BLAT standalone version - why is it so slow?

I am using BLAT for one of my class projects and have downloaded the standalone version's executables from and moved it to my class server. I ran BLAT using the following command:

~/blat_standalone/blat/blat ../GRCh38_latest_genomic.fna test_4.fa blat_out4.psl

As indicated above, I am running a test sequence against hg38. The test sequence is the mRNA sequence of POLR2A. When I ran the sequence on the web version of BLAT on UCSC it only took less than a second. However, when I tried to run the same sequence using my own standalone version, it took about 40 seconds. The standard output, while the program was running, is as follows:

  $ ~/blat_standalone/blat/blat ../GRCh38_latest_genomic.fna test_4.fa blat_out4.psl
  Loaded 3272089205 letters in 639 sequences
  Searched 6749 bases in 1 sequences

1) Why is my program so much slower than the web version and how do I make it faster?
I suspect it may have something to do with the fact that I am not using the -ooc option and an ooc file. My understanding is that I need to create the file, but I don't know how to make one.
2) can someone please tell me how to create a 11.ooc file from my database?
3) It took around 14 seconds for the program to load all of the sequences from the database (all 639 of them). Will using the -ooc option reduce this time? If not, will deleting all but the 25 primary assemblies significantly reduce this time?



Source link