Comet 2021.01 rev. 0 is now available

[Jimmy Eng]

Comet 2021.01 rev. 0 is now available. 

Release notes: http://comet-ms.sourceforge.net/release/release_2021001/

Download link:  https://sourceforge.net/projects/comet-ms/files/

Release notes:

• Update the expectation value (E-value) calculation by improving the determination of the tail region of the xcorr cumulative distribution for  the linear regression fit.
• New ThreadPool code by D. Shteynberg. The previous code apparently has  intermittent issues when using many (70+) threads.
• Make flanking (previous and next) residue reporting consistent when a  peptide is present in a protein multiple times and thus could have different flanking residues within the same protein. Previous versions did not consistently report the same set of flanking residues in repeated/replicate  searches. The flanking residues for the first occurrence of the peptide in a protein will now always be reported.
• Added a parameter "old_mods_encoding" to enable using the old character based modification encodings (e.g. DLYM*NCK) instead mass based encodings (e.g. DLYM[15.9949]NCK) in the SQT output files. Add "old_mods_encoding = 1" to the comet.params file to use the old modification character encodings. This functionality was added to support post-processing tools that have not been updated to handle the numeric modification encodings.
• The "print_expect_score" parameter is now deprecated; it will be treated as a hidden parameter. Anyone using SQT output who would rather have the Sp score instead of the E-value reported will now have to manually add "print_expect_score = 0" to their params file.
• Added a no digestion (aka "no_cut", aka don't cleave anywhere) entry to the comet.params file.
• The Windows Visual Studio solution is updated to compile with v142 build tools using Visual Studio 2019.
• This version of Comet will also run using comet.params files from the 2020.01 releases as there have been no significant changes to the parameter entries.

[Harald Barsnes]

Hi Jimmy,

I just tested the new release and it all seems to work fine except for that the progress display seems to be a bit too eager? As the progress displayed for "Search Progress" now almost immediately goes up to 99% and then spend most of the actual search time getting from 99 to 100%?

Hopefully not too difficult to fix?

Best regards,

Harald

[Jimmy Eng]

The eager progress reporting was due to the program pre-loading every sequence in the fasta file with the search progress reporting being based on progress through the fasta file.  So once the sequences were all pre-loaded, that was reflected in the 99% progress.  Pre-loading all sequences was not intended for the release and the issue is resolved.  Looks like the Comet website is down right now but here's the direct link to the release files:  https://sourceforge.net/projects/comet-ms/files/.  The comet_2021010.zip contains updated binaries to address the progress reporting.  Yet again, I appreciate the report on the issue!

Jimmy

[Harald Barsnes]

Hi Jimmy,

I can confirm that the progress display is now back to normal. Thanks for the quick fix!

Best regards,

Harald