector missing for df0 residue 85 in chain A in file /mnt/Input/raw/d2/6d2v_l_u.pdb
I0621 12:39:42.500828 140401309815360 run_docker.py:135] I0621 12:39:42.500077 139901744678720 dips_plus_utils.py:536] Normal vector missing for df0 residue 99 in chain A in file /mnt/Input/raw/d2/6d2v_l_u.pdb
I0621 12:39:42.552430 140401309815360 run_docker.py:135] I0621 12:39:42.551667 139901744678720 dips_plus_utils.py:536] Normal vector missing for df0 residue 107 in chain A in file /mnt/Input/raw/d2/6d2v_l_u.pdb
I0621 12:39:42.616647 140401309815360 run_docker.py:135] I0621 12:39:42.615720 139901744678720 dips_plus_utils.py:536] Normal vector missing for df0 residue 117 in chain A in file /mnt/Input/raw/d2/6d2v_l_u.pdb
I0621 12:39:42.743300 140401309815360 run_docker.py:135] I0621 12:39:42.742340 139901744678720 dips_plus_utils.py:536] Normal vector missing for df0 residue 137 in chain A in file /mnt/Input/raw/d2/6d2v_l_u.pdb
I0621 12:39:42.812014 140401309815360 run_docker.py:135] I0621 12:39:42.811212 139901744678720 dips_plus_utils.py:536] Normal vector missing for df0 residue 148 in chain A in file /mnt/Input/raw/d2/6d2v_l_u.pdb
I0621 12:39:42.849296 140401309815360 run_docker.py:135] I0621 12:39:42.848616 139901744678720 dips_plus_utils.py:536] Normal vector missing for df0 residue 154 in chain A in file /mnt/Input/raw/d2/6d2v_l_u.pdb
I0621 12:39:42.994962 140401309815360 run_docker.py:135] I0621 12:39:42.994056 139901744678720 dips_plus_utils.py:536] Normal vector missing for df0 residue 177 in chain A in file /mnt/Input/raw/d2/6d2v_l_u.pdb
I0621 12:39:43.006819 140401309815360 run_docker.py:135] I0621 12:39:43.006204 139901744678720 dips_plus_utils.py:536] Normal vector missing for df0 residue 179 in chain A in file /mnt/Input/raw/d2/6d2v_l_u.pdb
I0621 12:39:43.012657 140401309815360 run_docker.py:135] I0621 12:39:43.012028 139901744678720 dips_plus_utils.py:536] Normal vector missing for df0 residue 180 in chain A in file /mnt/Input/raw/d2/6d2v_l_u.pdb
I0621 12:39:43.025393 140401309815360 run_docker.py:135] I0621 12:39:43.024782 139901744678720 dips_plus_utils.py:536] Normal vector missing for df0 residue 182 in chain A in file /mnt/Input/raw/d2/6d2v_l_u.pdb
I0621 12:39:43.031161 140401309815360 run_docker.py:135] I0621 12:39:43.030568 139901744678720 dips_plus_utils.py:536] Normal vector missing for df0 residue 183 in chain A in file /mnt/Input/raw/d2/6d2v_l_u.pdb
I0621 12:39:43.108997 140401309815360 run_docker.py:135] I0621 12:39:43.108363 139901744678720 dips_plus_utils.py:536] Normal vector missing for df0 residue 195 in chain A in file /mnt/Input/raw/d2/6d2v_l_u.pdb
I0621 12:39:43.165647 140401309815360 run_docker.py:135] I0621 12:39:43.165016 139901744678720 dips_plus_utils.py:536] Normal vector missing for df0 residue 204 in chain A in file /mnt/Input/raw/d2/6d2v_l_u.pdb
I0621 12:39:43.372141 140401309815360 run_docker.py:135] I0621 12:39:43.371286 139901744678720 dips_plus_utils.py:536] Normal vector missing for df0 residue 237 in chain A in file /mnt/Input/raw/d2/6d2v_l_u.pdb
I0621 12:39:43.377866 140401309815360 run_docker.py:135] I0621 12:39:43.377245 139901744678720 dips_plus_utils.py:536] Normal vector missing for df0 residue 238 in chain A in file /mnt/Input/raw/d2/6d2v_l_u.pdb
I0621 12:39:43.408345 140401309815360 run_docker.py:135] I0621 12:39:43.407525 139901744678720 dips_plus_utils.py:536] Normal vector missing for df0 residue 243 in chain A in file /mnt/Input/raw/d2/6d2v_l_u.pdb
I0621 12:39:43.491838 140401309815360 run_docker.py:135] I0621 12:39:43.490914 139901744678720 dips_plus_utils.py:536] Normal vector missing for df0 residue 256 in chain A in file /mnt/Input/raw/d2/6d2v_l_u.pdb
I0621 12:39:43.665829 140401309815360 run_docker.py:135] I0621 12:39:43.664943 139901744678720 dips_plus_utils.py:536] Normal vector missing for df0 residue 283 in chain A in file /mnt/Input/raw/d2/6d2v_l_u.pdb
I0621 12:39:43.723889 140401309815360 run_docker.py:135] I0621 12:39:43.723078 139901744678720 dips_plus_utils.py:536] Normal vector missing for df0 residue 292 in chain A in file /mnt/Input/raw/d2/6d2v_l_u.pdb
