search

pFindStudio / pFind3

23 stars 7 forks source link

search stopped #25

Open caverliersun2003 opened 5 years ago

caverliersun2003 commented 5 years ago

Hi, pfind team, I'm using the pFind3.1.5 to search a set of 6 raw files. But it stopped in the middle without any error message.

here is the log message: [E:\DSP\20190131\SCX\pFindTask2\ : 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] - --------- BEGIN PARAMETERS ----------- [pParse] - 01: check_activationcenter = 1 [pParse] - 02: co-elute = 1 [pParse] - 03: cut_similiar_mono = 1 [pParse] - 04: datanum = 6 [pParse] - 05: datapath1 = E:\DSP\20190131\SCX\CY_acetyl_SCX1.raw [pParse] - 06: datapath2 = E:\DSP\20190131\SCX\CY_acetyl_SCX2.raw [pParse] - 07: datapath3 = E:\DSP\20190131\SCX\CY_acetyl_SCX3.raw [pParse] - 08: datapath4 = E:\DSP\20190131\SCX\CY_acetyl_SCX4.raw [pParse] - 09: datapath5 = E:\DSP\20190131\SCX\CY_acetyl_SCX5.raw [pParse] - 10: datapath6 = E:\DSP\20190131\SCX\CY_acetyl_SCX6.raw [pParse] - 11: delete_msn = 0 [pParse] - 12: input_format = raw [pParse] - 13: intensity = 1 [pParse] - 14: ipv_file = .\IPV.txt [pParse] - 15: isolation_width = 2.000000 [pParse] - 16: logfilepath = [pParse] - 17: m/z = 5 [pParse] - 18: mars_model = 4 [pParse] - 19: mars_threshold = -0.500000 [pParse] - 20: mstol = 20.000000 [pParse] - 21: mstolppm = 1 [pParse] - 22: output_mgf = 1 [pParse] - 23: output_pf = 1 [pParse] - 24: outputpath = [pParse] - 25: recalibrate_window = 7.000000 [pParse] - 26: rewrite_files = 0 [pParse] - --------- END PARAMETERS ------------- [pParse] - pParse writes logs in E:\DSP\20190131\SCX\pParsePlusLog.txt [pParse] - E:\DSP\20190131\SCX\CY_acetyl_SCX1.raw has existed results, skipping... [pParse] - E:\DSP\20190131\SCX\CY_acetyl_SCX2.raw has existed results, skipping... [pParse] - E:\DSP\20190131\SCX\CY_acetyl_SCX3.raw has existed results, skipping... [pParse] - E:\DSP\20190131\SCX\CY_acetyl_SCX4.raw has existed results, skipping... [pParse] - E:\DSP\20190131\SCX\CY_acetyl_SCX5.raw has existed results, skipping... [pParse] - E:\DSP\20190131\SCX\CY_acetyl_SCX6.raw has existed results, skipping... [pParse] - == == == Time elapsed: 1 seconds. == == == = [pFind] ######################################### [pFind] # # [pFind] # Welcome to use pFind search engine! # [pFind] # # [pFind] # version 3.1.5 # [pFind] # # [pFind] # http://pfind.ict.ac.cn # [pFind] # # [pFind] ######################################### [pFind] Fasta path: E:\database\uniprot-proteome_Human201901HBV_con.fasta [pFind] MSMS path: E:\DSP\20190131\SCX\CY_acetyl_SCX1_HCDFT.pf2 [pFind] <Search 1> Round: 1 / 1 [pFind] <Search 1>: 100% [pFind] Search time: 121.16 [pFind] Inferring proteins... [pFind] Inferring proteins completed. [pFind] : 100% [pFind] <Search 2> Round: 1 / 1 [pFind] <Search 2>: 100% [pFind] Time Used: 175.91. [pFind] Inferring proteins... [pFind] Inferring proteins completed. [pFind] : 100% [pFind] MSMS path: E:\DSP\20190131\SCX\CY_acetyl_SCX2_HCDFT.pf2 [pFind] <Search 1> Round: 1 / 1 [pFind] <Search 1>: 100% [pFind] Search time: 214.15 [pFind] Inferring proteins... [pFind] Inferring proteins completed. [pFind] : 100% [pFind] <Search 2> Round: 1 / 1 [pFind] <Search 2>: 100% [pFind] Time Used: 269.96. [pFind] Inferring proteins... [pFind] Inferring proteins completed. [pFind] : 100% [pFind] MSMS path: E:\DSP\20190131\SCX\CY_acetyl_SCX3_HCDFT.pf2 [pFind] <Search 1> Round: 1 / 1 [pFind] <Search 1>: 100% [pFind] Search time: 60.12 [pFind] Inferring proteins... [pFind] Inferring proteins completed. [pFind] : 100% [pFind] <Search 2> Round: 1 / 1 [pFind] <Search 2>: 100% [pFind] Time Used: 147.28. [pFind] Inferring proteins... [pFind] Inferring proteins completed. [pFind] : 100% [pFind] MSMS path: E:\DSP\20190131\SCX\CY_acetyl_SCX4_HCDFT.pf2

Can anyone help me to diagnose the problem? thank you very much!

