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lost some output files #1023

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xjhzjucas opened this issue Oct 6, 2024 · 0 comments
Open

lost some output files #1023

xjhzjucas opened this issue Oct 6, 2024 · 0 comments

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@xjhzjucas
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Hi developer, thank you for this nice tool!
I put 300 protein sequences into AF2, and some of them were run successfully, however some of them didn't get all output files. I used the same commond to run them.
For example, one specific protein seq was put into AF2 and output files were only features.pkl and msas, no pdb files.
error was like this :

Sun Oct  6 14:43:23 2024
+-----------------------------------------------------------------------------+
| NVIDIA-SMI 525.60.13    Driver Version: 525.60.13    CUDA Version: 12.0     |
|-------------------------------+----------------------+----------------------+
| GPU  Name        Persistence-M| Bus-Id        Disp.A | Volatile Uncorr. ECC |
| Fan  Temp  Perf  Pwr:Usage/Cap|         Memory-Usage | GPU-Util  Compute M. |
|                               |                      |               MIG M. |
|===============================+======================+======================|
|   0  Tesla V100-SXM2...  Off  | 00000000:19:00.0 Off |                    0 |
| N/A   32C    P0    40W / 300W |      0MiB / 32768MiB |      0%      Default |
|                               |                      |                  N/A |
+-------------------------------+----------------------+----------------------+

+-----------------------------------------------------------------------------+
| Processes:                                                                  |
|  GPU   GI   CI        PID   Type   Process name                  GPU Memory |
|        ID   ID                                                   Usage      |
|=============================================================================|
|  No running processes found                                                 |
+-----------------------------------------------------------------------------+
I1006 14:43:28.010590 23380422018880 templates.py:857] Using precomputed obsolete pdbs /opt/app/alphafold-2.2.0/datax/pdb_mmcif/obsolete.dat.
I1006 14:43:28.221988 23380422018880 xla_bridge.py:353] Unable to initialize backend 'tpu_driver': NOT_FOUND: Unable to find driver in registry given worker:
I1006 14:43:28.442123 23380422018880 xla_bridge.py:353] Unable to initialize backend 'rocm': NOT_FOUND: Could not find registered platform with name: "rocm". Available platform names are: Interpreter Host CUDA
I1006 14:43:28.442796 23380422018880 xla_bridge.py:353] Unable to initialize backend 'tpu': module 'jaxlib.xla_extension' has no attribute 'get_tpu_client'
