/scratch/user/jialiyu/software/crux-4.0.Linux.x86_64/bin/crux param-medic --spectrum-parser mstoolkit ms2/*ms2 --overwrite T
WARNING: The output directory 'crux-output' already exists.
Existing files will be overwritten.
WARNING: The file 'crux-output/param-medic.log.txt' already exists and will be overwritten.
INFO: CPU: tnxt-0306.cluster
INFO: Crux version: 4.0-b854e9b-2021-06-01
INFO: Mon Sep 13 10:02:45 CDT 2021
INFO: Beginning param-medic.
WARNING: The file 'crux-output/param-medic.txt' already exists and will be overwritten.
INFO: param-medic processing input file ms2/10.raw.ms2...
INFO: param-medic processing input file ms2/11.raw.ms2...
INFO: param-medic processing input file ms2/12.raw.ms2...
INFO: param-medic processing input file ms2/13.raw.ms2...
INFO: param-medic processing input file ms2/1.raw.ms2...
INFO: param-medic processing input file ms2/2.raw.ms2...
INFO: param-medic processing input file ms2/3.raw.ms2...
INFO: param-medic processing input file ms2/4.raw.ms2...
INFO: param-medic processing input file ms2/5.raw.ms2...
INFO: param-medic processing input file ms2/6.raw.ms2...
INFO: param-medic processing input file ms2/7.raw.ms2...
INFO: param-medic processing input file ms2/8.raw.ms2...
INFO: param-medic processing input file ms2/9.raw.ms2...
INFO:
INFO: Search parameter recommendations:
INFO: Processed 1213584 total spectra
INFO:   charge 0
INFO: Processed 0 qualifying spectra
INFO: Precursor pairs: 0
INFO: Fragment pairs: 0
INFO: Total spectra in the same bin as another: 0
INFO: Total spectra in the same bin as another and within m/z tol: 0
INFO: Total spectra in the same bin as another and within m/z tol and within scan range: 0
INFO:   charge 2
INFO: Processed 7725 qualifying spectra
INFO: Precursor pairs: 0
INFO: Fragment pairs: 0
INFO: Total spectra in the same bin as another: 1584
INFO: Total spectra in the same bin as another and within m/z tol: 306
INFO: Total spectra in the same bin as another and within m/z tol and within scan range: 66
INFO: Proportion of bins with multiple fragments: 0.02
INFO:   charge 3
INFO: Processed 7725 qualifying spectra
INFO: Precursor pairs: 0
INFO: Fragment pairs: 0
INFO: Total spectra in the same bin as another: 1245
INFO: Total spectra in the same bin as another and within m/z tol: 308
INFO: Total spectra in the same bin as another and within m/z tol and within scan range: 67
INFO: Proportion of bins with multiple fragments: 0.02
INFO:   charge 4
INFO: Processed 0 qualifying spectra
INFO: Precursor pairs: 0
INFO: Fragment pairs: 0
INFO: Total spectra in the same bin as another: 0
INFO: Total spectra in the same bin as another and within m/z tol: 0
INFO: Total spectra in the same bin as another and within m/z tol and within scan range: 0
INFO: Did not find spectra from known charges, so looking for unknown-charge spectra.
INFO: Precursor and fragment error summary:
ERROR: Precursor error calculation failed: Need >= 200 peak pairs to fit mixed distribution. Got only 0.
Details:
  Charge 0
Spectra in same averagine bin as another: 0
    ... and also within m/z tolerance: 0
    ... and also within scan range: 0
    ... and also with sufficient in-common fragments: 0
  Charge 2
Spectra in same averagine bin as another: 1584
    ... and also within m/z tolerance: 306
    ... and also within scan range: 66
    ... and also with sufficient in-common fragments: 0
  Charge 3
Spectra in same averagine bin as another: 1245
    ... and also within m/z tolerance: 308
    ... and also within scan range: 67
    ... and also with sufficient in-common fragments: 0
  Charge 4
Spectra in same averagine bin as another: 0
    ... and also within m/z tolerance: 0
    ... and also within scan range: 0
    ... and also with sufficient in-common fragments: 0

ERROR: Fragment error calculation failed: Need >= 200 peak pairs to fit mixed distribution. Got only 0.
Details:
  Charge 0
Spectra in same averagine bin as another: 0
    ... and also within m/z tolerance: 0
    ... and also within scan range: 0
    ... and also with sufficient in-common fragments: 0
  Charge 2
Spectra in same averagine bin as another: 1584
    ... and also within m/z tolerance: 306
    ... and also within scan range: 66
    ... and also with sufficient in-common fragments: 0
  Charge 3
Spectra in same averagine bin as another: 1245
    ... and also within m/z tolerance: 308
    ... and also within scan range: 67
    ... and also with sufficient in-common fragments: 0
  Charge 4
Spectra in same averagine bin as another: 0
    ... and also within m/z tolerance: 0
    ... and also within scan range: 0
    ... and also with sufficient in-common fragments: 0

INFO:
INFO:
WARNING: SILAC: No counts for any control separation pairs! Cannot estimate prevalance of SILAC separations.
INFO: iTRAQ: no reporter ions detected
INFO: TMT: no reporter ions detected
WARNING: No spectra usable for phosphorylation detection
INFO: No modifications detected requiring search parameter changes.
INFO: Elapsed time: 130 s
INFO: Finished crux param-medic.
INFO: Return Code:0