search

zhaoyanswill / RAPSearch2

Reduced Alphabet based Protein similarity Search
40 stars 15 forks source link

prerapsearch not splitting database automatically #12

Open deprekate opened 9 years ago

deprekate commented 9 years ago

Hi, I used prerapsearch to format NR for use with rapsesarch2. I have found that it does not automatically split the database. I know I can do this using the -s option, I just don't know what the best option is for rapsearches. And the help file says:

  1. For big similarity search database (like nr), prerapsearch automatically splits the database into several files to reduce the memory requirement. If you need further reduce the memory usage, you can choose to use -s option to run prerapsearch
deprekate commented 9 years ago

Hm, it appears that the -s flag does not work.

$ ~/opt/RAPSearch2/bin/prerapsearch -s 3 -d test.faa -n test now building hash file hash file saved to file test

Main END

$ ls test test.faa test.info

arivers commented 9 years ago

I just encountered this same error, the -s flag does not split the database.

zhaoyanswill commented 9 years ago

Sorry for the late reply! RAPSearch2 would put all pieces into one file to make the directory clean, no matter how many pieces you want.

Sincerely, Y. Z.

On 02/24/2015 07:25 PM, Adam Rivers wrote:

I just encountered this same error, the -s flag does not split the database.

— Reply to this email directly or view it on GitHub https://github.com/zhaoyanswill/RAPSearch2/issues/12#issuecomment-75881058.