I0621 12:39:43.854378 140401309815360 run_docker.py:135] I0621 12:39:43.853497 139901744678720 dips_plus_utils.py:630] Normal vector missing for df1 residue 3 in chain B in file /mnt/Input/raw/d2/6d2v_r_u.pdb
I0621 12:39:43.898285 140401309815360 run_docker.py:135] I0621 12:39:43.897567 139901744678720 dips_plus_utils.py:630] Normal vector missing for df1 residue 10 in chain B in file /mnt/Input/raw/d2/6d2v_r_u.pdb
I0621 12:39:43.903930 140401309815360 run_docker.py:135] I0621 12:39:43.903309 139901744678720 dips_plus_utils.py:630] Normal vector missing for df1 residue 11 in chain B in file /mnt/Input/raw/d2/6d2v_r_u.pdb
I0621 12:39:43.915581 140401309815360 run_docker.py:135] I0621 12:39:43.914965 139901744678720 dips_plus_utils.py:630] Normal vector missing for df1 residue 13 in chain B in file /mnt/Input/raw/d2/6d2v_r_u.pdb
I0621 12:39:44.040245 140401309815360 run_docker.py:135] I0621 12:39:44.039506 139901744678720 dips_plus_utils.py:630] Normal vector missing for df1 residue 33 in chain B in file /mnt/Input/raw/d2/6d2v_r_u.pdb
I0621 12:39:44.059344 140401309815360 run_docker.py:135] I0621 12:39:44.058759 139901744678720 dips_plus_utils.py:630] Normal vector missing for df1 residue 36 in chain B in file /mnt/Input/raw/d2/6d2v_r_u.pdb
I0621 12:39:44.077337 140401309815360 run_docker.py:135] I0621 12:39:44.076769 139901744678720 dips_plus_utils.py:630] Normal vector missing for df1 residue 39 in chain B in file /mnt/Input/raw/d2/6d2v_r_u.pdb
I0621 12:39:44.134004 140401309815360 run_docker.py:135] I0621 12:39:44.133355 139901744678720 dips_plus_utils.py:630] Normal vector missing for df1 residue 48 in chain B in file /mnt/Input/raw/d2/6d2v_r_u.pdb
I0621 12:39:44.208367 140401309815360 run_docker.py:135] I0621 12:39:44.207648 139901744678720 dips_plus_utils.py:630] Normal vector missing for df1 residue 60 in chain B in file /mnt/Input/raw/d2/6d2v_r_u.pdb
I0621 12:39:44.244361 140401309815360 run_docker.py:135] I0621 12:39:44.243762 139901744678720 dips_plus_utils.py:630] Normal vector missing for df1 residue 66 in chain B in file /mnt/Input/raw/d2/6d2v_r_u.pdb
I0621 12:39:44.344155 140401309815360 run_docker.py:135] I0621 12:39:44.343361 139901744678720 dips_plus_utils.py:630] Normal vector missing for df1 residue 82 in chain B in file /mnt/Input/raw/d2/6d2v_r_u.pdb
I0621 12:39:44.361849 140401309815360 run_docker.py:135] I0621 12:39:44.361222 139901744678720 dips_plus_utils.py:630] Normal vector missing for df1 residue 85 in chain B in file /mnt/Input/raw/d2/6d2v_r_u.pdb
I0621 12:39:44.446519 140401309815360 run_docker.py:135] I0621 12:39:44.445842 139901744678720 dips_plus_utils.py:630] Normal vector missing for df1 residue 99 in chain B in file /mnt/Input/raw/d2/6d2v_r_u.pdb
I0621 12:39:44.497653 140401309815360 run_docker.py:135] I0621 12:39:44.496819 139901744678720 dips_plus_utils.py:630] Normal vector missing for df1 residue 107 in chain B in file /mnt/Input/raw/d2/6d2v_r_u.pdb
I0621 12:39:44.560553 140401309815360 run_docker.py:135] I0621 12:39:44.559613 139901744678720 dips_plus_utils.py:630] Normal vector missing for df1 residue 117 in chain B in file /mnt/Input/raw/d2/6d2v_r_u.pdb
I0621 12:39:44.686419 140401309815360 run_docker.py:135] I0621 12:39:44.685462 139901744678720 dips_plus_utils.py:630] Normal vector missing for df1 residue 137 in chain B in file /mnt/Input/raw/d2/6d2v_r_u.pdb
I0621 12:39:44.755932 140401309815360 run_docker.py:135] I0621 12:39:44.754979 139901744678720 dips_plus_utils.py:630] Normal vector missing for df1 residue 148 in chain B in file /mnt/Input/raw/d2/6d2v_r_u.pdb
I0621 12:39:44.793098 140401309815360 run_docker.py:135] I0621 12:39:44.792411 139901744678720 dips_plus_utils.py:630] Normal vector missing for df1 residue 154 in chain B in file /mnt/Input/raw/d2/6d2v_r_u.pdb
I0621 12:39:44.937708 140401309815360 run_docker.py:135] I0621 12:39:44.936798 139901744678720 dips_plus_utils.py:630] Normal vector missing for df1 residue 177 in chain B in file /mnt/Input/raw/d2/6d2v_r_u.pdb
