# ERROR\_Active residue prediction **URL:** \ **Category:** Uncategorized\ **Created:** [June 2, 2025, 9:02pm UTC](https://ask.bioexcel.eu/t/error-active-residue-prediction/5719 "2025-06-02T21:02:26Z")\ **Posts on this page:** 1\ **Page:** 1
**Author:** ![Negin](https://avatars.discourse-cdn.com/v4/letter/n/45deac/32.png) [@Negin](https://ask.bioexcel.eu/u/Negin)\ **Post date:** [June 2, 2025, 9:02pm UTC](https://ask.bioexcel.eu/t/error-active-residue-prediction/5719/1 "2025-06-02T21:02:26Z")
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 # =========================================================================== 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.