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Nesvilab / FragPipe

A cross-platform proteomics data analysis suite
http://fragpipe.nesvilab.org
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java.lang.OutOfMemoryError: Java heap space #800

Closed jmcalist closed 2 years ago

jmcalist commented 2 years ago

We ran into a java.lang.OutOfMemoryError: Java heap space error. It is a reasonably big run (64 samples), and when I look at the System Summary for the computer it lists: Installed Physical Memory (RAM): 16.0 GB Available physical memory: 6.08 GB Total virtual memory: 32.7 GB Available virtual memory: 17.8 GB Page file space: 16.8 GB

Is this simply a RAM issue? For a run of this size what amount of RAM would you recommend?

One other question, these samples represent an infection study, therefore we want to add FASTA files for both the host and the pathogen. I see that you can download more that one FASTA file by entering Uniprot IDs separated by a comma, but one of the FASTA files is not from Uniprot (although should be in Uniprot format). I uploaded each of the two fasta files separately into Fragpipe, created decoys for them, then joined these two files together (simply appended one to the end of the other in the text file) and uploaded this combined fasta file to Fragpipe for our analysis. Should this work?

Thank you so much and please let me know if I can provide any additional information

All the best,

Jason

fcyu commented 2 years ago

Hi Jason,

Although your computer have 16 GB in total, there are only 5 GB free memory available. MSFragger couldn't load the raw files. You need to have at least 16 GB free memory.

I uploaded each of the two fasta files separately into Fragpipe, created decoys for them, then joined these two files together (simply appended one to the end of the other in the text file) and uploaded this combined fasta file to Fragpipe for our analysis. Should this work?

If should work. Need to double check that you didn't add the contaminants twice.

Best,

Fengchao

jmcalist commented 2 years ago

Hi Feng,

Thank you so much for your reply, I always tell everyone how your help center always replies so promptly, it is really amazing and very helpful!

We are going to run on a 64GB machine, so that should hopefully work :)

One question about the fasta files, just for my own curiosity. When you download fasta files in Fragpipe the number of entries is less than the number of proteins that might be listed in Uniprot, particularly given that 50% are decoys, is that correct? For example: Uniprot Fragpipe Proteins Entries Decoys UP000002515 5431 1594 797 UP000006548 39325 32552 16276 Combined 44756 33914 16957 Combined is downloading the two uniprot IDs together in Fragpipe

I am just curious what an entry is Fragpipe represents?

Thank you so much! We have been using MQ for a long time, but I am working on converting people šŸ™‚

Thanks again!

All the best,

Jason

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Hi Jason,

Although your computer have 16 GB in total, there are only 5 GB free memory available. MSFragger couldn't load the raw files. You need to have at least 16 GB free memory.

I uploaded each of the two fasta files separately into Fragpipe, created decoys for them, then joined these two files together (simply appended one to the end of the other in the text file) and uploaded this combined fasta file to Fragpipe for our analysis. Should this work?

If should work. Need to double check that you didn't add the contaminants twice.

Best,

Fengchao

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fcyu commented 2 years ago

Hi Jason,

Thanks for your kind words.

As to your question, what does your "entries" mean? Is that proteins? I tested with UP000002515, both FragPipe and UniProt website get 681 reviewed proteins. I am not sure what the issue is.

Best,

Fengchao