Hello, I am trying to use WHISCY webserver, but when I insert my alignment file (FASTA or .aln format), I am getting error: Run 3+r48DDe
Status: FAILED
See the error output below which might include an indication about why your run failed. If you need assistance please reach us out at ask.bioexcel.eu
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command: whiscy_setup model_01_1.pdb B --alignment rcsb_pdb_4RZK.fasta --alignment_format FASTA
exit status: 0
log:
2025-05-27 21:19:09,975 cli_setup:192 INFO - PDB structure with chain B saved to model_01_1_B.pdb
2025-05-27 21:19:10,056 cli_setup:199 INFO - Atom accessibility calculated to model_01_1_B.rsa
2025-05-27 21:19:10,057 cli_setup:203 INFO - Surface and buried residues calculated
2025-05-27 21:19:10,080 cli_setup:246 INFO - HSSP file not found, fallback to generating MSA with blastp
2025-05-27 21:19:10,257 cli_setup:310 INFO - Protdist calculated
2025-05-27 21:19:10,279 cli_setup:317 INFO - Conversion table file generated
2025-05-27 21:19:10,279 cli_setup:319 INFO - Whiscy setup finished
command: whiscy model_01_1_B.sur model_01_1_B.conv model_01_1_B.phylseq model_01_1_B.out -o model_01_1_B.cons
exit status: 0
log:
2025-05-27 21:19:09,975 cli_setup:192 INFO - PDB structure with chain B saved to model_01_1_B.pdb
2025-05-27 21:19:10,056 cli_setup:199 INFO - Atom accessibility calculated to model_01_1_B.rsa
2025-05-27 21:19:10,057 cli_setup:203 INFO - Surface and buried residues calculated
2025-05-27 21:19:10,080 cli_setup:246 INFO - HSSP file not found, fallback to generating MSA with blastp
2025-05-27 21:19:10,257 cli_setup:310 INFO - Protdist calculated
2025-05-27 21:19:10,279 cli_setup:317 INFO - Conversion table file generated
2025-05-27 21:19:10,279 cli_setup:319 INFO - Whiscy setup finished
whiscy [INFO] Parsing surface list…
whiscy [INFO] Loading conversion table…
whiscy [INFO] Converting…
whiscy [INFO] Initializing score calculation…
whiscy [ERROR] Can not read sequence number
command: whiscy model_01_1_B.lac model_01_1_B.conv model_01_1_B.phylseq model_01_1_B.out -o model_01_1_B.lcons
exit status: 0
log:
2025-05-27 21:19:09,975 cli_setup:192 INFO - PDB structure with chain B saved to model_01_1_B.pdb
2025-05-27 21:19:10,056 cli_setup:199 INFO - Atom accessibility calculated to model_01_1_B.rsa
2025-05-27 21:19:10,057 cli_setup:203 INFO - Surface and buried residues calculated
2025-05-27 21:19:10,080 cli_setup:246 INFO - HSSP file not found, fallback to generating MSA with blastp
2025-05-27 21:19:10,257 cli_setup:310 INFO - Protdist calculated
2025-05-27 21:19:10,279 cli_setup:317 INFO - Conversion table file generated
2025-05-27 21:19:10,279 cli_setup:319 INFO - Whiscy setup finished
whiscy [INFO] Parsing surface list…
whiscy [INFO] Loading conversion table…
whiscy [INFO] Converting…
whiscy [INFO] Initializing score calculation…
whiscy [ERROR] Can not read sequence number
whiscy [INFO] Parsing surface list…
whiscy [INFO] Loading conversion table…
whiscy [INFO] Converting…
whiscy [INFO] Initializing score calculation…
whiscy [ERROR] Can not read sequence number
command: whiscy_consadjust model_01_1_B.cons -o model_01_1_B.acons
exit status: 0
log:
2025-05-27 21:19:09,975 cli_setup:192 INFO - PDB structure with chain B saved to model_01_1_B.pdb
2025-05-27 21:19:10,056 cli_setup:199 INFO - Atom accessibility calculated to model_01_1_B.rsa
2025-05-27 21:19:10,057 cli_setup:203 INFO - Surface and buried residues calculated
2025-05-27 21:19:10,080 cli_setup:246 INFO - HSSP file not found, fallback to generating MSA with blastp
2025-05-27 21:19:10,257 cli_setup:310 INFO - Protdist calculated
2025-05-27 21:19:10,279 cli_setup:317 INFO - Conversion table file generated
2025-05-27 21:19:10,279 cli_setup:319 INFO - Whiscy setup finished
whiscy [INFO] Parsing surface list…
whiscy [INFO] Loading conversion table…
whiscy [INFO] Converting…
whiscy [INFO] Initializing score calculation…
whiscy [ERROR] Can not read sequence number
whiscy [INFO] Parsing surface list…
whiscy [INFO] Loading conversion table…
whiscy [INFO] Converting…
whiscy [INFO] Initializing score calculation…
whiscy [ERROR] Can not read sequence number
consadjust [ERROR] Conservation file model_01_1_B.cons does not exist
command: whiscy_resdist model_01_1_B.pdb model_01_1_B.conv model_01_1_B.rd
exit status: 0
log:
2025-05-27 21:19:09,975 cli_setup:192 INFO - PDB structure with chain B saved to model_01_1_B.pdb
2025-05-27 21:19:10,056 cli_setup:199 INFO - Atom accessibility calculated to model_01_1_B.rsa
