# WHISCY error, Can not read sequence number **URL:** \ **Category:** HADDOCK\ **Created:** [July 14, 2026, 8:41am UTC](https://ask.bioexcel.eu/t/whiscy-error-can-not-read-sequence-number/6190 "2026-07-14T08:41:14Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![F-Mars](https://avatars.discourse-cdn.com/v4/letter/f/f1d935/32.png) [@F-Mars](https://ask.bioexcel.eu/u/F-Mars)\ **Post date:** [July 14, 2026, 8:41am UTC](https://ask.bioexcel.eu/t/whiscy-error-can-not-read-sequence-number/6190/1 "2026-07-14T08:41:14Z")
I have run into a problem with WHISCY: set -euo pipefail - export MUSCLE\_BIN=/home/fabian/software/muscle3.8.1551/muscle - MUSCLE\_BIN=/home/fabian/software/muscle3.8.1551/muscle - export FREESASA\_BIN=/home/fabian/software/freesasa-2.0.3/bin/freesasa - FREESASA\_BIN=/home/fabian/software/freesasa-2.0.3/bin/freesasa - export PROTDIST\_BIN=/home/fabian/software/protdist/protdist - PROTDIST\_BIN=/home/fabian/software/protdist/protdist - export HSSPCONV\_BIN=/home/fabian/software/hssp-3.1.5/hsspconv - HSSPCONV\_BIN=/home/fabian/software/hssp-3.1.5/hsspconv ++ dirname /home/fabian/Desktop/PhD\_sequencing/Docking\_receptor\_A.pcons - cd /home/fabian/Desktop/PhD\_sequencing - python /home/fabian/PycharmProjects/Workflow\_v2/scripts/WHISCY.py /home/fabian/Desktop/PhD\_sequencing/Docking\_receptor.pdb A /home/fabian/Desktop/PhD\_sequencing/Docking\_receptor\_A.pcons Running: whiscy\_setup /home/fabian/Desktop/PhD\_sequencing/Docking\_receptor.pdb A 2026-07-13 16:39:36,934 cli\_setup:192 INFO - PDB structure with chain A saved to Docking\_receptor\_A.pdb 2026-07-13 16:39:37,101 cli\_setup:199 INFO - Atom accessibility calculated to Docking\_receptor\_A.rsa 2026-07-13 16:39:37,103 cli\_setup:203 INFO - Surface and buried residues calculated 2026-07-13 16:39:37,159 cli\_setup:246 INFO - HSSP file not found, fallback to generating MSA with blastp 2026-07-13 16:39:37,168 cli\_setup:268 INFO - Generating MSA using MUSCLE… 2026-07-13 16:39:37,760 cli\_setup:271 INFO - Done. 2026-07-13 16:39:37,760 cli\_setup:274 INFO - Converting MSA file to Phylseq format… 2026-07-13 16:39:37,761 cli\_setup:283 INFO - Docking\_receptor\_A.phylseq file written 2026-07-13 16:39:37,762 cli\_setup:310 INFO - Protdist calculated 2026-07-13 16:39:37,861 cli\_setup:317 INFO - Conversion table file generated 2026-07-13 16:39:37,861 cli\_setup:319 INFO - Whiscy setup finished Running: whiscy Docking\_receptor\_A.sur Docking\_receptor\_A.conv Docking\_receptor\_A.phylseq Docking\_receptor\_A.out -o Docking\_receptor\_A.cons 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 Running: whiscy\_consadjust Docking\_receptor\_A.cons -o Docking\_receptor\_A.acons consadjust [ERROR] Conservation file Docking\_receptor\_A.cons does not exist Running: whiscy\_resdist /home/fabian/Desktop/PhD\_sequencing/Docking\_receptor.pdb Docking\_receptor\_A.conv Docking\_receptor\_A.rd residue\_distance [INFO] Reading conversion table residue\_distance [INFO] Reading PDB structure from /home/fabian/Desktop/PhD\_sequencing/Docking\_receptor.pdb residue\_distance [INFO] Residue distances written to Docking\_receptor\_A.rd Running: whiscy\_parasmooth Docking\_receptor\_A.acons Docking\_receptor\_A.cons Docking\_receptor\_A.rd -o Docking\_receptor\_A.pscons parasmooth [INFO] Reading input files parasmooth [ERROR] [Errno 2] No such file or directory: ‘Docking\_receptor\_A.acons’ ERROR: Expected output file Docking\_receptor\_A.pscons was not generated. Is there an alternative tool I can use, or is there a fix for this? ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [July 17, 2026, 6:44am UTC](https://ask.bioexcel.eu/t/whiscy-error-can-not-read-sequence-number/6190/2 "2026-07-17T06:44:47Z")
The question is: Is this linked to your input data? Did you try with another protein? ---
**Author:** ![F-Mars](https://avatars.discourse-cdn.com/v4/letter/f/f1d935/32.png) [@F-Mars](https://ask.bioexcel.eu/u/F-Mars)\ **Post date:** [July 17, 2026, 7:32am UTC](https://ask.bioexcel.eu/t/whiscy-error-can-not-read-sequence-number/6190/3 "2026-07-17T07:32:32Z")
I did try it on another protein, but it also has the error of whiscy [ERROR] Can not read sequence number. ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [July 17, 2026, 7:50am UTC](https://ask.bioexcel.eu/t/whiscy-error-can-not-read-sequence-number/6190/4 "2026-07-17T07:50:59Z")
I suggest you try our web server version to see if the error persists. ---
**Author:** ![F-Mars](https://avatars.discourse-cdn.com/v4/letter/f/f1d935/32.png) [@F-Mars](https://ask.bioexcel.eu/u/F-Mars)\ **Post date:** [July 17, 2026, 8:32am UTC](https://ask.bioexcel.eu/t/whiscy-error-can-not-read-sequence-number/6190/5 "2026-07-17T08:32:11Z")
website error: Output not found, please report this error and the run\_id: 43FnB+oY ---
**Author:** ![F-Mars](https://avatars.discourse-cdn.com/v4/letter/f/f1d935/32.png) [@F-Mars](https://ask.bioexcel.eu/u/F-Mars)\ **Post date:** [July 28, 2026, 7:45am UTC](https://ask.bioexcel.eu/t/whiscy-error-can-not-read-sequence-number/6190/6 "2026-07-28T07:45:58Z")
Has anyone else managed to get WHISCY to work?