Open MarcIsak opened 4 years ago
Hi Marc,
There is probably an undetected bug in the PTM scoring. Can you share the PeptideShaker log file? You'll find it via the Welcome dialog > Settings & Help > Help > Bug Report.
Best regards, Harald
Hi Harald,
I tried to process new data in PeptideShaker 2.0.0-beta, and it stopped at Scoring Peptide Modification Localization again:
This time, I can provide you with the error log file, see attached.
Hi Marc,
Ok, so there is a bug in the localization of the PTMs. Which search engines are you using? And which variable PTMs?
And could you try running without PTM scoring? I.e. set the "Probabilistic Score" to "None" and "Confident Sites" under "Site Alignment" to "No" in the "PTM Localization" settings dialog.
Best regards, Harald
Hi Harald,
I used Comet, X!Tandem and MS Amanda. The searches went fine, even with MS Amanda this time.
I will try to run another analysis later today, where I have disabled the things mentioned above. I will get back to you after this.
Best,
Marc
...and I only used Oxidation on Methionine as variable mod.
Best,
Marc
Hi Harald, I managed to import the SearchGUI output.
Still, I cannot save the project locally as a psdb-file and load it (but I opened a new issue for this).
Hi Marc,
I used Comet, X!Tandem and MS Amanda. The searches went fine, even with MS Amanda this time.
Could you also try loading just the X! Tandem results?
Best regards, Harald
Hi Marc,
I'm having a hard time with the memory/database issues. Made some progress, but seem like I need help from the two other developers that were in charge of implementing the new database backend.
However, if only loading the X! Tandem data I am able to both load, save and reopen. Perhaps you can use that as a temporary fix until we're able to solve the other issues?
Best regards, Harald
Hi Harald,
I am using PeptideShaker 2.0-beta for Windows to process search results from Comet and X!Tandem in SearchGUI 4.0.0-beta. I have searched 7 RAW-files with sizes around 1 GB.
Unfortunately, there is a step in which processing in PeptideShaker always stops. It is at the Scoring Peptide Modification Localization. It is when 85% of the processing has been complete, see attached image.![error_peptshaker](https://user-images.githubusercontent.com/47174270/69815847-77a33380-11f7-11ea-8b9b-25f502c6a085.png)
My thought is that it could be related to memory issues.
I am using 6 cores with 24 GB allocated for Java 12.0.1 (JDK, 64-bit). So it should be 4 GB RAM available for each core. Still, I wonder if it is enough? How much memory do you allocate for each core when you process btw?
I just thought it could be interesting to mention, since it also could be a bug.
Best,
Marc