Errors running pFind3

[nelson42]

When running pFind3 the software always fails when looking for a certain file. From some testing it looks like it may be an issue to do with the MS instrument selection. When set to HCD-FTMS there is a missing file at this point with no explanation of why pFind didn't create it. When set to CID-ITMS at this stage pFind looks for the file "...CIDIT.pf2" rather than "...HCDFT.pf2" however this still doesn't work and pFind fails when trying to read it with no error. The log output is below.

[P:\pFind\pFindTask1\ : start from Data Extraction]

   *********************************************
  /       pParse2.0 (x64) from pFind Studio     \
 /        Email  :  pfind@ict.ac.cn              \
 \        Website:  http://pfind.ict.ac.cn       /
   *********************************************

The license will expire in 2020-1-1
[pParse] <INFO> - --------- BEGIN PARAMETERS -----------
[pParse] <INFO> - 01: check_activationcenter = 1
[pParse] <INFO> - 02: co-elute = 1
[pParse] <INFO> - 03: cut_similiar_mono = 1
[pParse] <INFO> - 04: datanum = 1
[pParse] <INFO> - 05: datapath1 = C:\Users\nelson\Desktop\Dan_FlyTC_set1_F3.mzML
[pParse] <INFO> - 06: delete_msn = 0
[pParse] <INFO> - 07: input_format = mzml
[pParse] <INFO> - 08: intensity = 1
[pParse] <INFO> - 09: ipv_file = .\IPV.txt
[pParse] <INFO> - 10: isolation_width = 2.000000
[pParse] <INFO> - 11: logfilepath = 
[pParse] <INFO> - 12: m/z = 5
[pParse] <INFO> - 13: mars_model = 4
[pParse] <INFO> - 14: mars_threshold = -0.500000
[pParse] <INFO> - 15: mstol = 20.000000
[pParse] <INFO> - 16: mstolppm = 1
[pParse] <INFO> - 17: output_mgf = 0
[pParse] <INFO> - 18: output_pf = 1
[pParse] <INFO> - 19: outputpath = 
[pParse] <INFO> - 20: recalibrate_window = 7.000000
[pParse] <INFO> - 21: rewrite_files = 0
[pParse] <INFO> - --------- END PARAMETERS -------------
[pParse] <INFO> - pParse writes logs in C:\Users\nelson\Desktop\pParsePlusLog.txt
[pParse] <INFO> - .\xtract_xml.exe -ms -a -i 1 -m 5 -o "C:\Users\nelson\Desktop" "C:\Users\nelson\Desktop\Dan_FlyTC_set1_F3.mzML"
[pXtract] <INFO> - The software will expire in 01/01/2020
[pXtract] <INFO> - Begin to extract C:\Users\nelson\Desktop\Dan_FlyTC_set1_F3.mzML
[pXtract] <INFO> - Reading Scans, Scan Num = 100
[pXtract] <INFO> - Reading Scans, Scan Num = 200
[pXtract] <INFO> - Reading Scans, Scan Num = 300
.
.
.
[pXtract] <INFO> - Reading Scans, Scan Num = 57500
[pXtract] <INFO> - Reading Scans, Scan Num = 57600
[pXtract] <INFO> - Reading Scans, Scan Num = 57700
[pXtract] <INFO> - Reading MS1:7466, MS2:25136, total:57709
[pXtract] <INFO> - Output Files Completed!
[pXtract] <INFO> - Extracted C:\Users\nelson\Desktop\Dan_FlyTC_set1_F3.mzML
[pXtract] <INFO> -  == == == Time elapsed: 36.514s. == == ==
[pParse] <INFO> - Start to process C:\Users\nelson\Desktop\Dan_FlyTC_set1_F3.ms1
[pParse] <INFO> - Start to process C:\Users\nelson\Desktop\Dan_FlyTC_set1_F3.ms2
[pParse] <INFO> - Start to process C:\Users\nelson\Desktop\Dan_FlyTC_set1_F3.pf1
[pParse] <INFO> - Start to process C:\Users\nelson\Desktop\Dan_FlyTC_set1_F3_CIDIT.pf2
[pParse] <INFO> - Extracting MS1, Scan Num = 1000
[pParse] <INFO> - Extracting MS2, Scan Num = 1000
[pParse] <INFO> - Extracting MS1, Scan Num = 2000
[pParse] <INFO> - Extracting MS2, Scan Num = 2000
[pParse] <INFO> - Extracting MS1, Scan Num = 3000
[pParse] <INFO> - Extracting MS2, Scan Num = 6000
[pParse] <INFO> - Extracting MS1, Scan Num = 4000
[pParse] <INFO> - Extracting MS2, Scan Num = 11000
[pParse] <INFO> - Extracting MS1, Scan Num = 5000
[pParse] <INFO> - Extracting MS2, Scan Num = 22000
[pParse] <INFO> - Extracting MS1, Scan Num = 6000
[pParse] <INFO> - Extracting MS2, Scan Num = 24000
[pParse] <INFO> - Extracting MS1, Scan Num = 7000
[pParse] <INFO> - Extracting MS2, Scan Num = 25000
[pParse] <INFO> - Closed C:\Users\nelson\Desktop\Dan_FlyTC_set1_F3.ms1
[pParse] <INFO> - Finished Operations on C:\Users\nelson\Desktop\Dan_FlyTC_set1_F3.ms1
[pParse] <INFO> - Scan Number in C:\Users\nelson\Desktop\Dan_FlyTC_set1_F3.ms1: 7466
[pParse] <INFO> - Closed C:\Users\nelson\Desktop\Dan_FlyTC_set1_F3.pf1
[pParse] <INFO> - Finished Operations on C:\Users\nelson\Desktop\Dan_FlyTC_set1_F3.pf1
[pParse] <INFO> - Scan Number in C:\Users\nelson\Desktop\Dan_FlyTC_set1_F3.pf1: 7466
[pParse] <INFO> - Closed C:\Users\nelson\Desktop\Dan_FlyTC_set1_F3.ms2
[pParse] <INFO> - Finished Operations on C:\Users\nelson\Desktop\Dan_FlyTC_set1_F3.ms2
[pParse] <INFO> - Scan Number in C:\Users\nelson\Desktop\Dan_FlyTC_set1_F3.ms2: 25136
[pParse] <INFO> - Closed C:\Users\nelson\Desktop\Dan_FlyTC_set1_F3_CIDIT.pf2
[pParse] <INFO> - Finished Operations on C:\Users\nelson\Desktop\Dan_FlyTC_set1_F3_CIDIT.pf2
[pParse] <INFO> - Scan Number in C:\Users\nelson\Desktop\Dan_FlyTC_set1_F3_CIDIT.pf2: 25136
[pParse] <INFO> - Closed C:\Users\nelson\Desktop\Dan_FlyTC_set1_F3.csv
[pParse] <INFO> - Finished Operations on C:\Users\nelson\Desktop\Dan_FlyTC_set1_F3.csv
[pParse] <INFO> - Scan Number in C:\Users\nelson\Desktop\Dan_FlyTC_set1_F3.csv: 25136
[pParse] <INFO> -  == == == Time elapsed: 45 seconds. == == == = 
[pFind] ALERT: Invalid_msmspath1_Path: [C:\Users\nelson\Desktop\Dan_FlyTC_set1_F3_HCDFT.pf2]

[xuesu]

@nelson42 that's because pparse and pfind runs seperately. When pparse tries to output potential precursors, it does not know your instrument settings in pfind and has to guess it. HCDFT means pparse will refine the precursor infos and others means pparse will do nothing. That's why they are different. pls use the one showed after using pparse instead of your former settings.