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compomics / peptide-shaker-2.0-issue-tracker

Issue tracker for the beta release of PeptideShaker 2.0
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PeptideShaker going into endless loop #59

Closed CarlaCristinaUranga closed 3 years ago

CarlaCristinaUranga commented 4 years ago

Hi, in a previous communication, it was discovered that PeptideShakerCLI on a large-memory server was going into an endless loop because of a bug in reading mgf files, which were generated via msconvert. I was able to overcome this using PeptideShakerGUI on my computer, but I am now running into the same issue using PeptideShakerGUI. No error is reported, the program simply stalls and does not output anything.

I was wondering how this bug fix is going, and why sometimes PeptideShakerGUI works, but PeptideShakerCLI never works. The database I am using is a custom generic 1.3 G database, any help is appreciated. Thanks!

hbarsnes commented 4 years ago

Hi Carla,

This bug has been fixed, but due to other unrelated issues we have not yet been able to update the beta release. I will let you know as soon as a new beta release is available.

Best regards, Harald

CarlaCristinaUranga commented 4 years ago

Ok. Well now is is evident that PeptideShaker freezes at the "Simplify Protein Groups" stage. Thank you and I am looking forward to the new version.

hbarsnes commented 3 years ago

This issue should hopefully be fixed in the new releases that have now been made available. If not, please let us know by opening a new issue here: https://github.com/compomics/peptide-shaker/issues.

CarlaCristinaUranga commented 3 years ago

YAY!!! Thank you Harald, how awesome. I am wondering, is it a new beta version or is this version available in the compomics website? Good to hear you are OK, I hope things are getting better where you are!

Best wishes,

Carla Uranga

On Wed, Nov 4, 2020 at 6:47 AM Harald Barsnes notifications@github.com wrote:

This issue should hopefully be fixed in the new releases that have now been made available. If not, please let us know by opening a new issue here: https://github.com/compomics/peptide-shaker/issues.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/compomics/peptide-shaker-2.0-issue-tracker/issues/59#issuecomment-721775524, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFK6HCZEI7ILNOOYWPCBW3LSOFSRZANCNFSM4NSIOPPA .

hbarsnes commented 3 years ago

Hi Carla,

I am wondering, is it a new beta version or is this version available in the compomics website?

The new normal releases are available via the standard download links. :)

Best regards, Harald