# Whiscy error message using fasta file **URL:** https://ask.bioexcel.eu/t/whiscy-error-message-using-fasta-file/5179 **Category:** HADDOCK **Created:** [July 7, 2024, 11:54am UTC](https://ask.bioexcel.eu/t/whiscy-error-message-using-fasta-file/5179 "2024-07-07T11:54:21Z") **Posts on this page:** 1 **Page:** 1
### Author: ![andrew1345](https://avatars.discourse-cdn.com/v4/letter/a/d9b06d/32.png) [@andrew1345](https://ask.bioexcel.eu/u/andrew1345) #### Post date: [July 7, 2024, 11:54am UTC](https://ask.bioexcel.eu/t/whiscy-error-message-using-fasta-file/5179/1 "2024-07-07T11:54:22Z")
I am attempting to use Whiscy using my own predicted pdb file and a sample alignment fasta file but I get the following error. How are my inputs incorrectly formatted? Full error message below: # =========================================================================== command: whiscy\_setup proteinOfInterest.pdb A --alignment proteinOfInterest.fasta --alignment\_format FASTA exit status: 0 log: 2024-07-04 17:50:26,782 cli\_setup:192 INFO - PDB structure with chain A saved to proteinOfInterest\_A.pdb 2024-07-04 17:50:26,942 cli\_setup:199 INFO - Atom accessibility calculated to proteinOfInterest\_A.rsa 2024-07-04 17:50:26,944 cli\_setup:203 INFO - Surface and buried residues calculated 2024-07-04 17:50:27,078 cli\_setup:246 INFO - HSSP file not found, fallback to generating MSA with blastp 2024-07-04 17:50:27,098 cli\_setup:310 INFO - Protdist calculated 2024-07-04 17:50:27,146 cli\_setup:317 INFO - Conversion table file generated 2024-07-04 17:50:27,146 cli\_setup:319 INFO - Whiscy setup finished command: whiscy proteinOfInterest\_A.sur proteinOfInterest\_A.conv proteinOfInterest\_A.phylseq proteinOfInterest\_A.out -o proteinOfInterest\_A.cons exit status: 0 log: 2024-07-04 17:50:26,782 cli\_setup:192 INFO - PDB structure with chain A saved to proteinOfInterest\_A.pdb 2024-07-04 17:50:26,942 cli\_setup:199 INFO - Atom accessibility calculated to proteinOfInterest\_A.rsa 2024-07-04 17:50:26,944 cli\_setup:203 INFO - Surface and buried residues calculated 2024-07-04 17:50:27,078 cli\_setup:246 INFO - HSSP file not found, fallback to generating MSA with blastp 2024-07-04 17:50:27,098 cli\_setup:310 INFO - Protdist calculated 2024-07-04 17:50:27,146 cli\_setup:317 INFO - Conversion table file generated 2024-07-04 17:50:27,146 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 [INFO] Calculating scores… whiscy [ERROR] Surface residue out of range command: whiscy proteinOfInterest\_A.lac proteinOfInterest\_A.conv proteinOfInterest\_A.phylseq proteinOfInterest\_A.out -o proteinOfInterest\_A.lcons exit status: 0 log: 2024-07-04 17:50:26,782 cli\_setup:192 INFO - PDB structure with chain A saved to proteinOfInterest\_A.pdb 2024-07-04 17:50:26,942 cli\_setup:199 INFO - Atom accessibility calculated to proteinOfInterest\_A.rsa 2024-07-04 17:50:26,944 cli\_setup:203 INFO - Surface and buried residues calculated 2024-07-04 17:50:27,078 cli\_setup:246 INFO - HSSP file not found, fallback to generating MSA with blastp 2024-07-04 17:50:27,098 cli\_setup:310 INFO - Protdist calculated 2024-07-04 17:50:27,146 cli\_setup:317 INFO - Conversion table file generated 2024-07-04 17:50:27,146 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 [INFO] Calculating scores… whiscy [ERROR] Surface residue out of range whiscy [INFO] Parsing surface list… whiscy [INFO] Loading conversion table… whiscy [INFO] Converting… whiscy [INFO] Initializing score calculation… whiscy [INFO] Calculating scores… whiscy [ERROR] Surface residue out of range command: whiscy\_consadjust proteinOfInterest\_A.cons -o proteinOfInterest\_A.acons exit status: 0 log: 2024-07-04 17:50:26,782 cli\_setup:192 INFO - PDB structure with chain A saved to proteinOfInterest\_A.pdb 2024-07-04 17:50:26,942 cli\_setup:199 INFO - Atom accessibility calculated to proteinOfInterest\_A.rsa 2024-07-04 17:50:26,944 cli\_setup:203 INFO - Surface and buried residues calculated 2024-07-04 17:50:27,078 cli\_setup:246 INFO - HSSP file not found, fallback to generating MSA with blastp 2024-07-04 17:50:27,098 cli\_setup:310 INFO - Protdist calculated 2024-07-04 17:50:27,146 cli\_setup:317 INFO - Conversion table file generated 2024-07-04 17:50:27,146 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 [INFO] Calculating scores… whiscy [ERROR] Surface residue out of range whiscy [INFO] Parsing surface list… whiscy [INFO] Loading conversion table… whiscy [INFO] Converting… whiscy [INFO] Initializing score