SRA Toolkit的下载安装及使用

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mb5fdb0fbba4f73 2021-07-31 12:08:00

文章标签 linux centos ico bash d3 文章分类 代码人生

1、下载进NCBI官网

SRA Toolkit的下载安装及使用_linux

2、

SRA Toolkit的下载安装及使用_centos_02

3、

SRA Toolkit的下载安装及使用_linux_03

4、根据系统选择版本，下载即可

SRA Toolkit的下载安装及使用_d3_04

5、查看自己系统

[root@PC3 software]# hostnamectl
   Static hostname: PC3
         Icon name: computer
           Chassis: n/a
        Machine ID: b7fae4ce730a4eb598ae4e92f7ad3683
           Boot ID: 8cedfc6564604ef088354f6fb76a1f50
    Virtualization: vmware
  Operating System: Red Hat Enterprise Linux Server 7.0 (Maipo)
       CPE OS Name: cpe:/o:redhat:enterprise_linux:7.0:GA:server
            Kernel: Linux 3.10.0-123.el7.x86_64
      Architecture: x86_64

6、centos和redhed 使用软件一致

因此选择：

SRA Toolkit的下载安装及使用_bash_05

7、

[root@PC3 test]# wget https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.11.0/sratoolkit.2.11.0-centos_linux64.tar.gz

8、进度

SRA Toolkit的下载安装及使用_bash_06

9、

[root@PC3 test]# ls
sratoolkit.2.11.0-centos_linux64.tar.gz

10、解压

[root@PC3 test]# tar -xzvf sratoolkit.2.11.0-centos_linux64.tar.gz

11、

[root@PC3 test]# ls
sratoolkit.2.11.0-centos_linux64  sratoolkit.2.11.0-centos_linux64.tar.gz

12、

[root@PC3 test]# cd sratoolkit.2.11.0-centos_linux64/
[root@PC3 sratoolkit.2.11.0-centos_linux64]# ls
bin  CHANGES  example  README-blastn  README.md  README-vdb-config  schema
[root@PC3 sratoolkit.2.11.0-centos_linux64]# cd bin/
[root@PC3 bin]# ls
abi-dump                  fasterq-dump-orig.2.11.0  pacbio-load           srapath-orig.2.11.0        test-sra.2.11.0
abi-dump.2                fastq-dump                pacbio-load.2         sra-pileup                 vdb-config
abi-dump.2.11.0           fastq-dump.2              pacbio-load.2.11.0    sra-pileup.2               vdb-config.2
abi-load                  fastq-dump.2.11.0         prefetch              sra-pileup.2.11.0          vdb-config.2.11.0
abi-load.2                fastq-dump-orig.2.11.0    prefetch.2            sra-pileup-orig.2.11.0     vdb-copy
abi-load.2.11.0           fastq-load                prefetch.2.11.0       sra-search                 vdb-copy.2
align-info                fastq-load.2              prefetch-orig.2.11.0  sra-search.2               vdb-copy.2.11.0
align-info.2              fastq-load.2.11.0         rcexplain             sra-search.2.11.0          vdb-decrypt
align-info.2.11.0         helicos-load              rcexplain.2           sra-sort                   vdb-decrypt.2
bam-load                  helicos-load.2            rcexplain.2.11.0      sra-sort.2                 vdb-decrypt.2.11.0
bam-load.2                helicos-load.2.11.0       remote-fuser          sra-sort.2.11.0            vdb-dump
bam-load.2.11.0           illumina-dump             remote-fuser.2        sra-sort-cg                vdb-dump.2
blastn_vdb                illumina-dump.2           remote-fuser.2.11.0   sra-sort-cg.2              vdb-dump.2.11.0
blastn_vdb.2              illumina-dump.2.11.0      sam-dump              sra-sort-cg.2.11.0         vdb-dump-orig.2.11.0
blastn_vdb.2.10.1-2.11.0  illumina-load             sam-dump.2            sra-stat                   vdb-encrypt
cache-mgr                 illumina-load.2           sam-dump.2.11.0       sra-stat.2                 vdb-encrypt.2
cache-mgr.2               illumina-load.2.11.0      sam-dump-orig.2.11.0  sra-stat.2.11.0            vdb-encrypt.2.11.0
cache-mgr.2.11.0          kar                       sff-dump              sra-tblastn                vdb-lock
cg-load                   kar.2                     sff-dump.2            sratools.2.11.0            vdb-lock.2
cg-load.2                 kar.2.11.0                sff-dump.2.11.0       srf-load                   vdb-lock.2.11.0
cg-load.2.11.0            kdbmeta                   sff-load              srf-load.2                 vdb-unlock
dump-ref-fasta            kdbmeta.2                 sff-load.2            srf-load.2.11.0            vdb-unlock.2
dump-ref-fasta.2          kdbmeta.2.11.0            sff-load.2.11.0       tblastn_vdb                vdb-unlock.2.11.0
dump-ref-fasta.2.11.0     latf-load                 sra-blastn            tblastn_vdb.2              vdb-validate
fasterq-dump              latf-load.2               srapath               tblastn_vdb.2.10.1-2.11.0  vdb-validate.2
fasterq-dump.2            latf-load.2.11.0          srapath.2             test-sra                   vdb-validate.2.11.0
fasterq-dump.2.11.0       ncbi                      srapath.2.11.0        test-sra.2