I1006 14:43:28.443102 23380422018880 xla_bridge.py:353] Unable to initialize backend 'plugin': xla_extension has no attributes named get_plugin_device_client. Compile TensorFlow with //tensorflow/compiler/xla/python:enable_plugin_device set to true (defaults to false) to enable this.
I1006 14:43:31.975059 23380422018880 run_alphafold.py:376] Have 5 models: ['model_1_pred_0', 'model_2_pred_0', 'model_3_pred_0', 'model_4_pred_0', 'model_5_pred_0']
I1006 14:43:31.975301 23380422018880 run_alphafold.py:393] Using random seed 587468596677303199 for the data pipeline
I1006 14:43:31.975554 23380422018880 run_alphafold.py:161] Predicting rdp_gene_799.part_201
I1006 14:43:31.978374 23380422018880 jackhmmer.py:133] Launching subprocess "/opt/app/anaconda3/envs/alphafold/bin/jackhmmer -o /dev/null -A /tmp/tmpsv9rdwy6/output.sto --noali --F1 0.0005 --F2 5e-05 --F3 5e-07 --incE 0.0001 -E 0.0001 --cpu 8 -N 1 /home/u12317037/rdp_gene_799/rdp_gene_799.faa.split/rdp_gene_799.part_201.faa /opt/app/alphafold-2.2.0/datax/uniref90/uniref90.fasta"
I1006 14:43:32.004555 23380422018880 utils.py:36] Started Jackhmmer (uniref90.fasta) query
I1006 15:02:23.145329 23380422018880 utils.py:40] Finished Jackhmmer (uniref90.fasta) query in 1131.141 seconds
I1006 15:02:23.196874 23380422018880 jackhmmer.py:133] Launching subprocess "/opt/app/anaconda3/envs/alphafold/bin/jackhmmer -o /dev/null -A /tmp/tmpmiu8_qhp/output.sto --noali --F1 0.0005 --F2 5e-05 --F3 5e-07 --incE 0.0001 -E 0.0001 --cpu 8 -N 1 /home/u12317037/rdp_gene_799/rdp_gene_799.faa.split/rdp_gene_799.part_201.faa /opt/app/alphafold-2.2.0/datax/mgnify/mgy_clusters_2018_12.fa"
I1006 15:02:23.221295 23380422018880 utils.py:36] Started Jackhmmer (mgy_clusters_2018_12.fa) query
I1006 15:22:53.923045 23380422018880 utils.py:40] Finished Jackhmmer (mgy_clusters_2018_12.fa) query in 1230.701 seconds
I1006 15:22:54.644595 23380422018880 hhsearch.py:85] Launching subprocess "/opt/app/anaconda3/envs/alphafold/bin/hhsearch -i /tmp/tmpc0el6jyi/query.a3m -o /tmp/tmpc0el6jyi/output.hhr -maxseq 1000000 -d /opt/app/alphafold-2.2.0/datax/pdb70/pdb70"
I1006 15:22:54.675355 23380422018880 utils.py:36] Started HHsearch query
I1006 15:29:19.083334 23380422018880 utils.py:40] Finished HHsearch query in 384.408 seconds
I1006 15:29:19.919570 23380422018880 jackhmmer.py:133] Launching subprocess "/opt/app/anaconda3/envs/alphafold/bin/jackhmmer -o /dev/null -A /tmp/tmpylar48de/output.sto --noali --F1 0.0005 --F2 5e-05 --F3 5e-07 --incE 0.0001 -E 0.0001 --cpu 8 -N 1 /home/u12317037/rdp_gene_799/rdp_gene_799.faa.split/rdp_gene_799.part_201.faa /opt/app/alphafold-2.2.0/datax/small_bfd/bfd-first_non_consensus_sequences.fasta"
I1006 15:29:19.944685 23380422018880 utils.py:36] Started Jackhmmer (bfd-first_non_consensus_sequences.fasta) query
I1006 15:35:38.325978 23380422018880 utils.py:40] Finished Jackhmmer (bfd-first_non_consensus_sequences.fasta) query in 378.381 seconds
