tide-index of Mus Musculus database

[abhishekdub...@gmail.com]

Dear all

I was trying to search a set of spectra against Mus Musculus RefSeq database that contains around 90k protein sequences. I used the following command for indexing :

crux tide-index --digestion partial-digest --missed-cleavages 1 --decoy-format peptide-reverse --mods-spec C+57.02146,2M+15.9949 mus_musculus.fasta db-index

The system on which I am doing this has 4GB RAM and Intel Core i3 2100 3.1 Ghz processor.

Is it even possible to index the database on this system in reasonable time (12hrs or so is fine for me. Should it take more time than that ?). Does it require HPC Cluster for doing such large database indexing or there is some workaround to avoid it ?

Best

Abhishek

[William S Noble]

Hi Abhishek,

In its current implementation, tide-index requires that the peptide database fit in memory. When you use the partial-digest option, the memory requirement will become quite large. It seems likely that you have exceeded the 4GB available on your computer, in which case the program is likely spending all its time writing to and from disk as it tries to use virtual memory. I think you will need to use full digestion or switch to a computer with more memory.

Bill

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[abhishekdub...@gmail.com]

Hi Bill

Thank you very much for your response. Indeed, I was able to get indexing done without using partial-digest option on a 4GB RAM.

Best

Abhishek