--
You received this message because you are subscribed to the Google Groups "crux-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to crux-users+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/crux-users/000d6fd2-88b1-4c35-b991-71b073849708n%40googlegroups.com.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Warning text added to this message by UW Information Technology he...@uw.edu ATTACHMENTS RENAMED This message came to the UW with an attached file with a name that ended in .zip or .exe. Because files of this type can automatically infect computers with a virus, the attachment has been renamed. o If the sender of the message is known to you, and you were expecting the message, you need simply save the attachment using the original name or save it as is and rename it back to the original name on your computer. o If the sender is not known to you, it is possible that the attachment contains a virus and you may simply delete the message. o If this message claims to be official and instructs you to open the attachment to get important information, it is likely to be fake. Virus writers are increasingly using sophisticated social engineering techniques to mislead people. UW-IT never sends important information about your account or password in an email attachment. Instead you will be directed to a web page on a UW-IT site. If you have further questions, please contact your local computing support or UW Information Technology email: he...@uw.edu phone: 206.221.5000 Warning text added to this message by UW Information Technology +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
To view this discussion on the web visit https://groups.google.com/d/msgid/crux-users/e3483902-f48c-4101-995c-d69027d07de5n%40googlegroups.com.
Hi Rita,Here's the percolator command I use to process comet output (actually for a different experiment but the issue is the same):crux percolator --overwrite T --subset-max-train 1000000 --klammer F --maxiter 10 --output-dir ./P3856/percolator-output-pasef-recalibrated --picked-protein ./fasta/Human_Yeast_Ecoli.fasta --protein T --protein-enzyme trypsin --search-input auto --verbosity 30 --fileroot P3856 ./comet-output-pasef-recalibrated/P3856_YHE211_1_Slot1-1_1_5104.comet.pinThe comet command I use is this:crux comet --parameter-file ./comet/TimsTOF-recalibration.params --output-dir ./comet-output-pasef-recalibrated --fileroot "P3856_YHE211_1_Slot1-1_1_5104" ./exp-P3856-run-P3856_YHE211_1_Slot1-1_1_5104-features-pasef-recalibrated.mgf ./fasta/Human_Yeast_Ecoli.fastaAttached is the MGF.Thanks,Daryl.