I1006 15:35:38.824839 23380422018880 templates.py:878] Searching for template for: MPDFFINNSRAQFNQDEETIKKMNQSSKSYWDEQNARMQQKNTEYVEDLQRYSVNIPQEQYNIIKDAIANAEIPEDEAYRWAAAMELNNQYKIPIQSAYQNLESINAALWGEQYDFTPKTNFKAIVDNGRIGKNTLKMGEIGNKIMLAESKLNGGAMFYGEEELQALYDEYAKLEQENASLADNQARPFVIEALKFGAQSVPFTGAVIGASALGTLLAPGVGTAAGFATSMANASGLQYIKLREAGSSQDAALGLSLVSGGLQALVEVSLGNVAGALGKKTVGDMAGKAVSETITGNLFKRLTYDGTFKTLALRLGKEYVKENFEEGLEEVIQDLIEKGTDALAAELGNYEITGLDAKTIARDAWENFRGGVMGSLVLGLPTSAIKVNADVKEFTKVRQLSEVVESQEMFNALTDESPIFRDMTTQEKREAQKTSWENGQARKEARATEDAKQIAEGLDAGEGAEERKVTYDENGNEIEEETAESVARDEKGRLFVQDQEYKDDDGKVTGGQFWAGNAEQSGKEAGNRYGYITYSQDENGDITIDTFKMTKGREGLREEMFDQFAQEHPDVKIEWNAIGSDTQAIKQSLIDANPSGAKNGLSRYTTESLNDPNNAARKRAMAEIGNVIHNIEEVRDTNGNLVRDENGRVKVKRTQLTQQQLAAAVSFVELGAKTISGLSLEEYMNKSYENGRFFGSTQDFINKTLAQGERVDNKNGGIRQGTAQQGWQKDGMIIKNVIYAAENADFATFVHEVAHGFRAQLSGQMLADAEAAFGVKDGNWDGLSKYKYADGSYMTYEEAFAYYAQDYFITGKAPTPQMENIFKRLAQFLAEAYSRLRKHLDISPEISKVFNELLADDDSVYNKALKAAREQENEYRANLKRQAEEAKATKEAEEQEAQKQAELEKEEAGEYTDYEQETTQQSAEEIEEQLEESNEEETGNAIDNALGNLELTDETKNQVAETLKDPTTTTPEKANAIVDAAGEQFDLFQRQEGLLYQLAGEPSIRRMAESEEKRRILADLDAAVNLEKIYKDFSAETRALRIRRATGWERDANGQWKYELDDSVNRIKGGAVLNGLMRTSPELLSQASKKAMLNLGDIYDAPELYKVFPYMKNVRVSFYSDPNAFRAVLTPEGIKVNMRYLQGIDGEKGLKGALVHEIQHVVQAMEYAESKGLQGADIEQLYNDMMDAMQAAGERKYDYDLTSLQQGLEAYMNDYGEIEARNVARRILMNPDKRRNTTLASTEDVKRQPKLLFQAVKNEIKADEMEGLKEITDDEFSKIADNLYSATIDYKSIPNLVLLPNVNESLKKELGIKGNLYITKNRFTHTNPKRKHAHGEQDFRLDEYKSIPKMIRNATYALQENNSKYNSFFITELDKQDNTKVNVVIFDEDKNGNLLTTIKKLPLTELRSGSYKIVGTGVEPAISHTVRVSPTALASSPNISNNTTLKSSLSNILFQEERDDEYRQAVESGDTEKAMQMLAEEAERKGYTTPEDYKDAHSAPVAQIEKKDFKNLEKLQELNDESWDVNLYGIANGIMNVDPDYFVHPNRFGYGDNVSMESAAAVNKVMREIQNGNEDATIKVYRAVPNNIKGNQLETSGQWVSPSREYAENHGLARFGEGEYRIIEQEVPATDLWFDFGDIKEWGYDDGTTNNVYKNTENNRKLFEITYDENGDLIPLSKRFDQNNPSILYQIAGEIGAQNLDDAETQEGVSRMQNLAIAKEMEAEGKDTKAIRLATGWEKGADGKWKYEIPDGVLEIPTQGQEVNSEGKFVPRKQKEGYLREYYKSDELYKAYPDLKYAWLRFVPLDVEGRAYYAGGDKIDLNINLLNYNQEDEIKSTIIHEIQHLIQRIEGFAKGGSEDTVRQKANDTIHYSLEEKQQSNWYPFYLREVGAADFALDKKRMMKNPELIKKTGYWQAHSWAVPKKGTKDYTDYLYDRINGWMQETEAAIVRNDGYGEVLKNYYTKSDEELKKIKARNKYQADKYKDLYFKINNLESKRKEYDQLTNYELYNRLAGEVEARNVETRMNFTPEQRLNTLIAATEDVAPKDKIILFQAAYHGSGASFDKFDTENYGLSGEGAMTFGYGTYLTDNEDIARSYAERQGNKGNIYGNYEDIFLQMYRQLRESEFFDEQKERWEASLKKSLEDKYGQINKVVIESLLKALSEITKDNVNKWDNVISKILENNTPLTHNLYTVEIPNADYLKWDETVSNEMLERIAPVYAEELYNRWLNDSEWQDVNYTEQQKEGIRKHFGEEILNTVKDDPTYDGAQLYKYIQRKLEYYDKDNAAKLTSKLLSKAGIVGMKYPAGTIHGNGNGAYNYVIFNDDDAKIVDKLLFQTNAELMQEAQGFESWQEFMDYCETFHVGVDEVSPIPSEADAQWYQSFWETAHGYQTEEEKNERAVQEKAAREDSTAPAMDALFKTYIRSNPEMLDDFLHEVARIDAIDLDSEEWRNAADEQDAAERDRIVQLKDAIKIIMVDFNWQSAMNRIQGGGEISEGLRKRLMGEMTDTMKARDFRALYAEVMEDAQYAVDEEDTTSAILTRKLQKNPKRYYDIVKPSEDISKMSPEKRKRIAEAMANRDIANKIRNGSLKLDDELDNYIKSLDRQIKDLQKQLNEQEIETKADYQRIADAERRRLLKLHEELLIAKSKVTQKNSDTARKINRGLKITEKYKRESQNLQANYDELFRKFNDLKIGIQITAEVQAALDRQEQVATVRENLNAKQKDRNLMAEVKKMRINLVKKTMRRVPFNRIDYENAKTIIAIQRMLEPNLIGGVNRFIGIDSPFLRGVISQVVTDSDYKEKLLNYLAKNSRSSEAFANFKKKLAELKSIKDFDSWTAKERKAAIKYLPKENWVRDLNLKELAKEREESIDLDIDTEEYSRPVYDEKTGEPKTYKDADGLEHNVTETAFRLRYSDELGQLVKDAVGADMFDRIVNRPFSEWTTEELEQLAQRIDELYTEGRDLLAAKNEAKKREAESIRKRVEDAIKETGIVINDDDTPEEKERKQKEINKILNLNSDLKGTEAGKDKGIKAKLDRLIHGYSDMNVLRFARMLDNQSEGENVYMLYRKEDECYNNKTRSINNRARSINEIMKANNITEGDLAMSIPVPSLNTEFTVDELLYFLAADKDYAEDETKLAKGLFGLDANDDWAATSRNAVMFGNMMSDTASQEQKEKWVELDKQMKEALENDTLTTEQKQLDALGRLDKTPGTSAYISYCHAKWETVLGAANSFIAEHPEYKALMEAIEADYASQYERMNEVSINEFNMPVHRVKAYVPLVRRESNGDTNVNQVKEDLLGAYGAASGKQWVNKGMTQRRVNISPLNQKPVQTGLFATWGSSVDRTEHFIAYAPYVRQLNAIYKSRDASYTRRFIESRYGKNAVKYLDDYINEVANPNAGKVREAGSEWLHTLRGRTAPAYLGWKFSAIVKQGLTSPWPYMQFVNPAEYASAALECTRKGTYDAIREKSVFMNNRVMDPMNELVEEMADEGKTKFDRALGKFGKKGMQGLEWIDWVCVAPGWLACYKKEYAKLQRASEARYDAKMEELRERNMYTDIGTSEYMTPDQMEAQARKEIEEDIETEAVRYADDCTRQCQPSSRAADLAPLFKNSSEAMKAFLQFQTSLNVIWQNIRYDMPYAVRNKQFNRIVGTIMGYVFAGIFMNSVMDGVTSGADDDDDKELQALRNLIFYSTTQFTDAVPIMGSELTNMMDQVITGKRGFMNSGTDMTPSATKMLSAFTNATKGNWQKAAELSAEAIGMAAGAPVSGIKEINKLLGKPLDEGDINLLRGLSDVYGVAGDILEE
I1006 15:35:38.825432 23380422018880 templates.py:718] hit 4uet_A did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.029218215319821005.
I1006 15:35:38.825563 23380422018880 templates.py:912] Skipped invalid hit 4UET_A NEMATODE FATTY ACID RETINOID BINDING; RETINOL-BINDING PROTEIN, FATTY ACID BINDING; NMR {NECATOR AMERICANUS}, error: None, warning: None
I1006 15:35:38.825635 23380422018880 templates.py:718] hit 4xcp_A did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.029218215319821005.
I1006 15:35:38.825684 23380422018880 templates.py:912] Skipped invalid hit 4XCP_A Fatty acid and retinol binding; Fatty acid retinol binding, retinol-binding; HET: PLM, MSE; 2.14A {Necator americanus}, error: None, warning: None
I1006 15:35:38.825747 23380422018880 templates.py:718] hit 5ijn_Z did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.022111081863648328.
I1006 15:35:38.825793 23380422018880 templates.py:912] Skipped invalid hit 5IJN_Z NUCLEAR PORE COMPLEX PROTEIN NUP155; Nuclear pore complex, Nucleocytoplasmic transport; 21.4A {Homo sapiens}, error: None, warning: None
I1006 15:35:38.825848 23380422018880 templates.py:718] hit 2w9y_A did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.029744669649907872.
I1006 15:35:38.825890 23380422018880 templates.py:912] Skipped invalid hit 2W9Y_A FATTY ACID/RETINOL BINDING PROTEIN PROTEIN; LIPID TRANSPORT, FATTY ACID AND; HET: CSX, SO4; 1.8A {CAENORHABDITIS ELEGANS}, error: None, warning: None
I1006 15:35:38.825940 23380422018880 templates.py:718] hit 2l0r_A did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.024216899183995787.
I1006 15:35:38.825980 23380422018880 templates.py:912] Skipped invalid hit 2L0R_A Lethal factor (E.C.3.4.24.83); protein, Anthrax Lethal Factor, catalytic; NMR {Bacillus anthracis}, error: None, warning: None
I1006 15:35:38.826032 23380422018880 templates.py:718] hit 4dv8_A did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.024480126349039222.
I1006 15:35:38.826073 23380422018880 templates.py:912] Skipped invalid hit 4DV8_A Lethal factor (E.C.3.4.24.83); endopeptidase, Zinc dependent, HYDROLASE; HET: 0LX; 1.632A {Bacillus anthracis}, error: None, warning: None
I1006 15:35:38.826123 23380422018880 templates.py:718] hit 5ijn_S did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.024743353514082654.