2025-05-27 21:19:10,057 cli_setup:203 INFO - Surface and buried residues calculated
2025-05-27 21:19:10,080 cli_setup:246 INFO - HSSP file not found, fallback to generating MSA with blastp
2025-05-27 21:19:10,257 cli_setup:310 INFO - Protdist calculated
2025-05-27 21:19:10,279 cli_setup:317 INFO - Conversion table file generated
2025-05-27 21:19:10,279 cli_setup:319 INFO - Whiscy setup finished
whiscy [INFO] Parsing surface list…
whiscy [INFO] Loading conversion table…
whiscy [INFO] Converting…
whiscy [INFO] Initializing score calculation…
whiscy [ERROR] Can not read sequence number
whiscy [INFO] Parsing surface list…
whiscy [INFO] Loading conversion table…
whiscy [INFO] Converting…
whiscy [INFO] Initializing score calculation…
whiscy [ERROR] Can not read sequence number
consadjust [ERROR] Conservation file model_01_1_B.cons does not exist
residue_distance [INFO] Reading conversion table
residue_distance [INFO] Reading PDB structure from model_01_1_B.pdb
residue_distance [INFO] Residue distances written to model_01_1_B.rd
command: whiscy_parasmooth model_01_1_B.acons model_01_1_B.lcons model_01_1_B.rd -o model_01_1_B.pscons
exit status: 0
log:
2025-05-27 21:19:09,975 cli_setup:192 INFO - PDB structure with chain B saved to model_01_1_B.pdb
2025-05-27 21:19:10,056 cli_setup:199 INFO - Atom accessibility calculated to model_01_1_B.rsa
2025-05-27 21:19:10,057 cli_setup:203 INFO - Surface and buried residues calculated
2025-05-27 21:19:10,080 cli_setup:246 INFO - HSSP file not found, fallback to generating MSA with blastp
2025-05-27 21:19:10,257 cli_setup:310 INFO - Protdist calculated
2025-05-27 21:19:10,279 cli_setup:317 INFO - Conversion table file generated
2025-05-27 21:19:10,279 cli_setup:319 INFO - Whiscy setup finished
whiscy [INFO] Parsing surface list…
whiscy [INFO] Loading conversion table…
whiscy [INFO] Converting…
whiscy [INFO] Initializing score calculation…
whiscy [ERROR] Can not read sequence number
whiscy [INFO] Parsing surface list…
whiscy [INFO] Loading conversion table…
whiscy [INFO] Converting…
whiscy [INFO] Initializing score calculation…
whiscy [ERROR] Can not read sequence number
consadjust [ERROR] Conservation file model_01_1_B.cons does not exist
residue_distance [INFO] Reading conversion table
residue_distance [INFO] Reading PDB structure from model_01_1_B.pdb
residue_distance [INFO] Residue distances written to model_01_1_B.rd
parasmooth [INFO] Reading input files
parasmooth [ERROR] [Errno 2] No such file or directory: ‘model_01_1_B.acons’
command: whiscy_bfactor model_01_1_B.pdb model_01_1_B_bfactor.pdb model_01_1_B.pscons
exit status: 1
log:
2025-05-27 21:19:09,975 cli_setup:192 INFO - PDB structure with chain B saved to model_01_1_B.pdb
2025-05-27 21:19:10,056 cli_setup:199 INFO - Atom accessibility calculated to model_01_1_B.rsa
2025-05-27 21:19:10,057 cli_setup:203 INFO - Surface and buried residues calculated
2025-05-27 21:19:10,080 cli_setup:246 INFO - HSSP file not found, fallback to generating MSA with blastp
2025-05-27 21:19:10,257 cli_setup:310 INFO - Protdist calculated
2025-05-27 21:19:10,279 cli_setup:317 INFO - Conversion table file generated
2025-05-27 21:19:10,279 cli_setup:319 INFO - Whiscy setup finished
whiscy [INFO] Parsing surface list…
whiscy [INFO] Loading conversion table…
whiscy [INFO] Converting…
whiscy [INFO] Initializing score calculation…
whiscy [ERROR] Can not read sequence number
whiscy [INFO] Parsing surface list…
whiscy [INFO] Loading conversion table…
whiscy [INFO] Converting…
whiscy [INFO] Initializing score calculation…
whiscy [ERROR] Can not read sequence number
consadjust [ERROR] Conservation file model_01_1_B.cons does not exist
residue_distance [INFO] Reading conversion table
residue_distance [INFO] Reading PDB structure from model_01_1_B.pdb
residue_distance [INFO] Residue distances written to model_01_1_B.rd
parasmooth [INFO] Reading input files
parasmooth [ERROR] [Errno 2] No such file or directory: ‘model_01_1_B.acons’
Traceback (most recent call last):
File “/usr/local/bin/whiscy_bfactor”, line 6, in
sys.exit(main())
^^^^^^
File “/opt/software/whiscy/src/whiscy/cli_bfactor.py”, line 68, in main
scores = parse_whiscy_scores(whiscy_scores_file_name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/opt/software/whiscy/src/whiscy/cli_bfactor.py”, line 31, in parse_whiscy_scores
with open(file_name) as input:
^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: ‘model_01_1_B.pscons’.
Please guide me through this.