calculation… whiscy [INFO] Calculating scores… whiscy [ERROR] Surface residue out of range consadjust [ERROR] Conservation file proteinOfInterest\_A.cons does not exist command: whiscy\_resdist proteinOfInterest\_A.pdb proteinOfInterest\_A.conv proteinOfInterest\_A.rd exit status: 0 log: 2024-07-04 17:50:26,782 cli\_setup:192 INFO - PDB structure with chain A saved to proteinOfInterest\_A.pdb 2024-07-04 17:50:26,942 cli\_setup:199 INFO - Atom accessibility calculated to proteinOfInterest\_A.rsa 2024-07-04 17:50:26,944 cli\_setup:203 INFO - Surface and buried residues calculated 2024-07-04 17:50:27,078 cli\_setup:246 INFO - HSSP file not found, fallback to generating MSA with blastp 2024-07-04 17:50:27,098 cli\_setup:310 INFO - Protdist calculated 2024-07-04 17:50:27,146 cli\_setup:317 INFO - Conversion table file generated 2024-07-04 17:50:27,146 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 [INFO] Calculating scores… whiscy [ERROR] Surface residue out of range whiscy [INFO] Parsing surface list… whiscy [INFO] Loading conversion table… whiscy [INFO] Converting… whiscy [INFO] Initializing score calculation… whiscy [INFO] Calculating scores… whiscy [ERROR] Surface residue out of range consadjust [ERROR] Conservation file proteinOfInterest\_A.cons does not exist residue\_distance [INFO] Reading conversion table residue\_distance [INFO] Reading PDB structure from proteinOfInterest\_A.pdb residue\_distance [INFO] Residue distances written to proteinOfInterest\_A.rd command: whiscy\_parasmooth proteinOfInterest\_A.acons proteinOfInterest\_A.lcons proteinOfInterest\_A.rd -o proteinOfInterest\_A.pscons exit status: 0 log: 2024-07-04 17:50:26,782 cli\_setup:192 INFO - PDB structure with chain A saved to proteinOfInterest\_A.pdb 2024-07-04 17:50:26,942 cli\_setup:199 INFO - Atom accessibility calculated to proteinOfInterest\_A.rsa 2024-07-04 17:50:26,944 cli\_setup:203 INFO - Surface and buried residues calculated 2024-07-04 17:50:27,078 cli\_setup:246 INFO - HSSP file not found, fallback to generating MSA with blastp 2024-07-04 17:50:27,098 cli\_setup:310 INFO - Protdist calculated 2024-07-04 17:50:27,146 cli\_setup:317 INFO - Conversion table file generated 2024-07-04 17:50:27,146 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 [INFO] Calculating scores… whiscy [ERROR] Surface residue out of range whiscy [INFO] Parsing surface list… whiscy [INFO] Loading conversion table… whiscy [INFO] Converting… whiscy [INFO] Initializing score calculation… whiscy [INFO] Calculating scores… whiscy [ERROR] Surface residue out of range consadjust [ERROR] Conservation file proteinOfInterest\_A.cons does not exist residue\_distance [INFO] Reading conversion table residue\_distance [INFO] Reading PDB structure from proteinOfInterest\_A.pdb residue\_distance [INFO] Residue distances written to proteinOfInterest\_A.rd parasmooth [INFO] Reading input files parasmooth [ERROR] [Errno 2] No such file or directory: ‘proteinOfInterest\_A.acons’ command: whiscy\_bfactor proteinOfInterest\_A.pdb proteinOfInterest\_A\_bfactor.pdb proteinOfInterest\_A.pscons exit status: 1 log: 2024-07-04 17:50:26,782 cli\_setup:192 INFO - PDB structure with chain A saved to proteinOfInterest\_A.pdb 2024-07-04 17:50:26,942 cli\_setup:199 INFO - Atom accessibility calculated to proteinOfInterest\_A.rsa 2024-07-04 17:50:26,944 cli\_setup:203 INFO - Surface and buried residues calculated 2024-07-04 17:50:27,078 cli\_setup:246 INFO - HSSP file not found, fallback to generating MSA with blastp 2024-07-04 17:50:27,098 cli\_setup:310 INFO - Protdist calculated 2024-07-04 17:50:27,146 cli\_setup:317 INFO - Conversion table file generated 2024-07-04 17:50:27,146 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 [INFO] Calculating scores… whiscy [ERROR] Surface residue out of range whiscy [INFO] Parsing surface list… whiscy [INFO] Loading conversion table… whiscy [INFO] Converting… whiscy [INFO] Initializing score calculation… whiscy [INFO] Calculating scores… whiscy [ERROR] Surface residue out of range consadjust [ERROR] Conservation file proteinOfInterest\_A.cons does not exist residue\_distance [INFO] Reading conversion table residue\_distance [INFO] Reading PDB structure from proteinOfInterest\_A.pdb residue\_distance [INFO] Residue distances written to proteinOfInterest\_A.rd parasmooth [INFO] Reading input files parasmooth [ERROR] [Errno 2] No such file or directory: ‘proteinOfInterest\_A.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: ‘proteinOfInterest\_A.pscons’