I have followed the steps in the tutorial and done everything as directed in it but getting an error on running the example command. i have gone through the previous issues reported regarding it but am confused what to do. Kindly help what should I do to run it successfully. I am providing below the command log and the command i passed. Please help!!
(RFAA) kinshuk@kinshuk-lab:/media/kinshuk/My Book/rossettafold/RoseTTAFold-All-Atom$ python -m rf2aa.run_inference --config-name protein
/home/kinshuk/anaconda3/envs/RFAA/lib/python3.10/site-packages/hydra/_internal/defaults_list.py:251: UserWarning: In 'protein': Defaults list is missing _self_. See https://hydra.cc/docs/1.2/upgrades/1.0_to_1.1/default_composition_order for more information
warnings.warn(msg, UserWarning)
Using the cif atom ordering for TRP.
./make_msa.sh examples/protein/7u7w_A.fasta 7u7w_protein/A 4 64 pdb100_2021Mar03/pdb100_2021Mar03
Predicting: 100%|██████████████████████████| 1/1 [00:01<00:00, 1.02s/sequences]
Running HHblits against UniRef30 with E-value cutoff 1e-10
10:43:42.179 ERROR: In /opt/conda/conda-bld/hhsuite_1709621322429/work/src/hhfilter.cpp:177: main:
10:43:42.179 ERROR: could not open file '7u7wprotein/A/hhblits/t000.1e-10.a3m'
grep: 7u7wprotein/A/hhblits/t000.1e-10.id90cov75.a3m: No such file or directory
grep: 7u7wprotein/A/hhblits/t000.1e-10.id90cov50.a3m: No such file or directory
Running HHblits against UniRef30 with E-value cutoff 1e-6
10:43:42.200 ERROR: In /opt/conda/conda-bld/hhsuite_1709621322429/work/src/hhfilter.cpp:177: main:
10:43:42.200 ERROR: could not open file '7u7wprotein/A/hhblits/t000.1e-6.a3m'
grep: 7u7wprotein/A/hhblits/t000.1e-6.id90cov75.a3m: No such file or directory
grep: 7u7wprotein/A/hhblits/t000.1e-6.id90cov50.a3m: No such file or directory
Running HHblits against UniRef30 with E-value cutoff 1e-3
10:43:42.220 ERROR: In /opt/conda/conda-bld/hhsuite_1709621322429/work/src/hhfilter.cpp:177: main:
10:43:42.220 ERROR: could not open file '7u7wprotein/A/hhblits/t000.1e-3.a3m'
grep: 7u7wprotein/A/hhblits/t000.1e-3.id90cov75.a3m: No such file or directory
grep: 7u7wprotein/A/hhblits/t000.1e-3.id90cov50.a3m: No such file or directory
Running HHblits against BFD with E-value cutoff 1e-3
10:43:42.240 ERROR: In /opt/conda/conda-bld/hhsuite_1709621322429/work/src/hhfilter.cpp:177: main:
10:43:42.240 ERROR: could not open file '7u7wprotein/A/hhblits/t000.1e-3.bfd.a3m'
grep: 7u7wprotein/A/hhblits/t000.1e-3.bfd.id90cov75.a3m: No such file or directory
grep: 7u7wprotein/A/hhblits/t000.1e-3.bfd.id90cov50.a3m: No such file or directory
cp: cannot stat '7u7wprotein/A/hhblits/t000.1e-3.bfd.id90cov50.a3m': No such file or directory
Running PSIPRED
Running hhsearch
cat: 7u7wprotein/A/t000.ss2: No such file or directory
cat: 7u7wprotein/A/t000.msa0.a3m: No such file or directory
10:43:42.508 ERROR: Error in /opt/conda/conda-bld/hhsuite_1709621322429/work/src/hhfunc.cpp:16: ReadQueryFile:
10:43:42.508 ERROR: 7u7wprotein/A/t000.msa0.ss2.a3m is empty!
Error executing job with overrides: []
Traceback (most recent call last):
File "/media/kinshuk/My Book/rossettafold/RoseTTAFold-All-Atom/rf2aa/run_inference.py", line 206, in main
runner.infer()
File "/media/kinshuk/My Book/rossettafold/RoseTTAFold-All-Atom/rf2aa/run_inference.py", line 153, in infer
self.parse_inference_config()
File "/media/kinshuk/My Book/rossettafold/RoseTTAFold-All-Atom/rf2aa/run_inference.py", line 46, in parse_inference_config
protein_input = generate_msa_and_load_protein(
File "/media/kinshuk/My Book/rossettafold/RoseTTAFold-All-Atom/rf2aa/data/protein.py", line 93, in generate_msa_and_load_protein
return load_protein(str(msa_file), str(hhr_file), str(atab_file), model_runner)
File "/media/kinshuk/My Book/rossettafold/RoseTTAFold-All-Atom/rf2aa/data/protein.py", line 56, in load_protein
msa, ins, taxIDs = parse_a3m(msa_file)
File "/media/kinshuk/My Book/rossettafold/RoseTTAFold-All-Atom/rf2aa/data/parsers.py", line 415, in parse_a3m
fstream = open(filename, 'r')
FileNotFoundError: [Errno 2] No such file or directory: '7u7wprotein/A/t000.msa0.a3m'
Set the environment variable HYDRA_FULL_ERROR=1 for a complete stack trace.
