search

HIT-ImmunologyLab / DBSCAN-SWA

29 stars 13 forks source link

DBSCAN-SWA ignores thread number for blast searches #12

Closed alexweisberg closed 2 years ago

alexweisberg commented 2 years ago

When I run DBSCAN-SWA using the --thread_num option, it uses 20 threads for the blast/diamond searches regardless of what value I input. In the code (dbscan-swa.py line 386, line 393, line 1523 etc) this 20 thread value is hard coded rather than using the thread number as input.

gancao commented 2 years ago

Hi,

The parameter "thread_num" means the number of threads for inputing multiple contigs.  I am sorry to set a fixed value for diamond blastp.  Now, I have updated the code and added a new parameter "diamond_thread_num", representing the thread number of diamond.  You could set it by yourself.

—

alexweisberg commented 2 years ago

Hi,

Thank you! I had modified the code on my machine to use the thread_num variable but I will update to the newest version with your fix.