I0621 12:39:44.949535 140401309815360 run_docker.py:135] I0621 12:39:44.948864 139901744678720 dips_plus_utils.py:630] Normal vector missing for df1 residue 179 in chain B in file /mnt/Input/raw/d2/6d2v_r_u.pdb
I0621 12:39:44.955188 140401309815360 run_docker.py:135] I0621 12:39:44.954590 139901744678720 dips_plus_utils.py:630] Normal vector missing for df1 residue 180 in chain B in file /mnt/Input/raw/d2/6d2v_r_u.pdb
I0621 12:39:44.967625 140401309815360 run_docker.py:135] I0621 12:39:44.967013 139901744678720 dips_plus_utils.py:630] Normal vector missing for df1 residue 182 in chain B in file /mnt/Input/raw/d2/6d2v_r_u.pdb
I0621 12:39:44.973296 140401309815360 run_docker.py:135] I0621 12:39:44.972724 139901744678720 dips_plus_utils.py:630] Normal vector missing for df1 residue 183 in chain B in file /mnt/Input/raw/d2/6d2v_r_u.pdb
I0621 12:39:45.050072 140401309815360 run_docker.py:135] I0621 12:39:45.049450 139901744678720 dips_plus_utils.py:630] Normal vector missing for df1 residue 195 in chain B in file /mnt/Input/raw/d2/6d2v_r_u.pdb
I0621 12:39:45.105908 140401309815360 run_docker.py:135] I0621 12:39:45.105209 139901744678720 dips_plus_utils.py:630] Normal vector missing for df1 residue 204 in chain B in file /mnt/Input/raw/d2/6d2v_r_u.pdb
I0621 12:39:45.311397 140401309815360 run_docker.py:135] I0621 12:39:45.310593 139901744678720 dips_plus_utils.py:630] Normal vector missing for df1 residue 237 in chain B in file /mnt/Input/raw/d2/6d2v_r_u.pdb
I0621 12:39:45.317076 140401309815360 run_docker.py:135] I0621 12:39:45.316379 139901744678720 dips_plus_utils.py:630] Normal vector missing for df1 residue 238 in chain B in file /mnt/Input/raw/d2/6d2v_r_u.pdb
I0621 12:39:45.347154 140401309815360 run_docker.py:135] I0621 12:39:45.346449 139901744678720 dips_plus_utils.py:630] Normal vector missing for df1 residue 243 in chain B in file /mnt/Input/raw/d2/6d2v_r_u.pdb
I0621 12:39:45.429866 140401309815360 run_docker.py:135] I0621 12:39:45.429168 139901744678720 dips_plus_utils.py:630] Normal vector missing for df1 residue 256 in chain B in file /mnt/Input/raw/d2/6d2v_r_u.pdb
I0621 12:39:45.603310 140401309815360 run_docker.py:135] I0621 12:39:45.602409 139901744678720 dips_plus_utils.py:630] Normal vector missing for df1 residue 283 in chain B in file /mnt/Input/raw/d2/6d2v_r_u.pdb
I0621 12:39:45.661534 140401309815360 run_docker.py:135] I0621 12:39:45.660705 139901744678720 dips_plus_utils.py:630] Normal vector missing for df1 residue 292 in chain B in file /mnt/Input/raw/d2/6d2v_r_u.pdb
I0621 12:39:45.928123 140401309815360 run_docker.py:135] I0621 12:39:45.927218 139901744678720 deepinteract_utils.py:773] Imputing missing feature values for given inputs
I0621 12:39:45.928877 140401309815360 run_docker.py:135] I0621 12:39:45.928412 139901744678720 parallel.py:46] Processing 31 inputs.
I0621 12:39:45.929104 140401309815360 run_docker.py:135] I0621 12:39:45.928501 139901744678720 parallel.py:62] Sequential Mode.
I0621 12:39:52.517787 140401309815360 run_docker.py:135] I0621 12:39:52.517032 139901744678720 lit_model_predict_docker.py:99] Loading complex for prediction, l_chain: /mnt/input_pdbs/6d2v_l_u.pdb, r_chain: /mnt/input_pdbs/6d2v_r_u.pdb
I0621 12:39:53.520499 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/torchmetrics/utilities/prints.py:36: UserWarning: Metric AUROC will save all targets and predictions in buffer. For large datasets this may lead to large memory footprint.
I0621 12:39:53.520946 140401309815360 run_docker.py:135] warnings.warn(*args, *kwargs)
I0621 12:39:53.521200 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/torchmetrics/utilities/prints.py:36: UserWarning: Metric AveragePrecision will save all targets and predictions in buffer. For large datasets this may lead to large memory footprint.
I0621 12:39:53.521423 140401309815360 run_docker.py:135] warnings.warn(args, **kwargs)
I0621 12:39:53.521636 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/pytorch_lightning/trainer/connectors/accelerator_connector.py:792: UserWarning: You are running on single node with no parallelization, so distributed has no effect.