I1006 15:35:38.826163 23380422018880 templates.py:912] Skipped invalid hit 5IJN_S NUCLEAR PORE COMPLEX PROTEIN NUP155; Nuclear pore complex, Nucleocytoplasmic transport; 21.4A {Homo sapiens}, error: None, warning: None
I1006 15:35:38.826213 23380422018880 templates.py:718] hit 6fpc_C did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.022637536193735194.
I1006 15:35:38.826254 23380422018880 templates.py:912] Skipped invalid hit 6FPC_C PPEP-2; Endopeptidase, Metalloprotease, Zinc, HYDROLASE; HET: CD, SO4; 1.75A {Paenibacillus alvei}, error: None, warning: None
I1006 15:35:38.826303 23380422018880 templates.py:718] hit 6r4z_A did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.021847854698604896.
I1006 15:35:38.826353 23380422018880 templates.py:912] Skipped invalid hit 6R4Z_A Pro-Pro endopeptidase-1, ACE-GLU-VAL-ASN-PRO; Pro-Pro endopeptidase 1, zinc metallopeptidase; 1.052A {Peptoclostridium difficile}, error: None, warning: None
I1006 15:35:38.826405 23380422018880 templates.py:718] hit 5ijn_Z did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.016583311397736247.
I1006 15:35:38.826445 23380422018880 templates.py:912] Skipped invalid hit 5IJN_Z NUCLEAR PORE COMPLEX PROTEIN NUP155; Nuclear pore complex, Nucleocytoplasmic transport; 21.4A {Homo sapiens}, error: None, warning: None
I1006 15:35:38.826494 23380422018880 templates.py:718] hit 5ijn_S did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.020005264543300868.
I1006 15:35:38.826535 23380422018880 templates.py:912] Skipped invalid hit 5IJN_S NUCLEAR PORE COMPLEX PROTEIN NUP155; Nuclear pore complex, Nucleocytoplasmic transport; 21.4A {Homo sapiens}, error: None, warning: None
I1006 15:35:38.826584 23380422018880 templates.py:718] hit 6ait_A did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.013161358252171624.
I1006 15:35:38.826625 23380422018880 templates.py:912] Skipped invalid hit 6AIT_A Beta-barrel assembly-enhancing protease (E.C.3.4.-.-); hydrolase, METAL BINDING PROTEIN; HET: TRS; 2.598A {Escherichia coli (strain K12)}, error: None, warning: None
I1006 15:35:38.826673 23380422018880 templates.py:718] hit 6ait_D did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.013161358252171624.
I1006 15:35:38.826713 23380422018880 templates.py:912] Skipped invalid hit 6AIT_D Beta-barrel assembly-enhancing protease (E.C.3.4.-.-); hydrolase, METAL BINDING PROTEIN; HET: TRS; 2.598A {Escherichia coli (strain K12)}, error: None, warning: None
I1006 15:35:38.826769 23380422018880 templates.py:718] hit 4pkv_A did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.011318768096867597.
I1006 15:35:38.826810 23380422018880 templates.py:912] Skipped invalid hit 4PKV_A Anthrax toxin lethal factor (E.C.3.4.24.83); Anthrax toxin, lethal factor, metalloproteinase; HET: 30R; 2.5A {Bacillus anthracis}, error: None, warning: None
I1006 15:35:38.826858 23380422018880 templates.py:718] hit 1j7n_A did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.011055540931824164.
I1006 15:35:38.826898 23380422018880 templates.py:912] Skipped invalid hit 1J7N_A Lethal Factor precursor; Anthrax, Lethal Toxin, Lethal Factor; HET: SO4; 2.3A {Bacillus anthracis} SCOP: d.166.1.1, d.92.1.14, error: None, warning: None
I1006 15:35:38.826946 23380422018880 templates.py:718] hit 1jky_A did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.011055540931824164.
I1006 15:35:38.826985 23380422018880 templates.py:912] Skipped invalid hit 1JKY_A Lethal Factor precursor/mitogen-activated protein kinase; Lethal Toxin, Mek2, MAPKK, Uncleaved; 3.9A {Bacillus anthracis} SCOP: d.92.1.14, d.166.1.1, error: None, warning: None
I1006 15:35:38.827032 23380422018880 templates.py:718] hit 6ait_A did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.010792313766780732.
