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ERROR in ISPRED #87

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ankush290307 opened this issue Oct 19, 2023 · 0 comments
Open

ERROR in ISPRED #87

ankush290307 opened this issue Oct 19, 2023 · 0 comments
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@rvhonorato

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@ankush290307
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I Installed cport and Encountered this error how can I fix that

cport example/1PPE.pdb A
2023-10-19 13:33:08.396271: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on your machine, GPU will not be used.
2023-10-19 13:33:08.529716: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on your machine, GPU will not be used.
2023-10-19 13:33:08.530431: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: AVX2 AVX512F FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
2023-10-19 13:33:10.259470: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT
[2023-10-19 13:33:11,839 cli:L142 INFO] ------------------------------------------
[2023-10-19 13:33:11,839 cli:L143 INFO] Welcome to CPORT v0.2.0-alpha
[2023-10-19 13:33:11,839 cli:L144 INFO] ------------------------------------------
[2023-10-19 13:33:11,840 loader:L357 INFO] Running method: scriber
[2023-10-19 13:33:11,840 scriber:L210 INFO] Running SCRIBER
[2023-10-19 13:33:11,841 loader:L357 INFO] Running method: sppider
[2023-10-19 13:33:11,841 scriber:L211 INFO] Will try 36 times waiting 30s between tries
[2023-10-19 13:33:11,841 loader:L357 INFO] Running method: scannet
[2023-10-19 13:33:11,841 sppider:L190 INFO] Running SPPIDER
[2023-10-19 13:33:11,842 scannet:L176 INFO] Running ScanNet
[2023-10-19 13:33:11,842 loader:L357 INFO] Running method: ispred4
[2023-10-19 13:33:11,842 sppider:L191 INFO] Will try 36 times waiting 45s between tries
[2023-10-19 13:33:11,842 scannet:L177 INFO] Will try 36 times waiting 30s between tries
[2023-10-19 13:33:11,843 ispred4:L198 INFO] Running ISPRED4
[2023-10-19 13:33:11,844 ispred4:L199 INFO] Will try 36 times waiting 60s between tries
/home/ankush/.local/lib/python3.10/site-packages/Bio/PDB/StructureBuilder.py:87: PDBConstructionWarning: WARNING: Chain E is discontinuous at line 2361.
warnings.warn("WARNING: Chain %s is discontinuous at line %i."
/home/ankush/.local/lib/python3.10/site-packages/Bio/PDB/StructureBuilder.py:87: PDBConstructionWarning: WARNING: Chain I is discontinuous at line 2487.
warnings.warn("WARNING: Chain %s is discontinuous at line %i."
/home/ankush/.local/lib/python3.10/site-packages/Bio/SeqIO/PdbIO.py:217: BiopythonWarning: Ignoring out-of-order residues after a gap
warnings.warn("Ignoring out-of-order residues after a gap",
Exception in thread scriber:
Traceback (most recent call last):
File "/home/ankush/miniconda3/envs/pgml/lib/python3.10/threading.py", line 1009, in _bootstrap_inner
self.run()
File "/home/ankush/cport/src/cport/modules/threadreturn.py", line 14, in run
self._return = self._target(self._args, **self._kwargs)
File "/home/ankush/cport/src/cport/modules/loader.py", line 359, in run_prediction
result = predictor_func()
File "/home/ankush/cport/src/cport/modules/loader.py", line 85, in run_scriber
