Running and Verifying pblat

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Run the following commands to create a test file directory and copy the test files:

   mkdir /path/to/PBLAT/test
   cp hg19.fa /path/to/PBLAT/test
   cp NONCODEv5_human.fa.gz /path/to/PBLAT/test

3. Run the following command to go to the test case directory:

   cd /path/to/PBLAT/test

4. Run the following command to process the test case files:

   gzip -d NONCODEv5_human.fa.gz
   cat NONCODEv5_human.fa | grep -v "^#" | head -799996 > test-799996.fa

5. Run the following command to perform a test:

   { time pblat -threads=96 hg19.fa test-799996.fa out.psl ; } 2>&1 |tee pblat-kunpeng.log

   Check the real value (in seconds) in the pblat-kunpeng.log file. A smaller value indicates higher performance.

   Figure 1 is an example of the output result.

   Figure 1 Result example