The amount of memory required to convert a .blib file to a .elib seems to depend on the total number of unique peptide sequences in the FASTA file.
You could reduce the amount of memory needed by using a smaller fasta file and/or by setting Max Missed Cleavages to a smaller number.

There is a little bit more information about this error here:
https://skyline.ms/announcements/home/support/thread.view?rowId=66269

If your computer has less than 24GB of RAM in it, then this might succeed if you did it on a computer with more RAM.
Skyline tells EncyclopeDIA to use the smaller of either 12GB or half the amount of memory in the computer, so increasing the RAM beyond 24GB is unlikely to fix the problem.

How much RAM does your computer have? I could probably send you a special version of Skyline which tells EncyclopeDIA to use more RAM so you can get past this problem if it's not feasible for you to use a smaller FASTA file and/or decrease the number of missed cleavages to get around this problem.
-- Nick

Hi Nick,

Thanks so much for the prompt response. I have 16.0 GB of RAM. I'm not sure if this is it, but I had a really hard time getting MSConvert to work on my overlapping files (kept getting the minWindowValue too low error) - I attempted to raise it, but it didn't fix it, so i droped the .raw files into the Skyline EncyclopeDIA tool - it's able to read them in, generate the koina blib, then it crashes shortly thereafter. My fasta file is large - I'll try chopping it into bits. Is the reason it's crashing because I'm converting them in the program?

This might be a dumb question (sorry if it is!), but if I have the blib, is there any way to start at that point in Skyline, where I could load the blib and start from the point of elib generation?

Thanks again,

Shay

Hi sorry to pop this on here again,

For this error- I think the reason why it's failing is because of how MSConvert reads the DIA scheme from my runs -

Is there any way to export the mzml files that are generated from EncyclopeDIA in skyline?

Thank you,,
Shay

If you are getting the error about the number of deconvolution windows changes, that is probably caused by them overlapping in a weird way.
You can find some information about getting past that error here:
https://sourceforge.net/p/proteowizard/mailman/message/37747772/

I am not sure about the answers to your other questions. Someone else might know.
-- Nick

..."How much RAM does your computer have? I could probably send you a special version of Skyline which tells EncyclopeDIA to use more RAM so you can get past this problem if it's not feasible for you to use a smaller FASTA file and/or decrease the number of missed cleavages to get around this problem".
-- Nick

Hi Nick,

I have the same problem Shay encountered. My computer has 128 GB of memory and I had 2 max cleavages for the FASTA file (human). I was wondering if you could kindly send me also, the special version of skyline which tells EncyclopeDIA to use more RAM so that I could complete my analysis.

Much appreciated,

John

John,

I have made a special build of Skyline-daily which removes the 12GB memory cap, so the EncyclopeDIA process that is currently running out of memory will now try to use up to half of the RAM in your computer.
You can install this special build from here:
https://proteome.gs.washington.edu/~nicksh/SpecialSkylines/EncyclopeDiaMemory/

This special build has not been cryptographically signed, so Windows will probably try to discourage you from installing it. You might have to hunt around for the "More Info" and "Run Anyway" buttons.
This special build will show up on the Windows Start Menu as "Skyline-daily EncyclopeDIA Memory".

Let me know whether this special build fixes your failure. If it works, I will try to incorporate this fix into a future release of Skyline-daily.
If it does not fix things for you, then please send me your files. It could be that your scenario requires even more memory than what this fix provides, in which case I will try to come up with a better fix.
-- Nick

Hi Nick,

Many thanks for the link to the special build Skyline. I ran data from the tutorial in the paper Pino et al 2020 on DIA/EncyclopeDIA. Unfortunately the problem still persist. Attached is the error I got,

Appreciated,

John

Oops. I think I made a mistake coding that fix before.
I have uploaded a new special Skyline which will hopefully fix this problem for you.
If you exit Skyline and restart it, it will probably notice that I have uploaded version 25.1.1.189.
-- Nick

Many thanks Nick,

I tried version 25.1.1.189 and it got rid of the RAM error. Unfortunately, I encountered a different error - "cannot reserve enough space for .... object heap".
Please see attachment.

Many thanks,

John

Oops. I was accidentally asking for a million times more memory than I was supposed to.
I have uploaded a new version (25.1.1.190) which should work now.
-- Nick