I1006 15:35:38.827072 23380422018880 templates.py:912] Skipped invalid hit 6AIT_A Beta-barrel assembly-enhancing protease (E.C.3.4.-.-); hydrolase, METAL BINDING PROTEIN; HET: TRS; 2.598A {Escherichia coli (strain K12)}, error: None, warning: None
I1006 15:35:38.827118 23380422018880 templates.py:718] hit 6ait_D did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.010792313766780732.
I1006 15:35:38.827157 23380422018880 templates.py:912] Skipped invalid hit 6AIT_D Beta-barrel assembly-enhancing protease (E.C.3.4.-.-); hydrolase, METAL BINDING PROTEIN; HET: TRS; 2.598A {Escherichia coli (strain K12)}, error: None, warning: None
I1006 15:35:38.827205 23380422018880 templates.py:718] hit 3c37_A did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.011055540931824164.
I1006 15:35:38.827251 23380422018880 templates.py:912] Skipped invalid hit 3C37_A Peptidase, M48 family; Q74D82, GsR143A, Peptidase, M48 family; HET: PEG; 1.7A {Geobacter sulfurreducens PCA}, error: None, warning: None
I1006 15:35:38.827302 23380422018880 templates.py:718] hit 4il3_B did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.011055540931824164.
I1006 15:35:38.827342 23380422018880 templates.py:912] Skipped invalid hit 4IL3_B Ste24p (E.C.3.4.24.84); membrane protein, alpha helical, CaaX; 3.102A {Saccharomyces mikatae}, error: None, warning: None
I1006 15:35:38.827389 23380422018880 templates.py:718] hit 6gw6_A did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.008949723611476704.
I1006 15:35:38.827429 23380422018880 templates.py:912] Skipped invalid hit 6GW6_A Toxin, Antitoxin; Toxin antitoxin type II system; HET: GOL, IMD; 2.205A {Pseudomonas putida KT2440}, error: None, warning: None
I1006 15:35:38.827477 23380422018880 templates.py:718] hit 6mdx_A did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.009212950776520137.
I1006 15:35:38.827516 23380422018880 templates.py:912] Skipped invalid hit 6MDX_A SprT-like domain-containing protein Spartan/DNA Complex; DPC repair, protease, DNA BINDING; HET: MSE, PGE, FLC, MLZ; 1.55A {Homo sapiens}, error: None, warning: None
I1006 15:35:38.827564 23380422018880 templates.py:718] hit 4qhf_A did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.008686496446433272.
I1006 15:35:38.827603 23380422018880 templates.py:912] Skipped invalid hit 4QHF_A Uncharacterized protein MJ1213; Minigluzincin, Proteolytic enzyme, HYDROLASE; 2.1A {Methanocaldococcus jannaschii}, error: None, warning: None
I1006 15:35:38.827650 23380422018880 templates.py:718] hit 6mdw_A did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.008949723611476704.
I1006 15:35:38.827689 23380422018880 templates.py:912] Skipped invalid hit 6MDW_A SprT-like domain-containing protein Spartan; DPC repair protease, DNA BINDING; HET: ADP, FLC, MLZ; 1.5A {Homo sapiens}, error: None, warning: None
I1006 15:35:38.827741 23380422018880 templates.py:718] hit 4qhj_B did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.008686496446433272.
I1006 15:35:38.827782 23380422018880 templates.py:912] Skipped invalid hit 4QHJ_B Uncharacterized protein MJ1213; Minigluzincin, Proteolytic enzyme, HYDROLASE; HET: ACT; 1.75A {Methanocaldococcus jannaschii}, error: None, warning: None
I1006 15:35:38.827829 23380422018880 templates.py:718] hit 4jix_A did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.008160042116346407.
I1006 15:35:38.827868 23380422018880 templates.py:912] Skipped invalid hit 4JIX_A Uncharacterized protein MJ0123; Hydrolase, Metallopeptidase Zymogen, Minigluzincin; HET: GOL, SO4; 2.0A {Methanocaldococcus jannaschii}, error: None, warning: None
I1006 15:35:38.827916 23380422018880 templates.py:718] hit 3cqb_A did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.008686496446433272.
I1006 15:35:38.827955 23380422018880 templates.py:912] Skipped invalid hit 3CQB_A Probable protease htpX homolog (E.C.3.4.24.-); Heat shock protein HtpX domain; HET: EDO; 1.86A {Vibrio parahaemolyticus RIMD 2210633}, error: None, warning: None
I1006 15:35:38.828003 23380422018880 templates.py:718] hit 3kwv_F did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.0047380889707817845.