13、

[root@PC3 bin]# ./fastq-dump
This sra toolkit installation has not been configured.
Before continuing, please run: vdb-config --interactive
For more information, see https://www.ncbi.nlm.nih.gov/sra/docs/sra-cloud/

14、

[root@PC3 bin]# ls
abi-dump                  fasterq-dump-orig.2.11.0  pacbio-load           srapath-orig.2.11.0        test-sra.2.11.0
abi-dump.2                fastq-dump                pacbio-load.2         sra-pileup                 vdb-config
abi-dump.2.11.0           fastq-dump.2              pacbio-load.2.11.0    sra-pileup.2               vdb-config.2
abi-load                  fastq-dump.2.11.0         prefetch              sra-pileup.2.11.0          vdb-config.2.11.0
abi-load.2                fastq-dump-orig.2.11.0    prefetch.2            sra-pileup-orig.2.11.0     vdb-copy
abi-load.2.11.0           fastq-load                prefetch.2.11.0       sra-search                 vdb-copy.2
align-info                fastq-load.2              prefetch-orig.2.11.0  sra-search.2               vdb-copy.2.11.0
align-info.2              fastq-load.2.11.0         rcexplain             sra-search.2.11.0          vdb-decrypt
align-info.2.11.0         helicos-load              rcexplain.2           sra-sort                   vdb-decrypt.2
bam-load                  helicos-load.2            rcexplain.2.11.0      sra-sort.2                 vdb-decrypt.2.11.0
bam-load.2                helicos-load.2.11.0       remote-fuser          sra-sort.2.11.0            vdb-dump
bam-load.2.11.0           illumina-dump             remote-fuser.2        sra-sort-cg                vdb-dump.2
blastn_vdb                illumina-dump.2           remote-fuser.2.11.0   sra-sort-cg.2              vdb-dump.2.11.0
blastn_vdb.2              illumina-dump.2.11.0      sam-dump              sra-sort-cg.2.11.0         vdb-dump-orig.2.11.0
blastn_vdb.2.10.1-2.11.0  illumina-load             sam-dump.2            sra-stat                   vdb-encrypt
cache-mgr                 illumina-load.2           sam-dump.2.11.0       sra-stat.2                 vdb-encrypt.2
cache-mgr.2               illumina-load.2.11.0      sam-dump-orig.2.11.0  sra-stat.2.11.0            vdb-encrypt.2.11.0
cache-mgr.2.11.0          kar                       sff-dump              sra-tblastn                vdb-lock
cg-load                   kar.2                     sff-dump.2            sratools.2.11.0            vdb-lock.2
cg-load.2                 kar.2.11.0                sff-dump.2.11.0       srf-load                   vdb-lock.2.11.0
cg-load.2.11.0            kdbmeta                   sff-load              srf-load.2                 vdb-unlock
dump-ref-fasta            kdbmeta.2                 sff-load.2            srf-load.2.11.0            vdb-unlock.2
dump-ref-fasta.2          kdbmeta.2.11.0            sff-load.2.11.0       tblastn_vdb                vdb-unlock.2.11.0
dump-ref-fasta.2.11.0     latf-load                 sra-blastn            tblastn_vdb.2              vdb-validate
fasterq-dump              latf-load.2               srapath               tblastn_vdb.2.10.1-2.11.0  vdb-validate.2
fasterq-dump.2            latf-load.2.11.0          srapath.2             test-sra                   vdb-validate.2.11.0
fasterq-dump.2.11.0       ncbi                      srapath.2.11.0        test-sra.2

