WHISCY error, Can not read sequence number

HADDOCK
1

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?

2

The question is: Is this linked to your input data? Did you try with another protein?

3

I did try it on another protein, but it also has the error of whiscy [ERROR] Can not read sequence number.

4

I suggest you try our web server version to see if the error persists.

5

website error:

Output not found, please report this error and the run_id: 43FnB+oY