I1006 15:35:38.828042 23380422018880 templates.py:912] Skipped invalid hit 3KWV_F Protective antigen PA-63, Lethal factor; Bacillus anthracis, protective antigen, lethal; 3.101A {Bacillus anthracis}, error: None, warning: None
I1006 15:35:38.828089 23380422018880 templates.py:718] hit 3lum_C did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.003421953145564622.
I1006 15:35:38.828135 23380422018880 templates.py:912] Skipped invalid hit 3LUM_C Ulilysin (E.C.3.4.24.-); metallopeptidase, hydrolase, metal ion binding; HET: VAL, ARG, CA, GOL; 1.7A {Methanosarcina acetivorans}, error: None, warning: None
I1006 15:35:38.828185 23380422018880 templates.py:718] hit 2cki_B did not pass prefilter: Proportion of residues aligned to query too small. Align ratio: 0.003421953145564622.
I1006 15:35:38.828225 23380422018880 templates.py:912] Skipped invalid hit 2CKI_B ULILYSIN; METALLOPROTEASE, HYDROLASE; HET: VAL, GOL, MSE, ARG; 1.7A {METHANOSARCINA ACETIVORANS}, error: None, warning: None
I1006 15:35:39.592017 23380422018880 pipeline.py:234] Uniref90 MSA size: 493 sequences.
I1006 15:35:39.592266 23380422018880 pipeline.py:235] BFD MSA size: 582 sequences.
I1006 15:35:39.592322 23380422018880 pipeline.py:236] MGnify MSA size: 501 sequences.
I1006 15:35:39.592370 23380422018880 pipeline.py:237] Final (deduplicated) MSA size: 1401 sequences.
I1006 15:35:39.592804 23380422018880 pipeline.py:239] Total number of templates (NB: this can include bad templates and is later filtered to top 4): 0.
I1006 15:35:39.671825 23380422018880 run_alphafold.py:190] Running model model_1_pred_0 on rdp_gene_799.part_201
I1006 15:35:45.916054 23380422018880 model.py:165] Running predict with shape(feat) = {'aatype': (4, 3799), 'residue_index': (4, 3799), 'seq_length': (4,), 'template_aatype': (4, 4, 3799), 'template_all_atom_masks': (4, 4, 3799, 37), 'template_all_atom_positions': (4, 4, 3799, 37, 3), 'template_sum_probs': (4, 4, 1), 'is_distillation': (4,), 'seq_mask': (4, 3799), 'msa_mask': (4, 508, 3799), 'msa_row_mask': (4, 508), 'random_crop_to_size_seed': (4, 2), 'template_mask': (4, 4), 'template_pseudo_beta': (4, 4, 3799, 3), 'template_pseudo_beta_mask': (4, 4, 3799), 'atom14_atom_exists': (4, 3799, 14), 'residx_atom14_to_atom37': (4, 3799, 14), 'residx_atom37_to_atom14': (4, 3799, 37), 'atom37_atom_exists': (4, 3799, 37), 'extra_msa': (4, 5120, 3799), 'extra_msa_mask': (4, 5120, 3799), 'extra_msa_row_mask': (4, 5120), 'bert_mask': (4, 508, 3799), 'true_msa': (4, 508, 3799), 'extra_has_deletion': (4, 5120, 3799), 'extra_deletion_value': (4, 5120, 3799), 'msa_feat': (4, 508, 3799, 49), 'target_feat': (4, 3799, 22)}
2024-10-06 15:37:57.878654: W external/org_tensorflow/tensorflow/tsl/framework/bfc_allocator.cc:290] Allocator (GPU_0_bfc) ran out of memory trying to allocate 6.90GiB with freed_by_count=0. The caller indicates that this is not a failure, but this may mean that there could be performance gains if more memory were available.
/opt/app/alphafold-2.2.4/alphafold/model/mapping.py:50: FutureWarning: jax.tree_flatten is deprecated, and will be removed in a future release. Use jax.tree_util.tree_flatten instead.
  values_tree_def = jax.tree_flatten(values)[1]
/opt/app/alphafold-2.2.4/alphafold/model/mapping.py:54: FutureWarning: jax.tree_unflatten is deprecated, and will be removed in a future release. Use jax.tree_util.tree_unflatten instead.
  return jax.tree_unflatten(values_tree_def, flat_axes)
/opt/app/alphafold-2.2.4/alphafold/model/mapping.py:129: FutureWarning: jax.tree_flatten is deprecated, and will be removed in a future release. Use jax.tree_util.tree_flatten instead.
