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compomics / peptide-shaker

Interpretation of proteomics identification results
http://compomics.github.io/projects/peptide-shaker.html
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Error in follow-up analysis export #472

Open indianAppl opened 2 years ago

indianAppl commented 2 years ago

Hello,

I executed SearchGUI followed by PeptideShaker on 30 fractionated cell line proteome to produce DDA search profile. The run executed perfectly and loaded on to PeptideShaker. But shows the following error while exporting mzid for skyline:

Error while loading spectrum sample=1 period=1 cycle=6985 experiment=2 of file Fract01.mgf

This sample previouly executed without error. It just appeared suddenly. What exactly am I doing wrong here ? Has the file got corrupted ??

Thanks in advance.

hbarsnes commented 2 years ago

Would it be possible for you to share the PeptideShaker log file? You will find it via the PeptideShaker Welcome Dialog > Settings & Help > Help > Bug Report. I will hopefully tell us a bit more about why the error occurs.

indianAppl commented 2 years ago

Definitely, Please find the file attached PeptideShaker 1.16.45 log.txt

hbarsnes commented 2 years ago

It seems like you are using a very old version of PeptideShaker. We are now at PeptideShaker version 2.2.2. I would recommend that you update to the most recent version and see if that solves the problem. If not, please send me the new log file and I will see what I can do.

indianAppl commented 2 years ago

I did execute the analysis in new version. Now the error shows up at the parsing stage only. The files were ok. Any clue why this might be happening ? PS_error.txt

hbarsnes commented 2 years ago

Can you send me the log file from the new version as well? Then I will have a closer look at the current code and hopefully come up with a fix.

indianAppl commented 2 years ago

Yes. Please find it attached. PeptideShaker 2.2.2 log.zip

hbarsnes commented 2 years ago

It looks like you are running into a known backend issue in which the only known solution is to increase the amount of memory you provide to PeptideShaker. You can do this via the PeptideShaker Welcome Dialog > Settings & Help > Settings > Java Settings > Memory. Can you try increasing the memory and see if that solves the problem?

indianAppl commented 2 years ago

I have already done that...given it 110Gb ram....in the previous version the same data was executed with 90Gb space !! This problem just popped up from nowhere. But I think I must inform you that I am trying to run two data viz one from nanoLC (one lab) and microLC (different lab)...can this be a problem ??!!

hbarsnes commented 2 years ago

I have already done that...given it 110Gb ram....in the previous version the same data was executed with 90Gb space !!

Ah, in that case I'm afraid I've run out of suggestions...

But I think I must inform you that I am trying to run two data viz one from nanoLC (one lab) and microLC (different lab)...can this be a problem ??!!

Not sure I understand exactly what you mean, but if you mean running both at the same time I would recommend rather running one at the time.

indianAppl commented 2 years ago

Ok I think I am in difficult soup :( ..... then once I am able to figure out a solution, I will come back and close the thread. Thanks for all the help.