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@googl >> egroups.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.
