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
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?