predictions = scriber.run()
File "/home/ankush/cport/src/cport/modules/scriber.py", line 213, in run
submitted_url = self.submit()
File "/home/ankush/cport/src/cport/modules/scriber.py", line 53, in submit
fasta_string = get_fasta_from_pdbfile(
File "/home/ankush/cport/src/cport/modules/utils.py", line 138, in get_fasta_from_pdbfile
return sequence
UnboundLocalError: local variable 'sequence' referenced before assignment
[2023-10-19 13:33:14,709 ispred4:L118 DEBUG] Waiting for ISPRED4 to finish... 36
Exception in thread scannet:
Traceback (most recent call last):
File "/home/ankush/miniconda3/envs/pgml/lib/python3.10/threading.py", line 1009, in _bootstrap_inner
self.run()
File "/home/ankush/cport/src/cport/modules/threadreturn.py", line 14, in run
self._return = self._target(self._args, **self._kwargs)
File "/home/ankush/cport/src/cport/modules/loader.py", line 359, in run_prediction
result = predictor_func()
File "/home/ankush/cport/src/cport/modules/loader.py", line 268, in run_scannet
predictions = scannet.run()
File "/home/ankush/cport/src/cport/modules/scannet.py", line 179, in run
submitted_url = self.submit()
File "/home/ankush/cport/src/cport/modules/scannet.py", line 64, in submit
browser.follow_link(browser.links()[7])
IndexError: list index out of range
[2023-10-19 13:34:15,419 ispred4:L118 DEBUG] Waiting for ISPRED4 to finish... 35
[2023-10-19 13:34:19,375 sppider:L106 DEBUG] Waiting for SPPIDER to finish... 36
[2023-10-19 13:35:16,100 ispred4:L118 DEBUG] Waiting for ISPRED4 to finish... 34
[2023-10-19 13:35:37,263 sppider:L106 DEBUG] Waiting for SPPIDER to finish... 35
[2023-10-19 13:36:16,808 ispred4:L118 DEBUG] Waiting for ISPRED4 to finish... 33
[2023-10-19 13:36:54,362 sppider:L106 DEBUG] Waiting for SPPIDER to finish... 34
[2023-10-19 13:37:17,532 ispred4:L118 DEBUG] Waiting for ISPRED4 to finish... 32
[2023-10-19 13:37:40,849 loader:L109 INFO] {'active': [38, 39, 57, 61, 62, 74, 75, 92, 93, 96, 114, 117, 119, 120, 121, 122, 125, 127, 132, 133, 135, 137, 151, 159, 202, 203, 236, 239, 240], 'passive': []}
[2023-10-19 13:38:18,356 ispred4:L118 DEBUG] Waiting for ISPRED4 to finish... 3 1
[2023-10-19 13:39:19,044 ispred4:L118 DEBUG] Waiting for ISPRED4 to finish... 3 0
[2023-10-19 13:40:19,747 ispred4:L118 DEBUG] Waiting for ISPRED4 to finish... 2 9
[2023-10-19 13:41:20,422 ispred4:L118 DEBUG] Waiting for ISPRED4 to finish... 2 8
[2023-10-19 13:42:21,113 ispred4:L118 DEBUG] Waiting for ISPRED4 to finish... 2 7
[2023-10-19 13:43:21,928 ispred4:L118 DEBUG] Waiting for ISPRED4 to finish... 2 6
[2023-10-19 13:44:22,622 ispred4:L118 DEBUG] Waiting for ISPRED4 to finish... 2 5
[2023-10-19 13:45:23,383 ispred4:L118 DEBUG] Waiting for ISPRED4 to finish... 2 4
[2023-10-19 13:46:24,079 ispred4:L118 DEBUG] Waiting for ISPRED4 to finish... 2 3
[2023-10-19 13:47:24,772 ispred4:L118 DEBUG] Waiting for ISPRED4 to finish... 2 2
[2023-10-19 13:48:25,595 ispred4:L118 DEBUG] Waiting for ISPRED4 to finish... 2 1
[2023-10-19 13:49:26,287 ispred4:L118 DEBUG] Waiting for ISPRED4 to finish... 2 0
[2023-10-19 13:50:26,958 ispred4:L118 DEBUG] Waiting for ISPRED4 to finish... 1 9
[2023-10-19 13:51:27,637 ispred4:L118 DEBUG] Waiting for ISPRED4 to finish... 18
