Hi Bob, Brian mentioned something that brought stalled applications to mind. Sometimes a virus scanner can halt the application at its start without warning you, leaving it in limbo indefinitely. If you are using a virus scanner, you can try disabling it to see if it solves the problem. If so, then create a rule that allows comet to run.
Cheers, Mike From: [email protected] [mailto:[email protected]] On Behalf Of Brian Hampton Sent: Monday, March 21, 2016 3:39 PM To: spctools-discuss Subject: Re: [spctools-discuss] Comet search performance issue Hello Bob, Go to Task Manager and look at Processes to see if comet is still actually running. If so look at Performance and see if it is using the number of threads that you specified in the parameter file. This might give a clue as to why it is taking so long, for example if you somehow told it to use only one thread. Did you specify an enzyme or no enzyme search? The latter will take a long time. Might help if you posted your comet parameters file. Also, I have found that running TPP processes from the command line produces useful output to help debug problems. You can "cheat" and run it via Petunia, then copy paste the command from there to a cmd window and watch the output. Sometimes you will receive errors or warnings that will give you a clue as to what is happening. You might also try generating a new comet params file and then editing it to suit your conditions. WRT msconvert, I usually just do peak picking on those MS levels where you have profile data and leave rest to defaults. I am not certain what msconvert does with profile data by default so I specify that parameter. It would be nice if others would share their msconvert parameters. Brian Brian Hampton Protein Analysis Lab Center for Vascular and Inflammatory Diseases University of Maryland School of Medicine 655 West Baltimore Street BRB 7-018 Baltimore MD 21201 V: 410-706-8207 On Mon, Mar 21, 2016 at 5:11 PM, <[email protected]> wrote: Hi everyone, I started a Comet search in TPP three days ago and it is still going three days later. I must have messed up something without knowing because TPP did not generate any error message. Did anyone else have similar experience? Please see my system and TPP info below. HP Z600 Workstation Windows 7 Professional Processor: Intel(R) Xeon(R) CPU E5640 @ 2.67GHz 2.66 GHz Installed memory (RAM): 24.0 GB System type: 64-bit Operating System TPP v4.8.0 PHILAE, Build 201411201551-6764 (mingw-i686) Comet search mzXML input file: mydata.mzXML (110 MB) generated using command line msconvert C:/Inetpub/tpp-bin/msconvert mydata.raw --mzXML --filter "mslevel 2" --filter "threshold count 100 most-intense" Comet Parameters file: comet.params (default, came with TPP installation) Sequence database: human_uniprot_sprot.fasta Any advice/pointer is greatly appreciated. Thanks, Bob Xiong -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout. -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout. -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