I0621 12:39:53.521881 140401309815360 run_docker.py:135] rank_zero_warn("You are running on single node with no parallelization, so distributed has no effect.")
I0621 12:39:53.522081 140401309815360 run_docker.py:135] GPU available: False, used: False
I0621 12:39:53.522280 140401309815360 run_docker.py:135] TPU available: False, using: 0 TPU cores
I0621 12:39:53.522469 140401309815360 run_docker.py:135] IPU available: False, using: 0 IPUs
I0621 12:39:53.585114 140401309815360 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/pytorch_lightning/trainer/data_loading.py:105: UserWarning: The dataloader, predict dataloader 0, does not have many workers which may be a bottleneck. Consider increasing the value of the num_workers argument(try 64 which is the number of cpus on this machine) in theDataLoader` init to improve performance.
I0621 12:39:53.585383 140401309815360 run_docker.py:135] rank_zero_warn(
I0621 12:39:53.585540 140401309815360 run_docker.py:135] Setting the default backend to "pytorch". You can change it in the ~/.dgl/config.json file or export the DGLBACKEND environment variable. Valid options are: pytorch, mxnet, tensorflow (all lowercase)
I0621 12:40:01.792003 140401309815360 run_docker.py:135] I0621 12:40:01.791101 139901744678720 lit_model_predict_docker.py:298] Saved predicted contact probability map for 6d2v as /mnt/input_pdbs/6d2v_contact_prob_map.npy
I0621 12:40:01.798268 140401309815360 run_docker.py:135] I0621 12:40:01.797450 139901744678720 lit_model_predict_docker.py:307] Saved learned node representations for the first chain graph of 6d2v as /mnt/input_pdbs/6d2v_graph1_node_feats.npy
I0621 12:40:01.798567 140401309815360 run_docker.py:135] I0621 12:40:01.797590 139901744678720 lit_model_predict_docker.py:308] Saved learned edge representations for the first chain graph of 6d2v as /mnt/input_pdbs/6d2v_graph1_edge_feats.npy
I0621 12:40:01.798772 140401309815360 run_docker.py:135] I0621 12:40:01.797632 139901744678720 lit_model_predict_docker.py:309] Saved learned node representations for the second chain graph of 6d2v as /mnt/input_pdbs/6d2v_graph2_node_feats.npy
I0621 12:40:01.798954 140401309815360 run_docker.py:135] I0621 12:40:01.797671 139901744678720 lit_model_predict_docker.py:310] Saved learned edge representations for the second chain graph of 6d2v as /mnt/input_pdbs/6d2v_graph2_edge_feats.npy
Predicting: 100%|██████████| 1/1 [00:08<00:00, 8.20s/it]Predicting: 0it [00:00, ?it/s]
amorehead
When I try to run: python3 docker/run_docker.py --left_pdb_filepath project/test_data/4heq_l_u.pdb --right_pdb_filepath project/test_data/4heq_r_u.pdb --input_dataset_dir project/datasets/CASP_CAPRI --ckpt_name project/checkpoints/LitGINI-GeoTran-DilResNet.ckpt --hhsuite_db ~/Data/Databases/uniclust30/uniclust30_2018_08/uniclust30_2018_08
I get these logs:
I0621 12:54:27.512626 139977373710144 run_docker.py:59] Mounting /home/ryc/pro/DeepInteract/project/test_data -> /mnt/input_pdbs I0621 12:54:27.512762 139977373710144 run_docker.py:59] Mounting /home/ryc/pro/DeepInteract/project/test_data -> /mnt/input_pdbs I0621 12:54:27.512836 139977373710144 run_docker.py:59] Mounting /home/ryc/pro/DeepInteract/project/datasets/CASP_CAPRI -> /mnt/Input I0621 12:54:27.512908 139977373710144 run_docker.py:59] Mounting /home/ryc/pro/DeepInteract/project/checkpoints -> /mnt/checkpoints I0621 12:54:27.512977 139977373710144 run_docker.py:59] Mounting /home/ryc/Data/Databases/uniclust30/uniclust30_2018_08 -> /mnt/hhsuite_db I0621 12:54:30.589913 139977373710144 run_docker.py:135] DGL backend not selected or invalid. Assuming PyTorch for now. I0621 12:54:30.590292 139977373710144 run_docker.py:135] Using backend: pytorch I0621 12:54:30.594311 139977373710144 run_docker.py:135] I0621 12:54:30.593440 140113106646848 deepinteract_utils.py:1098] Seeding everything with random seed 42 I0621 12:54:30.594596 139977373710144 run_docker.py:135] Global seed set to 42 I0621 12:54:30.643066 139977373710144 run_docker.py:135] cp: cannot stat '/mnt/input_pdbs/4heq_l_u.pdb': No such file or directory I0621 12:54:30.654789 139977373710144 run_docker.py:135] cp: cannot stat '/mnt/input_pdbs/4heq_r_u.pdb': No such file or directory I0621 12:54:30.655230 139977373710144 