For a huge run, irrespective of whether it's converted in profile or centroid mode (the # of MS/MS scans is more important), be sure to set the parameter "spectrum_batch_size" to something non-zero. If this parameter value is set to 0, Comet will try to load all spectra into memory at once. With your huge file, you likely don't have enough system memory for this to work and the program will likely crash or possibly slow to a crawl with disk swapping. Off the top of my head, I can't remember what "spectrum_batch_size" value corresponds to approximately what memory use (as this also depends on the bin size parameter). Try starting with a value of 10000 and monitor your search progress to see if it's progressing.
On Tue, Jan 24, 2017 at 11:13 AM, Eric Deutsch <[email protected]> wrote: > Aha, that’s probably the problem. During your conversion from wiff to > mzML, you should turn ON peak picking. Otherwise your profile mode data > will be huge and the searches will take a very long time. > > > > Regards, > > Eric > > > > > > *From:* Joel Christie [mailto:[email protected]] > *Sent:* Tuesday, January 24, 2017 10:42 AM > *To:* Eric Deutsch > *Subject:* Re: [spctools-discuss] Error while conversion of files > > > > One more thing, the .mzML file after the conversion from .Wiff was of > nearly 18 GB. > > > > > > On Wed, Jan 25, 2017 at 12:01 AM, Joel Christie < > [email protected]> wrote: > > Hi, > > > > I am using the params files that were taught at TPP workshop at Delhi > except the SILAC modifications. > > > > Other thing I would like to ask is what specifications of Computer you are > suggesting me to use to analyse a IDA run of cancer cell line, where around > 2000 proteins with 95% confidence are assigned using Protein Pilot of Ab > Sciex. > > > > Today I have started searching for Tandem as well, till the time I left > the lab it was still loading the spectra. > > > > For Comet, I am attaching one screenshot with this post. Please have a > look at it. When I tried to kill the Job, I couldn't. > > > > Thank you very much for your support. > > > > regards, > > Joel. > > > > > > On Tue, Jan 24, 2017 at 11:48 PM, Eric Deutsch < > [email protected]> wrote: > > Well, normally it should not, but depending on your data file(s) and > parameters you’ve set as well as the computer you’re running on, it > certainly may. Comet very rarely just keeps running without making > progress, so the search you’ve specified is probably just too expensive for > the computing power you’re making available to it. Using more threads, > fewer mass mods, fully tryptic search, large MS2 binsize, smaller sequence > database may all help. But without posting specifics, it is hard to guess > what the problem might be. Posting your comet.params file might help. > > > > Regards, > > Eric > > > > > > *From:* Joel Christie [mailto:[email protected]] > *Sent:* Tuesday, January 24, 2017 9:55 AM > *To:* spctools-discuss > *Cc:* [email protected] > *Subject:* Re: [spctools-discuss] Error while conversion of files > > > > Thanks it worked for me. Now I have different problem.Its been two days > still Comet search is not over. I don't know whether it should take this > much of time? > > > > On Saturday, 21 January 2017 00:25:08 UTC+5:30, Eric Deutsch wrote: > > Hi Joel, the problem is a space in your folder names. Some tools are > confused by this. If you rename “Joel Data” to “JoelData” (without the > space) and remove any other spaces in file name and folder names, things > should work a lot better. > > > > Regards, > > Eric > > > > > > *From:* [email protected] [mailto:[email protected] > <[email protected]>] *On Behalf Of *Joel Christie > *Sent:* Friday, January 20, 2017 9:14 AM > *To:* spctools-discuss <[email protected]> > *Subject:* [spctools-discuss] Error while conversion of files > > > > Dear all, > > > > I am facing an error while converting files from Sciex's .wiff files to > MzML, I am uploading an error msg with this post. Please check and suggest > me a solution. > > > > I am just beginning to use TPP. > > > > Much Thanks in Advance, > > Joel > > -- > 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.