15、

[root@PC3 bin]# ./vdb-config --interactive

SRA Toolkit的下载安装及使用_bash_07

16、直接输入f选择（默认）

SRA Toolkit的下载安装及使用_ico_08

17、输入y选择yes

SRA Toolkit的下载安装及使用_bash_09

18、输入o

SRA Toolkit的下载安装及使用_d3_10

19、输入x 离开

SRA Toolkit的下载安装及使用_d3_11

20、输入y保存修改

SRA Toolkit的下载安装及使用_linux_12

21、输入o即可

22、测试软件

[root@PC3 bin]# ./fastq-dump

Usage:
  /home/software/sratoolkit.2.11.0-centos_linux64/bin/fastq-dump.2.11.0 [options] <path> [<path>...]
  /home/software/sratoolkit.2.11.0-centos_linux64/bin/fastq-dump.2.11.0 [options] <accession>

Use option --help for more information

/home/software/sratoolkit.2.11.0-centos_linux64/bin/fastq-dump.2.11.0 : 2.11.0

23、添加环境变量

[root@PC3 bin]# pwd
/home/software/sratoolkit.2.11.0-centos_linux64/bin

24、路径是上一条命令pwd输出的路径，后面是追加>>, 千万不要写成重定向>.

[root@PC3 bin]# echo "export PATH=$PATH:/home/software/sratoolkit.2.11.0-centos_linux64/bin" >> ~/.bashrc

25、加载

[root@PC3 bin]# source ~/.bashrc

26、测试

[root@PC3 bin]# fastq-dump

Usage:
  /home/software/sratoolkit.2.11.0-centos_linux64/bin/fastq-dump.2.11.0 [options] <path> [<path>...]
  /home/software/sratoolkit.2.11.0-centos_linux64/bin/fastq-dump.2.11.0 [options] <accession>

Use option --help for more information

/home/software/sratoolkit.2.11.0-centos_linux64/bin/fastq-dump.2.11.0 : 2.11.0

27、使用数据测试，下载好的两个样本的测试数据

[root@PC3 test]# ls
SRR1135309.1  SRR1138358.1

28、单样本测试，没有问题

[root@PC3 test]# fastq-dump --gzip --split-3 SRR1135309.1 -O test

29、写成循环

[root@PC3 test]# ls
SRR1135309.1  SRR1138358.1

[root@PC3 test]# ls SRR* | while read id; do fastq-dump --gzip --split-3 $id -O result$id; done

30、无中断运行

[root@PC3 test]# nohup ls SRR* | while read id; do fastq-dump --gzip --split-3 $id -O result$id; done >log 2>&1 &                    [1] 5781
[root@PC3 test]# nohup: ignoring input and redirecting stderr to stdout