I have followed the steps in the tutorial and done everything as directed in it but getting an error on running the example command. i have gone through the previous issues reported regarding it but am confused what to do. Kindly help what should I do to run it successfully. I am providing below the command log and the command i passed. Please help!!
(RFAA) kinshuk@kinshuk-lab:/media/kinshuk/My Book/rossettafold/RoseTTAFold-All-Atom$ python -m rf2aa.run_inference --config-name protein /home/kinshuk/anaconda3/envs/RFAA/lib/python3.10/site-packages/hydra/_internal/defaults_list.py:251: UserWarning: In 'protein': Defaults list is missing
_self_. See https://hydra.cc/docs/1.2/upgrades/1.0_to_1.1/default_composition_order for more information warnings.warn(msg, UserWarning) Using the cif atom ordering for TRP. ./make_msa.sh examples/protein/7u7w_A.fasta 7u7w_protein/A 4 64 pdb100_2021Mar03/pdb100_2021Mar03 Predicting: 100%|██████████████████████████| 1/1 [00:01<00:00, 1.02s/sequences] Running HHblits against UniRef30 with E-value cutoff 1e-1010:43:42.153 WARNING: Ignoring unknown option Book/rossettafold/RoseTTAFold-All-Atom/UniRef30_2023_02/UniRef30_2023_02
10:43:42.153 ERROR: In /opt/conda/conda-bld/hhsuite_1709621322429/work/src/ffindexdatabase.cpp:11: FFindexDatabase:
10:43:42.153 ERROR: could not open file '/media/kinshuk_cs219.ffdata'
10:43:42.175 INFO: Input file = 7u7wprotein/A/hhblits/t000.1e-10.a3m
10:43:42.175 INFO: Output file = 7u7wprotein/A/hhblits/t000.1e-10.id90cov75.a3m
10:43:42.175 ERROR: In /opt/conda/conda-bld/hhsuite_1709621322429/work/src/hhfilter.cpp:177: main:
10:43:42.175 ERROR: could not open file '7u7wprotein/A/hhblits/t000.1e-10.a3m'
10:43:42.179 INFO: Input file = 7u7wprotein/A/hhblits/t000.1e-10.a3m
10:43:42.179 INFO: Output file = 7u7wprotein/A/hhblits/t000.1e-10.id90cov50.a3m
10:43:42.179 ERROR: In /opt/conda/conda-bld/hhsuite_1709621322429/work/src/hhfilter.cpp:177: main:
10:43:42.179 ERROR: could not open file '7u7wprotein/A/hhblits/t000.1e-10.a3m'
grep: 7u7wprotein/A/hhblits/t000.1e-10.id90cov75.a3m: No such file or directory grep: 7u7wprotein/A/hhblits/t000.1e-10.id90cov50.a3m: No such file or directory Running HHblits against UniRef30 with E-value cutoff 1e-6
10:43:42.191 WARNING: Ignoring unknown option Book/rossettafold/RoseTTAFold-All-Atom/UniRef30_2023_02/UniRef30_2023_02
10:43:42.191 ERROR: In /opt/conda/conda-bld/hhsuite_1709621322429/work/src/ffindexdatabase.cpp:11: FFindexDatabase:
10:43:42.191 ERROR: could not open file '/media/kinshuk_cs219.ffdata'
10:43:42.195 INFO: Input file = 7u7wprotein/A/hhblits/t000.1e-6.a3m
10:43:42.195 INFO: Output file = 7u7wprotein/A/hhblits/t000.1e-6.id90cov75.a3m
10:43:42.195 ERROR: In /opt/conda/conda-bld/hhsuite_1709621322429/work/src/hhfilter.cpp:177: main:
10:43:42.195 ERROR: could not open file '7u7wprotein/A/hhblits/t000.1e-6.a3m'
10:43:42.199 INFO: Input file = 7u7wprotein/A/hhblits/t000.1e-6.a3m
10:43:42.200 INFO: Output file = 7u7wprotein/A/hhblits/t000.1e-6.id90cov50.a3m
10:43:42.200 ERROR: In /opt/conda/conda-bld/hhsuite_1709621322429/work/src/hhfilter.cpp:177: main:
10:43:42.200 ERROR: could not open file '7u7wprotein/A/hhblits/t000.1e-6.a3m'
grep: 7u7wprotein/A/hhblits/t000.1e-6.id90cov75.a3m: No such file or directory grep: 7u7wprotein/A/hhblits/t000.1e-6.id90cov50.a3m: No such file or directory Running HHblits against UniRef30 with E-value cutoff 1e-3
10:43:42.211 WARNING: Ignoring unknown option Book/rossettafold/RoseTTAFold-All-Atom/UniRef30_2023_02/UniRef30_2023_02
10:43:42.211 ERROR: In /opt/conda/conda-bld/hhsuite_1709621322429/work/src/ffindexdatabase.cpp:11: FFindexDatabase:
