---
title: 运行和验证
description: "1. 使用PuTTY工具，以root用户登录服务器。"
url: https://www.hikunpeng.com/document/detail/zh/kunpenghpcs/hpcindapp/prtg-osc/kunpengvelvet_02_0007.html
sourcePath: /source/zh/kunpenghpcs/hpcindapp/prtg-osc/kunpengvelvet_02_0007.html
indexId: 33f8f962e4130f2b6624449690def4e9514255cf556c1e6973503b080e949e3d68
---
# 运行和验证

#### 操作步骤

1. 使用PuTTY工具，以root用户登录服务器。
2. 执行以下命令进入测试目录。

```
cd
/path/to/VELVET
/velvet-1.2.10
```


3. 执行以下命令运行可执行文件“velveth”， 准备数据。

```
./velveth output/ 31 -shortPaired -fastq.gz tests/read1.fq.gz -shortPaired -fastq.gz tests/read2.fq.gz
```


  “output”：代表输出结果的目录。 “shortPaired”：指定测序类型。 “Fastaq”：指定的序列格式，通过不同的参数指定指定输入文件的格式：-fasta对应fasta格式；-fastq对应fastq格式；-fastq.gz对应fastq.gz格式；-fasta.gz对应fasta.gz格式；-sam对应sam格式；-bam对应bam格式。

  输出结果样例回显信息如下所示。

```
[0.000000] Reading FastQ file tests/read1.fq.gz;
[0.083994] 25000 sequences found
[0.084004] Done
[0.084266] Reading FastQ file tests/read2.fq.gz;
[0.162083] 25000 sequences found
[0.162091] Done
[0.364858] Reading read set file output//Sequences;
[0.376048] 50000 sequences found
[0.427913] Done
[0.427929] 50000 sequences in total.
[0.428268] Writing into roadmap file output//Roadmaps...
[0.468365] Inputting sequences...
[0.468486] Inputting sequence 0 / 50000
[1.182309]  === Sequences loaded in 0.713954 s
[1.303762] Done inputting sequences
[1.303770] Destroying splay table
[1.305914] Splay table destroyed
```


4. 执行以下命令运行可执行文件“velvetg”，进行基因组组装。

```
./velvetg output/ -min_contig_lgth 100
```


  “output”：代表3输出结果的目录。 “min_contig_lgth”：代表Contig的最小长度，小于该长度的Contig会被删除，不会出现在最终的结果中。运行结束后，输出目录下的contigs.fa就是最终的组装结果。

  输出结果样例回显信息如下所示。

```
[1.258599] Concatenation over!
[1.259034] Writing contigs into output//contigs.fa...
[1.292427] Writing into stats file output//stats.txt...
[1.327635] Writing into graph file output//LastGraph...
Final graph has 987 nodes and n50 of 199, max 2546, total 110172, using 0/50000 reads
```