Running and Verifying CANU

Use PuTTY to log in to a server as the root user.
Run the following command to install Java 1.8.0:
```
yum install java-1.8.0-openjdk* gnuplot -y
```
The Yum source is a local source of the CentOS 7.6 image. You can modify the files in the /etc/yum.repos.d directory as required.
Run the following command to obtain the case file:
```
curl -L -o oxford.fastq http://gembox.cbcb.umd.edu/mhap/raw/ecoli_p6_25x.filtered.fastq
```
Access to the external network is required. You can download and convert the case file by using a server that is connected to the external network, and then copy the case file to the test directory.

Run the following command to start CANU:

{ time canu -p ecoli -d ecoli-pacbio genomeSize=4.8m corPartitions=384 corMemory=3  corPartitionMin=1000 corThreads=1 useGrid=false obtovlThreads=96 obtOvlHashBlockLength=682496000 utgOvlHashBlockLength=682496000 utgovlThreads=96  gridEngineMemoryOption="-l vf=MEMORY" -nanopore-raw oxford.fastq ; } 2>&1 |tee -a canu.log

Table 1 describes the command parameters.

**Table 1** CANU command parameters
Parameter	Description
useGrid	Whether to run under Grid Control. The default value is true. Change the value to false.
-p	assembly-prefix component index. Set this parameter based on the case.
-d	assembly-directory component directory. The value of this parameter is user-defined.
genmoeSize	Genome size. Set this parameter based on the case.
-nanopore-raw	Select the required gene file format based on the case.
corPartitions	Number of tasks. You are advised to set this parameter to a multiple of the number of cores. The recommended value is 4 times the number of cores.
corThreads	Number of threads in each process. The recommended value is 1.
obtovlThreads	Number of threads for running obtovl. You are advised to set this parameter to the number of cores.
utgovlThreads	Number of threads for running utgov. You are advised to set this parameter to the number of cores.

Parent topic: CANU 1.8 Porting Guide (CentOS 7.6)