10:43:42.211 ERROR: could not open file '/media/kinshuk_cs219.ffdata'
10:43:42.216 INFO: Input file = 7u7wprotein/A/hhblits/t000.1e-3.a3m
10:43:42.216 INFO: Output file = 7u7wprotein/A/hhblits/t000.1e-3.id90cov75.a3m
10:43:42.216 ERROR: In /opt/conda/conda-bld/hhsuite_1709621322429/work/src/hhfilter.cpp:177: main:
10:43:42.216 ERROR: could not open file '7u7wprotein/A/hhblits/t000.1e-3.a3m'
10:43:42.220 INFO: Input file = 7u7wprotein/A/hhblits/t000.1e-3.a3m
10:43:42.220 INFO: Output file = 7u7wprotein/A/hhblits/t000.1e-3.id90cov50.a3m
10:43:42.220 ERROR: In /opt/conda/conda-bld/hhsuite_1709621322429/work/src/hhfilter.cpp:177: main:
10:43:42.220 ERROR: could not open file '7u7wprotein/A/hhblits/t000.1e-3.a3m'
grep: 7u7wprotein/A/hhblits/t000.1e-3.id90cov75.a3m: No such file or directory grep: 7u7wprotein/A/hhblits/t000.1e-3.id90cov50.a3m: No such file or directory Running HHblits against BFD with E-value cutoff 1e-3
10:43:42.231 WARNING: Ignoring unknown option Book/rossettafold/RoseTTAFold-All-Atom/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt
10:43:42.231 ERROR: In /opt/conda/conda-bld/hhsuite_1709621322429/work/src/ffindexdatabase.cpp:11: FFindexDatabase:
10:43:42.231 ERROR: could not open file '/media/kinshuk_cs219.ffdata'
10:43:42.236 INFO: Input file = 7u7wprotein/A/hhblits/t000.1e-3.bfd.a3m
10:43:42.236 INFO: Output file = 7u7wprotein/A/hhblits/t000.1e-3.bfd.id90cov75.a3m
10:43:42.236 ERROR: In /opt/conda/conda-bld/hhsuite_1709621322429/work/src/hhfilter.cpp:177: main:
10:43:42.236 ERROR: could not open file '7u7wprotein/A/hhblits/t000.1e-3.bfd.a3m'
10:43:42.240 INFO: Input file = 7u7wprotein/A/hhblits/t000.1e-3.bfd.a3m
10:43:42.240 INFO: Output file = 7u7wprotein/A/hhblits/t000.1e-3.bfd.id90cov50.a3m
10:43:42.240 ERROR: In /opt/conda/conda-bld/hhsuite_1709621322429/work/src/hhfilter.cpp:177: main:
10:43:42.240 ERROR: could not open file '7u7wprotein/A/hhblits/t000.1e-3.bfd.a3m'
grep: 7u7wprotein/A/hhblits/t000.1e-3.bfd.id90cov75.a3m: No such file or directory grep: 7u7wprotein/A/hhblits/t000.1e-3.bfd.id90cov50.a3m: No such file or directory cp: cannot stat '7u7wprotein/A/hhblits/t000.1e-3.bfd.id90cov50.a3m': No such file or directory Running PSIPRED Running hhsearch cat: 7u7wprotein/A/t000.ss2: No such file or directory cat: 7u7wprotein/A/t000.msa0.a3m: No such file or directory
10:43:42.508 ERROR: Error in /opt/conda/conda-bld/hhsuite_1709621322429/work/src/hhfunc.cpp:16: ReadQueryFile:
10:43:42.508 ERROR: 7u7wprotein/A/t000.msa0.ss2.a3m is empty!
Error executing job with overrides: [] Traceback (most recent call last): File "/media/kinshuk/My Book/rossettafold/RoseTTAFold-All-Atom/rf2aa/run_inference.py", line 206, in main runner.infer() File "/media/kinshuk/My Book/rossettafold/RoseTTAFold-All-Atom/rf2aa/run_inference.py", line 153, in infer self.parse_inference_config() File "/media/kinshuk/My Book/rossettafold/RoseTTAFold-All-Atom/rf2aa/run_inference.py", line 46, in parse_inference_config protein_input = generate_msa_and_load_protein( File "/media/kinshuk/My Book/rossettafold/RoseTTAFold-All-Atom/rf2aa/data/protein.py", line 93, in generate_msa_and_load_protein return load_protein(str(msa_file), str(hhr_file), str(atab_file), model_runner) File "/media/kinshuk/My Book/rossettafold/RoseTTAFold-All-Atom/rf2aa/data/protein.py", line 56, in load_protein msa, ins, taxIDs = parse_a3m(msa_file) File "/media/kinshuk/My Book/rossettafold/RoseTTAFold-All-Atom/rf2aa/data/parsers.py", line 415, in parse_a3m fstream = open(filename, 'r') FileNotFoundError: [Errno 2] No such file or directory: '7u7wprotein/A/t000.msa0.a3m'
Set the environment variable HYDRA_FULL_ERROR=1 for a complete stack trace.