[2023-10-19 13:52:28,314 ispred4:L118 DEBUG] Waiting for ISPRED4 to finish... 17
[2023-10-19 13:53:29,134 ispred4:L118 DEBUG] Waiting for ISPRED4 to finish... 16
[2023-10-19 13:54:29,815 ispred4:L118 DEBUG] Waiting for ISPRED4 to finish... 15
[2023-10-19 13:55:30,506 ispred4:L118 DEBUG] Waiting for ISPRED4 to finish... 14
[2023-10-19 13:56:31,183 ispred4:L118 DEBUG] Waiting for ISPRED4 to finish... 13
[2023-10-19 13:57:31,889 ispred4:L118 DEBUG] Waiting for ISPRED4 to finish... 12
[2023-10-19 13:58:32,708 ispred4:L118 DEBUG] Waiting for ISPRED4 to finish... 11
[2023-10-19 13:59:33,412 ispred4:L118 DEBUG] Waiting for ISPRED4 to finish... 10
[2023-10-19 14:00:34,114 ispred4:L118 DEBUG] Waiting for ISPRED4 to finish... 9
[2023-10-19 14:01:34,812 ispred4:L118 DEBUG] Waiting for ISPRED4 to finish... 8
[2023-10-19 14:02:35,484 ispred4:L118 DEBUG] Waiting for ISPRED4 to finish... 7
[2023-10-19 14:03:36,310 ispred4:L118 DEBUG] Waiting for ISPRED4 to finish... 6
[2023-10-19 14:04:37,003 ispred4:L118 DEBUG] Waiting for ISPRED4 to finish... 5
[2023-10-19 14:05:37,693 ispred4:L118 DEBUG] Waiting for ISPRED4 to finish... 4
[2023-10-19 14:06:38,383 ispred4:L118 DEBUG] Waiting for ISPRED4 to finish... 3
[2023-10-19 14:07:39,068 ispred4:L118 DEBUG] Waiting for ISPRED4 to finish... 2
[2023-10-19 14:08:39,893 ispred4:L118 DEBUG] Waiting for ISPRED4 to finish... 1
[2023-10-19 14:09:40,582 ispred4:L125 ERROR] ISPRED4 server is not responding, url was https://ispred4.biocomp.unibo.it/ispred/default/job_summary?jobid=7ed2a43a-b55b-4fc0-8097-addc024355fc
/home/ankush/.local/lib/python3.10/site-packages/Bio/PDB/StructureBuilder.py:87: PDBConstructionWarning: WARNING: Chain E is discontinuous at line 2361.
warnings.warn("WARNING: Chain %s is discontinuous at line %i."
/home/ankush/.local/lib/python3.10/site-packages/Bio/PDB/StructureBuilder.py:87: PDBConstructionWarning: WARNING: Chain I is discontinuous at line 2487.
warnings.warn("WARNING: Chain %s is discontinuous at line %i."
Traceback (most recent call last):
File "/home/ankush/miniconda3/envs/pgml/bin/cport", line 33, in
sys.exit(load_entry_point('cport', 'console_scripts', 'cport')())
File "/home/ankush/cport/src/cport/cli.py", line 117, in maincli
cli(argument_parser, main)
File "/home/ankush/cport/src/cport/cli.py", line 112, in cli
main_func(**vars(cmd))
File "/home/ankush/cport/src/cport/cli.py", line 192, in main
format_output(
File "/home/ankush/cport/src/cport/modules/utils.py", line 153, in format_output
standardized_dic = standardize_residues(result_dic, chain_id, pdb_file)
File "/home/ankush/cport/src/cport/modules/utils.py", line 259, in standardize_residues
reslist = get_residue_list(pdb_file, chain_id)
File "/home/ankush/cport/src/cport/modules/utils.py", line 337, in get_residue_list
chain = model[chain_id]
File "/home/ankush/.local/lib/python3.10/site-packages/Bio/PDB/Entity.py", line 40, in getitem
return self.child_dict[id]
KeyError: 'A'
@rvhonorato rvhonorato self-assigned this Oct 20, 2023
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87-error-in-ispred haddocking/cport
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@rvhonorato @ankush290307