ERROR XTandemAdapter

Dear All,
I am using XTandemAdapter for peptide identification along with OMSSA in
Knime Analytics Platform. OMSSA works fine but XTandemAdapter is giving error
for some of my mzML files. I have downloaded raw data and converted it into
mzML using Proteowizard.
ERROR XTandemAdapter 0:581 Spectrum-to-sequence matching process in
progress | 8400 ks , Spectru sequences modelled = 8407 ks, Model
refinement:, Creating report:, initial calculations … done., sorting
… done., finding repeats … done., evaluating results … done.,
calculating expectations … done., writing results … done., , Valid
models = 1097, Unique models = 772, Estimated false positives = 22 ± 5,
, , Error: Unable to read file (Cannot convert string to amino acid sequence:
unexpected character ’ ’ in: GGGGSGSSGGGGSSVSSGSSV SSGYSSGT)]
ERROR XTandemAdapter 0:581 Failing process stderr:
ERROR XTandemAdapter 0:581 Execute failed: Failed to execute node
XTandemAdapter
Please help.

Hi Sangita,

there seems to be something strange with your FASTA database. It includes whitespaces, which it usually should not. Maybe OMSSA ignores this fact but I suggest to fix it.
Can you try to redownload or regenerate your database?

Cheers
Julianus