Hi Brian, It appears that all of the UNMAPPED results are to DECOY proteins. Is it possible that you regenerated the DECOYS at some point but kept the database name the same? DECOYS get reshuffled so you are not guaranteed to have the same DECOYS peptides that you had the first time you created the DECOYS. I would suggest you apply RefreshParser using the same database you used in the search or redo the search.
Thanks, -David On Tue, Jan 29, 2019 at 10:45 AM Hampton, Brian <[email protected]> wrote: > Hi David, > > Thanks for having a look. I sent you a link to the interact…pep.xml and > the database files to download at your convenience. > > Brian > > On Jan 29, 2019, at 1:09 PM, David Shteynberg < > [email protected]> wrote: > > Hi Brian, > > Can you post the files for me to trace the execution of RefreshParser and > troubleshoot the issue? > > Thanks, > -David > > On Tue, Jan 29, 2019 at 7:24 AM Hampton, Brian <[email protected]> > wrote: > >> Hello, >> >> I cannot determine why RefreshParser would not be able to remap all >> entries. Since the PSMs are derived from the fasta db used in the search, I >> would expect all PSMs to map to their respective database entries. For >> example: >> >> running: "/usr/local/tpp/bin/RefreshParser >> '/tmp/X33oJO/data/SMC/16-18-27-6094/source/interact-a-2.pep.xml' >> '/usr/local/tpp/data/dbase/human-reviewed-190128_DECOY-crap.fasta'" - >> Building Commentz-Walter keyword tree... >> - Searching the tree... >> - Linking duplicate entries... >> - Printing results... >> Warning: could not map 3081 entries >> >> command completed in 5 sec >> >> Thanks in advance for any help. >> >> Brian >> >> -- >> 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. > -- 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.