run_docker.py:135] I0621 12:54:30.654651 140113106646848 deepinteract_utils.py:608] Making interim data set from raw data I0621 12:54:30.675874 139977373710144 run_docker.py:135] I0621 12:54:30.675035 140113106646848 parse.py:43] 62 requested keys, 60 produced keys, 2 work keys I0621 12:54:30.676792 139977373710144 run_docker.py:135] I0621 12:54:30.675550 140113106646848 parallel.py:46] Processing 2 inputs. I0621 12:54:30.676914 139977373710144 run_docker.py:135] I0621 12:54:30.676569 140113106646848 parallel.py:62] Sequential Mode. I0621 12:54:30.677030 139977373710144 run_docker.py:135] I0621 12:54:30.676633 140113106646848 parse.py:63] Reading /mnt/Input/raw/he/4heq_r_u.pdb I0621 12:54:30.711622 139977373710144 run_docker.py:135] I0621 12:54:30.710961 140113106646848 parse.py:65] Writing /mnt/Input/raw/he/4heq_r_u.pdb to /mnt/Input/interim/parsed/he/4heq_r_u.pdb.pkl I0621 12:54:30.713438 139977373710144 run_docker.py:135] I0621 12:54:30.712913 140113106646848 parse.py:67] Done writing /mnt/Input/raw/he/4heq_r_u.pdb to /mnt/Input/interim/parsed/he/4heq_r_u.pdb.pkl I0621 12:54:30.713546 139977373710144 run_docker.py:135] I0621 12:54:30.713084 140113106646848 parse.py:63] Reading /mnt/Input/raw/he/4heq_l_u.pdb I0621 12:54:30.744368 139977373710144 run_docker.py:135] I0621 12:54:30.743873 140113106646848 parse.py:65] Writing /mnt/Input/raw/he/4heq_l_u.pdb to /mnt/Input/interim/parsed/he/4heq_l_u.pdb.pkl I0621 12:54:30.745597 139977373710144 run_docker.py:135] I0621 12:54:30.745240 140113106646848 parse.py:67] Done writing /mnt/Input/raw/he/4heq_l_u.pdb to /mnt/Input/interim/parsed/he/4heq_l_u.pdb.pkl I0621 12:54:30.745825 139977373710144 run_docker.py:135] I0621 12:54:30.745505 140113106646848 complex.py:38] Getting filenames... I0621 12:54:30.749119 139977373710144 run_docker.py:135] I0621 12:54:30.748700 140113106646848 complex.py:40] Getting complexes... I0621 12:54:30.770302 139977373710144 run_docker.py:135] I0621 12:54:30.769680 140113106646848 pair.py:79] 31 requested keys, 30 produced keys, 1 work keys I0621 12:54:30.770423 139977373710144 run_docker.py:135] I0621 12:54:30.769779 140113106646848 parallel.py:46] Processing 1 inputs. I0621 12:54:30.770527 139977373710144 run_docker.py:135] I0621 12:54:30.769842 140113106646848 parallel.py:62] Sequential Mode. I0621 12:54:30.770629 139977373710144 run_docker.py:135] I0621 12:54:30.769901 140113106646848 pair.py:97] Working on 4heq I0621 12:54:30.773638 139977373710144 run_docker.py:135] I0621 12:54:30.773111 140113106646848 pair.py:102] For complex 4heq found 1 pairs out of 2 chains I0621 12:54:31.086785 139977373710144 run_docker.py:135] I0621 12:54:31.085926 140113106646848 deepinteract_utils.py:689] Generating PSAIA features from PDB files in /mnt/Input/interim/parsed I0621 12:54:31.090075 139977373710144 run_docker.py:135] I0621 12:54:31.089508 140113106646848 conservation.py:361] 0 PDB files to process with PSAIA I0621 12:54:31.090215 139977373710144 run_docker.py:135] I0621 12:54:31.089650 140113106646848 parallel.py:46] Processing 1 inputs. I0621 12:54:31.090428 139977373710144 run_docker.py:135] I0621 12:54:31.089698 140113106646848 parallel.py:62] Sequential Mode. I0621 12:54:31.090618 139977373710144 run_docker.py:135] I0621 12:54:31.089743 140113106646848 conservation.py:43] PSAIA'ing /mnt/Input/interim/external_feats/PSAIA/INPUT/pdb_list.fls I0621 12:54:31.114144 139977373710144 run_docker.py:135] I0621 12:54:31.113151 140113106646848 conservation.py:200] For generating protrusion indices, spent 00.02 PSAIA'ing, 00.00 writing, and 00.02 overall. I0621 12:54:31.114319 139977373710144 run_docker.py:135] I0621 12:54:31.113927 140113106646848 deepinteract_utils.py:706] Generating profile HMM features from PDB files in /mnt/Input/interim/parsed I0621 12:54:31.125687 139977373710144 run_docker.py:135] I0621 12:54:31.125225 140113106646848 conservation.py:458] 62 requested keys, 60 produced keys, 2 work filenames I0621 12:54:31.125820 139977373710144 run_docker.py:135] I0621 12:54:31.125341 140113106646848 conservation.py:464] 2 work filenames I0621 12:54:31.126219 139977373710144 run_docker.py:135] I0621 12:54:31.125793 140113106646848 parallel.py:46] Processing 2 inputs. I0621 12:54:31.126399 