MatthewThe

For a test set of 16M PSMs (8M target and 8M decoy), the wall clock time speed up is also roughly 2: 6.7h on a single core vs 3.4h with...

Looks like a problem with linking the external libraries. Did you use the `admin/builders/centos64_build.sh` script? If not, could you post the command you used to start the build?

Fixed by #289

Added in e487451900f357275669123321635628c7873683 Flag is `--no-analytics`

Hi, sorry for the slow reply. Changing it could break some other downstream applications that expect m/z instead of mass. I'll do a quick check of the main downstream packages...

Since the 3.0 release we have included a temporary fix using [std::tmpnam](http://en.cppreference.com/w/cpp/io/c/tmpnam). However, there is a [theoretical chance this fails, as well as a security issue](http://stackoverflow.com/questions/21295974/are-there-any-reasons-to-avoid-using-tmpnam-to-get-a-name-for-a-temporary-file). Somehow changing to [std::tmpfile](http://www.cplusplus.com/reference/cstdio/tmpfile/)...

We have revised the logic and error messages in a commit (40f6798) after the 3.01 release, after earlier complaints from other users regarding this issue: The new help message regarding...

I can indeed reproduce your results on some data of my own. We are investigating this further, I'll try to get back to you next week.

You can override this automatic detection by using the `--search-input` argument. We try to detect the type of input (concatenated or separate) based on the scan numbers provided. If we...

You can find all the current command line parameters by executing `percolator -h`. The page you refer to needs to be updated, thanks for raising that issue!