Sun

xuesu commented 4 years ago

can you give me more logs? it looks good. sometimes it did suspend since you do not enough room...

kiallsuazo commented 3 years ago

Hi.

I was using pFind and it was fine. However, it was not working when I used some .raw data acquired through ETHCD. I was not sure if this kind of data is not suitable for pFind or I am just missing something out. Please let me know how to fix the issue on the msmspath error. I am pasting here the error log. Thank you so much!

Process 1: Process 1: Process 1: / pParse2.0 (x64) from pFind Studio \ Process 1: / Email : pfind@ict.ac.cn \ Process 1: \ Website: http://pfind.ict.ac.cn / Process 1: Process 1: Process 1: The license will expire in 2100-1-1 Process 1: [pParse] - --------- BEGIN PARAMETERS ----------- Process 1: [pParse] - 01: check_activationcenter = 1 Process 1: [pParse] - 02: co-elute = 1 Process 1: [pParse] - 03: cut_similiar_mono = 1 Process 1: [pParse] - 04: datanum = 1 Process 1: [pParse] - 05: datapath1 = C:\Users\suazo003\Documents\Rab7aSSSC_pFind\KS_11202020_Rab7aSSSC_untargeted1.raw Process 1: [pParse] - 06: delete_msn = 0 Process 1: [pParse] - 07: input_format = raw Process 1: [pParse] - 08: intensity = 1 Process 1: [pParse] - 09: ipv_file = .\IPV.txt Process 1: [pParse] - 10: isolation_width = 2.000000 Process 1: [pParse] - 11: logfilepath = C:\Users\suazo003\Documents\Rab7aSSSC_pFind.proc1 Process 1: [pParse] - 12: m/z = 4 Process 1: [pParse] - 13: mars_model = 4 Process 1: [pParse] - 14: mars_threshold = -0.500000 Process 1: [pParse] - 15: mstol = 20.000000 Process 1: [pParse] - 16: mstolppm = 1 Process 1: [pParse] - 17: output_mgf = 1 Process 1: [pParse] - 18: output_msb = 0 Process 1: [pParse] - 19: output_pf = 1 Process 1: [pParse] - 20: outputpath = Process 1: [pParse] - 21: recalibrate_window = 7.000000 Process 1: [pParse] - 22: rewrite_files = 0 Process 1: [pParse] - --------- END PARAMETERS ------------- Process 1: [pParse] - pParse writes logs in C:\Users\suazo003\Documents\Rab7aSSSC_pFind.proc1\pParsePlusLog.txt Process 1: [pParse] - .\xtract_raw.exe -ms -a -i 1 -m 4 -o "C:\Users\suazo003\Documents\Rab7aSSSC_pFind" "C:\Users\suazo003\Documents\Rab7aSSSC_pFind\KS_11202020_Rab7aSSSC_untargeted1.raw" Process 1: [pXtract] - The software will expire in 1/1/2100 Process 1: [pXtract] - Begin to extract C:\Users\suazo003\Documents\Rab7aSSSC_pFind\KS_11202020_Rab7aSSSC_untargeted1.raw Process 1: [pXtract] - Try to generate new rawinfo. Process 1: [pXtract] - : 99.95% Process 1: [pXtract] - Output Files Completed! Process 1: [pXtract] - Extracted C:\Users\suazo003\Documents\Rab7aSSSC_pFind\KS_11202020_Rab7aSSSC_untargeted1.raw Process 1: [pXtract] - == == == Time elapsed: 23.053s. == == == Process 1: [pParse] - Start to process C:\Users\suazo003\Documents\Rab7aSSSC_pFind\KS_11202020_Rab7aSSSC_untargeted1.ms1 Process 1: [pParse] - Start to process C:\Users\suazo003\Documents\Rab7aSSSC_pFind\KS_11202020_Rab7aSSSC_untargeted1.ms2 Process 1: [pParse] - Start to process C:\Users\suazo003\Documents\Rab7aSSSC_pFind\KS_11202020_Rab7aSSSC_untargeted1.pf1 Process 1: [pParse] - Start to process C:\Users\suazo003\Documents\Rab7aSSSC_pFind\KS_11202020_Rab7aSSSC_untargeted1_ETHCDFT.pf2 Process 1: [pParse] - Start to process C:\Users\suazo003\Documents\Rab7aSSSC_pFind\KS_11202020_Rab7aSSSC_untargeted1_ETHCDFT.mgf Process 1: [pParse] - Extracting MS1, Scan Num = 1000 