ERROR OMSSAAdapter

Dear all,

When i am running OMSSAAdapter for my mzML data, i am getting following error, how can i slove this problem.

ERROR OMSSAAdapter         2:8        Failing process stdout: [Progress of 'loading spectra list':, ,   1.99 %               ,   13.58 %               ,   21.09 %               ,   28.63 %               ,   36.07 %               ,   42.98 %               ,   50.18 %               ,   59.79 %               ,   77.03 %               ,   90.07 %               , -- done [took 6.69 s (CPU), 10.07 s (Wall)] -- , Progress of 'loading chromatogram list':, , -- done [took 0.00 s (CPU), 0.00 s (Wall)] -- , Chunk size is <=0; disabling chunking of input! If OMSSA crashes due to memory allocation errors, try setting 'chunk_size' to a value below 30000 (e.g., 10000 is usually ok)., Error: Unexpected internal error (The value '16479' was used but is not valid! Spectrum to be written as MGF has more than 10.000 peaks, which is the maximum upper limit. Only centroided data is allowed. This is most likely raw data.)]

ERROR OMSSAAdapter         2:8        Failing process stderr: []

ERROR OMSSAAdapter         2:8        Execute failed: Failed to execute node OMSSAAdapter

ERROR OMSSAAdapter         2:8        Failing process stdout: [Progress of 'loading spectra list':, ,   0.29 %               ,   15.47 %               ,   27.38 %               ,   38.66 %               ,   49.86 %               ,   64.94 %               ,   86.95 %               , -- done [took 6.59 s (CPU), 6.79 s (Wall)] -- , Progress of 'loading chromatogram list':, , -- done [took 0.00 s (CPU), 0.00 s (Wall)] -- , Chunk size is <=0; disabling chunking of input! If OMSSA crashes due to memory allocation errors, try setting 'chunk_size' to a value below 30000 (e.g., 10000 is usually ok)., Error: Unexpected internal error (The value '16479' was used but is not valid! Spectrum to be written as MGF has more than 10.000 peaks, which is the maximum upper limit. Only centroided data is allowed. This is most likely raw data.)]

ERROR OMSSAAdapter         2:8        Failing process stderr: []

ERROR OMSSAAdapter         2:8        Execute failed: Failed to execute node OMSSAAdapter

ERROR OMSSAAdapter         2:8        Failing process stdout: [Progress of 'loading spectra list':, ,   3.94 %               ,   17.91 %               ,   29.86 %               ,   41.28 %               ,   52.47 %               ,   68.67 %               ,   89.98 %               , -- done [took 6.61 s (CPU), 6.81 s (Wall)] -- , Progress of 'loading chromatogram list':, , -- done [took 0.00 s (CPU), 0.00 s (Wall)] -- , Error: Unexpected internal error (The value '16479' was used but is not valid! Spectrum to be written as MGF has more than 10.000 peaks, which is the maximum upper limit. Only centroided data is allowed. This is most likely raw data.)]

ERROR OMSSAAdapter         2:8        Failing process stderr: []

ERROR OMSSAAdapter         2:8        Execute failed: Failed to execute node OMSSAAdapter

ERROR OMSSAAdapter         2:8        Failing process stdout: [Progress of 'loading spectra list':, ,   15.02 %               ,   26.85 %               ,   38.44 %               ,   49.49 %               ,   64.00 %               ,   85.80 %               , -- done [took 6.64 s (CPU), 6.84 s (Wall)] -- , Progress of 'loading chromatogram list':, , -- done [took 0.00 s (CPU), 0.00 s (Wall)] -- , Error: Unexpected internal error (The value '16479' was used but is not valid! Spectrum to be written as MGF has more than 10.000 peaks, which is the maximum upper limit. Only centroided data is allowed. This is most likely raw data.)]

ERROR OMSSAAdapter         2:8        Failing process stderr: []

ERROR OMSSAAdapter         2:8        Execute failed: Failed to execute node OMSSAAdapter

ERROR OMSSAAdapter         2:8        Failing process stdout: [Progress of 'loading spectra list':, ,   4.78 %               ,   18.52 %               ,   30.62 %               ,   42.09 %               ,   54.00 %               ,   72.71 %               ,   92.41 %               , -- done [took 6.51 s (CPU), 6.70 s (Wall)] -- , Progress of 'loading chromatogram list':, , -- done [took 0.00 s (CPU), 0.00 s (Wall)] -- , Error: Unexpected internal error (The value '16479' was used but is not valid! Spectrum to be written as MGF has more than 10.000 peaks, which is the maximum upper limit. Only centroided data is allowed. This is most likely raw data.)]

ERROR OMSSAAdapter         2:8        Failing process stderr: []

ERROR OMSSAAdapter         2:8        Execute failed: Failed to execute node OMSSAAdapter

 

Dear all,

Kindly help me to slove this problem

Hello,

I will add an answer from our mailing list here (Thanks to Chris):

 

According to the error 

Error: Unexpected internal error (The value '16479' was used but is not valid!
 Spectrum to be written as MGF has more than 10.000 peaks,
 which is the maximum upper limit. Only centroided data is allowed.
 This is most likely raw data.)]

It seems your MS/MS spectra are still in profile mode.

Usually a search engine (including OMSSA) requires the spectra to be 

centroided. So, insert a PeakPicker node prior to searching and the 

error will disappear.

 

Best

Julianus

It doesn't work.

ERROR OMSSAAdapter         0:75       Failing process stdout: [Progress of 'loading spectra list':, , -- done [took 0.75 s (CPU), 0.75 s (Wall)] -- , Progress of 'loading chromatogram list':, , -- done [took 0.00 s (CPU), 0.00 s (Wall)] -- , Error: File empty (the file 'Error: No MS2 spectra in input file.' is empty)]
ERROR OMSSAAdapter         0:75       Failing process stderr: []
ERROR OMSSAAdapter         0:75       Execute failed: Failed to execute node OMSSAAdapter

Hi,

that seems to be another error. There seem to be no MS2 spectra in your file.

You would have to upload the file somewhere to say more. Can you tell us more about your input data?