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pFindStudio / pLink2

pLink is a software dedicated for the analysis of chemically cross-linked proteins or protein complexes using mass spectrometry.
http://pfind.ict.ac.cn/software/pLink/index.html
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search engine initializing #81

Open labguyatscripps opened 3 years ago

labguyatscripps commented 3 years ago

Hi I tried to use Plink to search a cross-link data. However, the search is halted at the step of “search engine initializing” and “generating reverse database”. BTW, I customized the mass shift for cross-linker. Thank you for your support. Best, Ming pParsePlusLog.txt image

01joy commented 3 years ago

Please show your parameter file *.plink.

Please make sure the fasta file does exist, and you have write permission to the folder of the fasta.

labguyatscripps commented 3 years ago

Thank you. You are right. My fasta file is located in a folder with whitespace in the folder name. I correct it with no whitespace. This time I make sure that my fasta file exist and have no whitespace. Also, we check the security setting for the folder. It allows the system and the administrator to visit the folder. I run it again. It’s still suck in the step of initializing the engine. I snapshot the output report. My MS sample was obtained from QE instrument that don’t have HCD (I think). I tried both HCD and CID-ETD, but it doesn’t work in both parameter. I attached the relevant files for your diagnosis. Thank you very much for your support. With best regards, Ming [cid:image002.png@01D6CEBF.DC1F6A10]

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From: bitJoymailto:notifications@github.com Sent: Wednesday, December 9, 2020 7:38 PM To: pFindStudio/pLink2mailto:pLink2@noreply.github.com Cc: Cheng, Mingmailto:ming.cheng@wustl.edu; Authormailto:author@noreply.github.com Subject: Re: [pFindStudio/pLink2] search engine initializing (#81)

Please show your parameter file *.plink.

Please make sure the fasta file does exist, and you have write permission to the folder of the fasta.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/pFindStudio/pLink2/issues/81#issuecomment-742217339, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ASCCIKP3ZF36HRSVJQGN3DDSUA7EFANCNFSM4UUM7U2A.

Thu Dec 10 06:26:38 2020 pParse.exe -D C:\Users\labguy\Desktop\ProjectAtScripps\BTFACrosslink\Rawdata\CMJL_1205_5.raw -t -0.5 -z 5 -i 1 -C 1 -a 0 -p 1 -S 1 Calling pXtract to export MS1 and MS2 files... MS1list completes. Processing CMJL_1205_5.MS1 Loading MS1 and MS2 files... Loading MS1 Spectra Number: 18978 Loading MS2 Spectra Number: 14163 Writing MS1 to PF... Evaluting by the classifier... Filtering by the threshold... Writing CSV... Releasing resources... Saving CSV to disk... Exported 29530 precursors. Found 0 duplicate scans. == == == Time elapsed: 94 seconds. == == == =