139977373710144 run_docker.py:135] I0621 12:54:31.125915 140113106646848 parallel.py:62] Sequential Mode. I0621 12:54:31.160443 139977373710144 run_docker.py:135] I0621 12:54:31.159958 140113106646848 conservation.py:152] HHblits'ing /mnt/Input/interim/external_feats/he/work/4heq_l_u.pdb-1-A.fa I0621 12:55:03.191800 139977373710144 run_docker.py:135] I0621 12:55:03.190688 140113106646848 conservation.py:238] For 1 profile HMMs generated from 4heq_l_u.pdb, spent 32.06 blitsing, 00.00 writing, and 32.06 overall. I0621 12:55:03.224250 139977373710144 run_docker.py:135] I0621 12:55:03.223448 140113106646848 conservation.py:152] HHblits'ing /mnt/Input/interim/external_feats/he/work/4heq_r_u.pdb-1-B.fa I0621 12:55:37.966540 139977373710144 run_docker.py:135] I0621 12:55:37.965222 140113106646848 conservation.py:238] For 1 profile HMMs generated from 4heq_r_u.pdb, spent 34.77 blitsing, 00.00 writing, and 34.77 overall. I0621 12:55:37.966913 139977373710144 run_docker.py:135] I0621 12:55:37.965721 140113106646848 deepinteract_utils.py:722] Starting postprocessing for all unprocessed pairs in /mnt/Input/interim/pairs I0621 12:55:37.967144 139977373710144 run_docker.py:135] I0621 12:55:37.965833 140113106646848 deepinteract_utils.py:729] Looking for all pairs in /mnt/Input/interim/pairs I0621 12:55:37.972153 139977373710144 run_docker.py:135] I0621 12:55:37.971457 140113106646848 deepinteract_utils.py:743] Found 1 work pair(s) in /mnt/Input/interim/pairs I0621 12:55:37.972460 139977373710144 run_docker.py:135] I0621 12:55:37.971827 140113106646848 parallel.py:46] Processing 1 inputs. I0621 12:55:37.972671 139977373710144 run_docker.py:135] I0621 12:55:37.971918 140113106646848 parallel.py:62] Sequential Mode. I0621 12:55:41.316108 139977373710144 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/vectors.py:357: RuntimeWarning: invalid value encountered in double_scalars I0621 12:55:41.316489 139977373710144 run_docker.py:135] c = (self other) / (n1 n2) I0621 12:55:41.316720 139977373710144 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/Bio/PDB/vectors.py:357: RuntimeWarning: invalid value encountered in double_scalars I0621 12:55:41.316918 139977373710144 run_docker.py:135] c = (self other) / (n1 n2) I0621 12:55:41.317103 139977373710144 run_docker.py:135] I0621 12:55:41.314721 140113106646848 dips_plus_utils.py:536] Normal vector missing for df0 residue 9 in chain A in file /mnt/Input/raw/he/4heq_l_u.pdb I0621 12:55:41.336150 139977373710144 run_docker.py:135] I0621 12:55:41.335281 140113106646848 dips_plus_utils.py:536] Normal vector missing for df0 residue 13 in chain A in file /mnt/Input/raw/he/4heq_l_u.pdb I0621 12:55:41.356255 139977373710144 run_docker.py:135] I0621 12:55:41.355384 140113106646848 dips_plus_utils.py:536] Normal vector missing for df0 residue 17 in chain A in file /mnt/Input/raw/he/4heq_l_u.pdb I0621 12:55:41.427843 139977373710144 run_docker.py:135] I0621 12:55:41.426913 140113106646848 dips_plus_utils.py:536] Normal vector missing for df0 residue 30 in chain A in file /mnt/Input/raw/he/4heq_l_u.pdb I0621 12:55:41.506287 139977373710144 run_docker.py:135] I0621 12:55:41.505459 140113106646848 dips_plus_utils.py:536] Normal vector missing for df0 residue 45 in chain A in file /mnt/Input/raw/he/4heq_l_u.pdb I0621 12:55:41.526054 139977373710144 run_docker.py:135] I0621 12:55:41.525439 140113106646848 dips_plus_utils.py:536] Normal vector missing for df0 residue 49 in chain A in file /mnt/Input/raw/he/4heq_l_u.pdb I0621 12:55:41.560204 139977373710144 run_docker.py:135] I0621 12:55:41.559483 140113106646848 dips_plus_utils.py:536] Normal vector missing for df0 residue 56 in chain A in file /mnt/Input/raw/he/4heq_l_u.pdb I0621 12:55:41.585425 139977373710144 run_docker.py:135] I0621 12:55:41.584762 140113106646848 dips_plus_utils.py:536] Normal vector missing for df0 residue 61 in chain A in file /mnt/Input/raw/he/4heq_l_u.pdb I0621 12:55:41.686717 139977373710144 run_docker.py:135] I0621 12:55:41.686072 140113106646848 dips_plus_utils.py:536] Normal vector missing for df0 residue 82 in chain A in file /mnt/Input/raw/he/4heq_l_u.pdb I0621 12:55:41.720789 139977373710144 run_docker.py:135] I0621 12:55:41.720090 140113106646848 