  flat_sizes = jax.tree_flatten(in_sizes)[0]
Traceback (most recent call last):
  File "/opt/app/alphafold-2.2.4/run_alphafold.py", line 422, in <module>
    app.run(main)
  File "/opt/app/anaconda3/envs/alphafold/lib/python3.8/site-packages/absl/app.py", line 312, in run
    _run_main(main, args)
  File "/opt/app/anaconda3/envs/alphafold/lib/python3.8/site-packages/absl/app.py", line 258, in _run_main
    sys.exit(main(argv))
  File "/opt/app/alphafold-2.2.4/run_alphafold.py", line 398, in main
    predict_structure(
  File "/opt/app/alphafold-2.2.4/run_alphafold.py", line 198, in predict_structure
    prediction_result = model_runner.predict(processed_feature_dict,
  File "/opt/app/alphafold-2.2.4/alphafold/model/model.py", line 167, in predict
    result = self.apply(self.params, jax.random.PRNGKey(random_seed), feat)
  File "/opt/app/anaconda3/envs/alphafold/lib/python3.8/site-packages/jax/_src/traceback_util.py", line 162, in reraise_with_filtered_traceback
    return fun(*args, **kwargs)
  File "/opt/app/anaconda3/envs/alphafold/lib/python3.8/site-packages/jax/_src/api.py", line 622, in cache_miss
    execute = dispatch._xla_call_impl_lazy(fun_, *tracers, **params)
  File "/opt/app/anaconda3/envs/alphafold/lib/python3.8/site-packages/jax/_src/dispatch.py", line 236, in _xla_call_impl_lazy
    return xla_callable(fun, device, backend, name, donated_invars, keep_unused,
  File "/opt/app/anaconda3/envs/alphafold/lib/python3.8/site-packages/jax/linear_util.py", line 303, in memoized_fun
    ans = call(fun, *args)
  File "/opt/app/anaconda3/envs/alphafold/lib/python3.8/site-packages/jax/_src/dispatch.py", line 359, in _xla_callable_uncached
    return lower_xla_callable(fun, device, backend, name, donated_invars, False,
  File "/opt/app/anaconda3/envs/alphafold/lib/python3.8/site-packages/jax/_src/dispatch.py", line 996, in compile
    self._executable = XlaCompiledComputation.from_xla_computation(
  File "/opt/app/anaconda3/envs/alphafold/lib/python3.8/site-packages/jax/_src/dispatch.py", line 1194, in from_xla_computation
    compiled = compile_or_get_cached(backend, xla_computation, options,
  File "/opt/app/anaconda3/envs/alphafold/lib/python3.8/site-packages/jax/_src/dispatch.py", line 1077, in compile_or_get_cached
    return backend_compile(backend, serialized_computation, compile_options,
  File "/opt/app/anaconda3/envs/alphafold/lib/python3.8/site-packages/jax/_src/profiler.py", line 314, in wrapper
    return func(*args, **kwargs)
  File "/opt/app/anaconda3/envs/alphafold/lib/python3.8/site-packages/jax/_src/dispatch.py", line 1012, in backend_compile
    return backend.compile(built_c, compile_options=options)
jax._src.traceback_util.UnfilteredStackTrace: jaxlib.xla_extension.XlaRuntimeError: RESOURCE_EXHAUSTED: Out of memory while trying to allocate 7406166528 bytes.

The stack trace below excludes JAX-internal frames.
The preceding is the original exception that occurred, unmodified.

--------------------

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/opt/app/alphafold-2.2.4/run_alphafold.py", line 422, in <module>
    app.run(main)
  File "/opt/app/anaconda3/envs/alphafold/lib/python3.8/site-packages/absl/app.py", line 312, in run
    _run_main(main, args)
  File "/opt/app/anaconda3/envs/alphafold/lib/python3.8/site-packages/absl/app.py", line 258, in _run_main
    sys.exit(main(argv))
  File "/opt/app/alphafold-2.2.4/run_alphafold.py", line 398, in main
    predict_structure(
  File "/opt/app/alphafold-2.2.4/run_alphafold.py", line 198, in predict_structure
    prediction_result = model_runner.predict(processed_feature_dict,
  File "/opt/app/alphafold-2.2.4/alphafold/model/model.py", line 167, in predict
    result = self.apply(self.params, jax.random.PRNGKey(random_seed), feat)
jaxlib.xla_extension.XlaRuntimeError: RESOURCE_EXHAUSTED: Out of memory while trying to allocate 7406166528 bytes.

How can I deal with this? Thank you so much!
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