How much memory/RAM do you have on your computer? It won't make a huge difference but larger spectrum batch sizes are more efficient. So see if you have enough free memory to run with that parameter set at say 5000. With our 16GB linux computers performing high-res ms/ms searches, I use batch sizes of 10000.
On Wed, Aug 10, 2016 at 12:27 AM, Eslam Nouri <eslamno...@gmail.com> wrote: > Thanks a lot Jimmy. It is a relief to know that I am doing the best that I > can do with my current system. > > I have already removed all the dynamic modifications that I had (no > methionine oxidation or phosphorylations were defined). I have also > confined the analysis to 1000 spectra batch size. Database search takes a > long time, but it identifies a large number of microbiome proteins with > high confidence. > > Eslam > > On Tue, Aug 9, 2016 at 11:39 PM, Jimmy Eng <jke...@gmail.com> wrote: > >> Eslam, >> >> Setting "num_threads = 0" is the best you can do. There's no free lunch >> ... a database that's 100 times larger than the human UniProt fasta will >> take approximately 100 times longer to run, e.g. a 10 minute human search >> would translate to a 17 hour search if the database were 100 times larger. >> You can give things up (no variable modifications, no missed cleavages, >> narrow precursor mass tolerance, etc.) to hopefully speed things up a >> little bit. Otherwise you just have to throw more horsepower at it. You >> can get Broadwell-class Xeon processors with up to 24 cores in them. >> >> On Tue, Aug 9, 2016 at 11:30 PM, Eslam Nouri <eslamno...@gmail.com> >> wrote: >> >>> Hi Eric, >>> >>> I am using comet. In my comet file the number of threads is equal to >>> zero "num_threads = 0". I have attached my system information. Is there >>> any way to increase the data analysis time by defining a thread number? >>> >>> Thanks, Eslam >>> >>> On Tue, Aug 9, 2016 at 11:18 PM, Eric Deutsch < >>> edeut...@systemsbiology.org> wrote: >>> >>>> Which search engine are you using? Comet? Tandem? >>>> >>>> >>>> >>>> Comet has num_threads: >>>> >>>> http://comet-ms.sourceforge.net/parameters/parameters_201601 >>>> /num_threads.php >>>> >>>> >>>> >>>> Tandem has threads: >>>> >>>> http://www.thegpm.org/TANDEM/api/st.html >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> *From:* spctools-discuss@googlegroups.com [mailto: >>>> spctools-discuss@googlegroups.com] *On Behalf Of *Eslam Nouri >>>> *Sent:* Tuesday, August 9, 2016 11:05 PM >>>> *To:* spctools-discuss@googlegroups.com >>>> *Subject:* [spctools-discuss] Multi core analysis >>>> >>>> >>>> >>>> Hello_ >>>> >>>> >>>> >>>> I am using TPP for the database search of microbiome proteins. Since >>>> the fasta file that I have is more than 100 times larger than human uniprot >>>> fasta file, the database search for a single DDA run takes more than 12 >>>> hours. Is there any way to have faster analysis using multi-cores? >>>> >>>> >>>> >>>> Thanks, Eslam >>>> >>>> Proteomics core facility >>>> >>>> University of southern California >>>> >>>> -- >>>> 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 spctools-discuss+unsubscr...@googlegroups.com. >>>> To post to this group, send email to spctools-discuss@googlegroups.com. >>>> 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 spctools-discuss+unsubscr...@googlegroups.com. >>>> To post to this group, send email to spctools-discuss@googlegroups.com. >>>> 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 spctools-discuss+unsubscr...@googlegroups.com. >>> To post to this group, send email to spctools-discuss@googlegroups.com. >>> 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 spctools-discuss+unsubscr...@googlegroups.com. >> To post to this group, send email to spctools-discuss@googlegroups.com. >> 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 spctools-discuss+unsubscr...@googlegroups.com. > To post to this group, send email to spctools-discuss@googlegroups.com. > 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. 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