Memory issue

Vanessa Casas

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Apr 9, 2020, 2:02:30 AM4/9/20

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Hello,

I am using Peptide Shaker v 1.16.44 and Search Gui 3.3.17 to open 5 files (2 Gb in total). The problem is that when Peptide Shaker tries to calculate the FDR the sytem runs out of memory.

Following the Java instructions I have a Java version higher than 1.7, a 64 bit system and 32 gb RAM (please , find attached a pdf with my system configuration).

The database that I am using has 2200 entries (4400 when the GUI adds the decoys).

I have used PS before, with other versions, and I do not know what is happening here...any suggestion, please??

Thank you very much, best regards

Vanessa Casas

PeptideShaker_bugreport_200409.txt

PS_configuration.pdf

Harald Barsnes

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Apr 9, 2020, 6:04:11 AM4/9/20

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Hi Vanessa,

I'm afraid you've come across an error with our backend that we have been trying to solve for a long time. There are beta versions you can test: https://groups.google.com/forum/#!topic/peptide-shaker/1ecY0IyMOBM. However, when we were close to officially releasing these versions we found an error in opening saved projects, resulting in that we had to make even more changes, which we are still working on. With the beta releases you should be able to process your data and export the results though.

Best regards,

Harald

Vanessa Casas

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Apr 9, 2020, 3:14:47 PM4/9/20

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Hi again Harald,

Finally I was able to open my data with the beta version, but now I have a problem trying to export the spectra of non validated peptides and proteins.

I do not understand why, because the spectra of non validated PSMs were exported without problem.

Do you have any suggestion??

Thanks again, best regards

Vanessa

Harald Barsnes

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Apr 10, 2020, 12:05:45 PM4/10/20

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Hi Vanessa,

I can reproduce the error with the protein report but not for the peptides. Probably a similar error though.

Can you share the error log? You can find it via Help > Bug Report in the main PeptideShaker window, or via the Welcome dialog > Settings & Help > Help > Bug Report.

Should hopefully be easy to fix.

Best regards,

Harald

Vanessa Casas

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Apr 10, 2020, 2:19:26 PM4/10/20

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Hi Harald,

Please, find attached the txt document with the error for the mgf exportation of non validated peptides and proteins. I also have problems when I try to open a project (error_openingfile).

Thank you very much, best regards

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PS_error_exportation mgf.txt

PS_error_openingfile.txt

Harald Barsnes

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Apr 10, 2020, 2:51:55 PM4/10/20

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Hi Vanessa,

Here is an updated beta version that should solve the export issues: http://vedlegg.uib.no/?id=64ba7c5fad02da9df3bc4a6d7f9e38d1.

Note that you my need to recreate your identification settings file.

As for the problems with reopening saved projects, I'm afraid this is a known issue that we have yet to solve (https://github.com/compomics/peptide-shaker-2.0-issue-tracker/issues/47) and the main reason why the beta release has not been officially released.