Process 1: [pParse] - Extracting MS2, Scan Num = 2000 Process 1: [pParse] - Extracting MS1, Scan Num = 2000 Process 1: [pParse] - Extracting MS2, Scan Num = 7000 Process 1: [pParse] - Extracting MS1, Scan Num = 3000 Process 1: [pParse] - Extracting MS2, Scan Num = 10000 Process 1: [pParse] - Extracting MS1, Scan Num = 4000 Process 1: [pParse] - Extracting MS2, Scan Num = 11000 Process 1: [pParse] - Extracting MS1, Scan Num = 5000 Process 1: [pParse] - Extracting MS2, Scan Num = 12000 Process 1: [pParse] - Extracting MS1, Scan Num = 6000 Process 1: [pParse] - Extracting MS1, Scan Num = 7000 Process 1: [pParse] - Extracting MS2, Scan Num = 13000 Process 1: [pParse] - Extracting MS1, Scan Num = 8000 Process 1: [pParse] - Extracting MS1, Scan Num = 9000 Process 1: [pParse] - Extracting MS1, Scan Num = 10000 Process 1: [pParse] - Extracting MS1, Scan Num = 11000 Process 1: [pParse] - Extracting MS1, Scan Num = 12000 Process 1: [pParse] - Extracting MS1, Scan Num = 13000 Process 1: [pParse] - Closed C:\Users\suazo003\Documents\Rab7aSSSC_pFind\KS_11202020_Rab7aSSSC_untargeted1.ms1 Process 1: [pParse] - Finished Operations on C:\Users\suazo003\Documents\Rab7aSSSC_pFind\KS_11202020_Rab7aSSSC_untargeted1.ms1 Process 1: [pParse] - Scan Number in C:\Users\suazo003\Documents\Rab7aSSSC_pFind\KS_11202020_Rab7aSSSC_untargeted1.ms1: 13799 Process 1: [pParse] - Closed C:\Users\suazo003\Documents\Rab7aSSSC_pFind\KS_11202020_Rab7aSSSC_untargeted1.pf1 Process 1: [pParse] - Finished Operations on C:\Users\suazo003\Documents\Rab7aSSSC_pFind\KS_11202020_Rab7aSSSC_untargeted1.pf1 Process 1: [pParse] - Scan Number in C:\Users\suazo003\Documents\Rab7aSSSC_pFind\KS_11202020_Rab7aSSSC_untargeted1.pf1: 13799 Process 1: [pParse] - Closed C:\Users\suazo003\Documents\Rab7aSSSC_pFind\KS_11202020_Rab7aSSSC_untargeted1.ms2 Process 1: [pParse] - Finished Operations on C:\Users\suazo003\Documents\Rab7aSSSC_pFind\KS_11202020_Rab7aSSSC_untargeted1.ms2 Process 1: [pParse] - Scan Number in C:\Users\suazo003\Documents\Rab7aSSSC_pFind\KS_11202020_Rab7aSSSC_untargeted1.ms2: 13814 Process 1: [pParse] - Closed C:\Users\suazo003\Documents\Rab7aSSSC_pFind\KS_11202020_Rab7aSSSC_untargeted1_ETHCDFT.pf2 Process 1: [pParse] - Finished Operations on C:\Users\suazo003\Documents\Rab7aSSSC_pFind\KS_11202020_Rab7aSSSC_untargeted1_ETHCDFT.pf2 Process 1: [pParse] - Scan Number in C:\Users\suazo003\Documents\Rab7aSSSC_pFind\KS_11202020_Rab7aSSSC_untargeted1_ETHCDFT.pf2: 13814 Process 1: [pParse] - Closed C:\Users\suazo003\Documents\Rab7aSSSC_pFind\KS_11202020_Rab7aSSSC_untargeted1_ETHCDFT.mgf Process 1: [pParse] - Finished Operations on C:\Users\suazo003\Documents\Rab7aSSSC_pFind\KS_11202020_Rab7aSSSC_untargeted1_ETHCDFT.mgf Process 1: [pParse] - Scan Number in C:\Users\suazo003\Documents\Rab7aSSSC_pFind\KS_11202020_Rab7aSSSC_untargeted1_ETHCDFT.mgf: 13814 Process 1: [pParse] - Closed C:\Users\suazo003\Documents\Rab7aSSSC_pFind\KS_11202020_Rab7aSSSC_untargeted1.csv Process 1: [pParse] - Finished Operations on C:\Users\suazo003\Documents\Rab7aSSSC_pFind\KS_11202020_Rab7aSSSC_untargeted1.csv Process 1: [pParse] - Scan Number in C:\Users\suazo003\Documents\Rab7aSSSC_pFind\KS_11202020_Rab7aSSSC_untargeted1.csv: 13814 Process 1: [pParse] - == == == Time elapsed: 80 seconds. == == == = [pFind] ALERT: Invalid_msmspath1_Path: [C:\Users\suazo003\Documents\Rab7aSSSC_pFind\KS_11202020_Rab7aSSSC_untargeted1_HCDFT.pf2]