dips_plus_utils.py:536] Normal vector missing for df0 residue 89 in chain A in file /mnt/Input/raw/he/4heq_l_u.pdb I0621 12:55:41.735666 139977373710144 run_docker.py:135] I0621 12:55:41.735008 140113106646848 dips_plus_utils.py:536] Normal vector missing for df0 residue 92 in chain A in file /mnt/Input/raw/he/4heq_l_u.pdb I0621 12:55:41.745175 139977373710144 run_docker.py:135] I0621 12:55:41.744497 140113106646848 dips_plus_utils.py:536] Normal vector missing for df0 residue 94 in chain A in file /mnt/Input/raw/he/4heq_l_u.pdb I0621 12:55:41.788900 139977373710144 run_docker.py:135] I0621 12:55:41.788190 140113106646848 dips_plus_utils.py:536] Normal vector missing for df0 residue 103 in chain A in file /mnt/Input/raw/he/4heq_l_u.pdb I0621 12:55:41.852835 139977373710144 run_docker.py:135] I0621 12:55:41.852125 140113106646848 dips_plus_utils.py:536] Normal vector missing for df0 residue 116 in chain A in file /mnt/Input/raw/he/4heq_l_u.pdb I0621 12:55:41.909060 139977373710144 run_docker.py:135] I0621 12:55:41.908362 140113106646848 dips_plus_utils.py:536] Normal vector missing for df0 residue 128 in chain A in file /mnt/Input/raw/he/4heq_l_u.pdb I0621 12:55:42.041210 139977373710144 run_docker.py:135] I0621 12:55:42.040462 140113106646848 dips_plus_utils.py:630] Normal vector missing for df1 residue 9 in chain B in file /mnt/Input/raw/he/4heq_r_u.pdb I0621 12:55:42.059900 139977373710144 run_docker.py:135] I0621 12:55:42.059195 140113106646848 dips_plus_utils.py:630] Normal vector missing for df1 residue 13 in chain B in file /mnt/Input/raw/he/4heq_r_u.pdb I0621 12:55:42.079119 139977373710144 run_docker.py:135] I0621 12:55:42.078433 140113106646848 dips_plus_utils.py:630] Normal vector missing for df1 residue 17 in chain B in file /mnt/Input/raw/he/4heq_r_u.pdb I0621 12:55:42.143947 139977373710144 run_docker.py:135] I0621 12:55:42.143125 140113106646848 dips_plus_utils.py:630] Normal vector missing for df1 residue 30 in chain B in file /mnt/Input/raw/he/4heq_r_u.pdb I0621 12:55:42.215802 139977373710144 run_docker.py:135] I0621 12:55:42.215100 140113106646848 dips_plus_utils.py:630] Normal vector missing for df1 residue 45 in chain B in file /mnt/Input/raw/he/4heq_r_u.pdb I0621 12:55:42.234920 139977373710144 run_docker.py:135] I0621 12:55:42.234243 140113106646848 dips_plus_utils.py:630] Normal vector missing for df1 residue 49 in chain B in file /mnt/Input/raw/he/4heq_r_u.pdb I0621 12:55:42.267936 139977373710144 run_docker.py:135] I0621 12:55:42.267218 140113106646848 dips_plus_utils.py:630] Normal vector missing for df1 residue 56 in chain B in file /mnt/Input/raw/he/4heq_r_u.pdb I0621 12:55:42.292104 139977373710144 run_docker.py:135] I0621 12:55:42.291366 140113106646848 dips_plus_utils.py:630] Normal vector missing for df1 residue 61 in chain B in file /mnt/Input/raw/he/4heq_r_u.pdb I0621 12:55:42.392189 139977373710144 run_docker.py:135] I0621 12:55:42.391432 140113106646848 dips_plus_utils.py:630] Normal vector missing for df1 residue 82 in chain B in file /mnt/Input/raw/he/4heq_r_u.pdb I0621 12:55:42.426449 139977373710144 run_docker.py:135] I0621 12:55:42.425676 140113106646848 dips_plus_utils.py:630] Normal vector missing for df1 residue 89 in chain B in file /mnt/Input/raw/he/4heq_r_u.pdb I0621 12:55:42.440944 139977373710144 run_docker.py:135] I0621 12:55:42.440204 140113106646848 dips_plus_utils.py:630] Normal vector missing for df1 residue 92 in chain B in file /mnt/Input/raw/he/4heq_r_u.pdb I0621 12:55:42.450548 139977373710144 run_docker.py:135] I0621 12:55:42.449811 140113106646848 dips_plus_utils.py:630] Normal vector missing for df1 residue 94 in chain B in file /mnt/Input/raw/he/4heq_r_u.pdb I0621 12:55:42.494798 139977373710144 run_docker.py:135] I0621 12:55:42.493852 140113106646848 dips_plus_utils.py:630] Normal vector missing for df1 residue 103 in chain B in file /mnt/Input/raw/he/4heq_r_u.pdb I0621 12:55:42.557198 139977373710144 run_docker.py:135] I0621 12:55:42.556405 140113106646848 dips_plus_utils.py:630] Normal vector missing for df1 residue 116 in chain B in file /mnt/Input/raw/he/4heq_r_u.pdb I0621 12:55:42.614418 139977373710144 run_docker.py:135] I0621 12:55:42.613722 140113106646848 dips_plus_utils.py:630] Normal vector missing