search

DiltheyLab / MetaMaps

Long-read metagenomic analysis
Other
96 stars 23 forks source link

Can a database be added via shared memory? #67

Closed jsonProgram closed 12 months ago

jsonProgram commented 2 years ago

Loading the database is slow... Any ideas to speed up this step? For example shared memory method

AlexanderDilthey commented 12 months ago

Hi @jsonProgram,

We do currently not support shared memory, but you can try to build the index and then store it to disk, like so (using the undocumented mapAgainstIndex command):

./metamaps index -i databases/miniSeq+H/DB.short.idx -r databases/miniSeq+H/DB.short.fa
./metamaps mapAgainstIndex --all -i databases/miniSeq+H/DB.short.idx -q test.fastq -o classification_results
AlexanderDilthey commented 12 months ago

Also, there was a bug in the code that implemented mapping against a pre-built index; if you want to try this feature, do a fresh pull and re-compile MetaMaps.

-A