Abacus error, freezes at 20% progress

[Linda Switzar]

Dear Damian,

after a few minor hick-ups, I think I now have all the right files and settings to run Abacus via the GUI. Unfortunately, the program freezes at 20% of the progress at the step of "recalculating peptide weights for combined..." (see attached screenshot). This also happens when using the sample data. Any ideas or suggestions?

Kind regards,

Linda Switzar

[dfermin]

Hi Linda,

Sorry so see you are having problems.

I need a little debugging information to try to figure out what's going wrong.

Could you launch Abacus from the command prompt in Windows?

Just open a command prompt, go to the folder where the Abacus jar file is located and type:
java -jar abacus.jar

Then run Abacus normally.

When it freezes, the error text will appear in the command prompt.
If you could send me that information along with the names of the XML files I should be able to diagnose the problem.

Damian

[Linda Switzar]

Hello Damian,

Thanks for your swift reply! when I ran Abacus from the command prompt, there was no problem anymore!

Do you have any suggestions for the probability settings? For instance, is it best to use similar ones as in TPP to obtain 1% FDR?

Thanks,

Linda