Hi! When I tried to do more motif extraction , I ran into this error:
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/hydroxyl_torsion_preference.txt
core.import_pose.import_pose: File '/home/gaon/cao_protocol/protocol_test_E/input/output/rif_64_output_sca0.8_noKR.rif.gz_target_chainchanged.pdb' automatically determined to be of type PDB
core.conformation.Conformation: Found disulfide between residues 3 22
core.conformation.Conformation: Found disulfide between residues 117 145
core.io.silent.SilentFileData: Reading all structures from /home/gaon/cao_protocol/protocol_test_E/input/10000_design_splits/fd_output_splits/xac.silent
core.io.silent: [ WARNING ] parse error: found 2 RT lines for a fold-tree with 1 for decoy tag HHH_bc_13421_000000004_0001
Traceback (most recent call last):
File "/home/gaon/cao_protocol/cao_2021_protocol/motif_extraction.py", line 240, in <module>
sfd_in.read_file(silent)
RuntimeError:
File: /home/benchmark/rosetta/source/src/core/io/silent/SilentFileData.cc:828
failure to read decoy HHH_bc_13421_000000004_0001 from silent-file /home/gaon/cao_protocol/protocol_test_E/input/10000_design_splits/fd_output_splits/xac.silent
There are 16 commands in the list but only this command report this error:
/home/gaon/cao_protocol/cao_2021_protocol/motif_extraction.py -in:file:silent /home/gaon/cao_protocol/protocol_test_E/input/10000_design_splits/fd_output_splits/xac.silent -ref_pdb /home/gaon/cao_protocol/protocol_test_E/input/output/rif_64_output_sca0.8_noKR.rif.gz_target_chainchanged.pdb -out_prefix mot_
Has anyone encountered this problem?Could anyone please help me solve this problem?I will be grateful if you could help.