for df1 residue 128 in chain B in file /mnt/Input/raw/he/4heq_r_u.pdb I0621 12:55:42.718224 139977373710144 run_docker.py:135] I0621 12:55:42.717459 140113106646848 deepinteract_utils.py:773] Imputing missing feature values for given inputs I0621 12:55:42.719177 139977373710144 run_docker.py:135] I0621 12:55:42.718771 140113106646848 parallel.py:46] Processing 31 inputs. I0621 12:55:42.719329 139977373710144 run_docker.py:135] I0621 12:55:42.718858 140113106646848 parallel.py:62] Sequential Mode. I0621 12:55:48.405303 139977373710144 run_docker.py:135] I0621 12:55:48.404334 140113106646848 lit_model_predict_docker.py:99] Loading complex for prediction, l_chain: /mnt/input_pdbs/4heq_l_u.pdb, r_chain: /mnt/input_pdbs/4heq_r_u.pdb I0621 12:55:49.322944 139977373710144 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/torchmetrics/utilities/prints.py:36: UserWarning: Metric
AUROCwill save all targets and predictions in buffer. For large datasets this may lead to large memory footprint. I0621 12:55:49.323281 139977373710144 run_docker.py:135] warnings.warn(*args, *kwargs) I0621 12:55:49.323480 139977373710144 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/torchmetrics/utilities/prints.py:36: UserWarning: MetricAveragePrecisionwill save all targets and predictions in buffer. For large datasets this may lead to large memory footprint. I0621 12:55:49.323687 139977373710144 run_docker.py:135] warnings.warn(args, **kwargs) I0621 12:55:49.323897 139977373710144 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/pytorch_lightning/trainer/connectors/accelerator_connector.py:792: UserWarning: You are running on single node with no parallelization, so distributed has no effect. I0621 12:55:49.324064 139977373710144 run_docker.py:135] rank_zero_warn("You are running on single node with no parallelization, so distributed has no effect.") I0621 12:55:49.324226 139977373710144 run_docker.py:135] GPU available: False, used: False I0621 12:55:49.324383 139977373710144 run_docker.py:135] TPU available: False, using: 0 TPU cores I0621 12:55:49.324540 139977373710144 run_docker.py:135] IPU available: False, using: 0 IPUs I0621 12:55:49.377713 139977373710144 run_docker.py:135] Setting the default backend to "pytorch". You can change it in the ~/.dgl/config.json file or export the DGLBACKEND environment variable. Valid options are: pytorch, mxnet, tensorflow (all lowercase) I0621 12:55:49.378072 139977373710144 run_docker.py:135] /opt/conda/lib/python3.8/site-packages/pytorch_lightning/trainer/data_loading.py:105: UserWarning: The dataloader, predict dataloader 0, does not have many workers which may be a bottleneck. Consider increasing the value of thenum_workersargument(try 64 which is the number of cpus on this machine) in theDataLoader` init to improve performance. I0621 12:55:49.378295 139977373710144 run_docker.py:135] rank_zero_warn( I0621 12:55:50.089681 139977373710144 run_docker.py:135] I0621 12:55:50.088823 140113106646848 lit_model_predict_docker.py:298] Saved predicted contact probability map for 4heq as /mnt/input_pdbs/4heq_contact_prob_map.npy I0621 12:55:50.092932 139977373710144 run_docker.py:135] I0621 12:55:50.092391 140113106646848 lit_model_predict_docker.py:307] Saved learned node representations for the first chain graph of 4heq as /mnt/input_pdbs/4heq_graph1_node_feats.npy I0621 12:55:50.093075 139977373710144 run_docker.py:135] I0621 12:55:50.092499 140113106646848 lit_model_predict_docker.py:308] Saved learned edge representations for the first chain graph of 4heq as /mnt/input_pdbs/4heq_graph1_edge_feats.npy I0621 12:55:50.093154 139977373710144 run_docker.py:135] I0621 12:55:50.092547 140113106646848 lit_model_predict_docker.py:309] Saved learned node representations for the second chain graph of 4heq as /mnt/input_pdbs/4heq_graph2_node_feats.npy I0621 12:55:50.093222 139977373710144 run_docker.py:135] I0621 12:55:50.092598 140113106646848 lit_model_predict_docker.py:310] Saved learned edge representations for the second chain graph of 4heq as /mnt/input_pdbs/4heq_graph2_edge_feats.npy Predicting: 100%|██████████| 1/1 [00:00<00:00, 1.41it/s]Predicting: 0it [00:00, ?it/s]This results in the final generated dill file not working properly