--- 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/kunpengtophat2_02_0009.html sourcePath: /source/zh/kunpenghpcs/hpcindapp/prtg-osc/kunpengtophat2_02_0009.html indexId: a540bf0765720f435016628aaab3b6bf4548658723a9e3d0ec890feca1b8305d69 --- # 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. 执行以下命令设置TopHat2环境变量。 ``` export PATH= /path/to/TOPHAT2 / bin: $PATH ``` 3. 执行以下命令进入测试算例存放目录。 ``` cd /path/to/CASE ``` 4. 执行以下命令解压缩算例。 ``` gzip -d Drosophila_melanogaster.BDGP6.dna.toplevel.fa.gz gzip -d R1.fq.gz gzip -d R2.fq.gz mv Drosophila_melanogaster.BDGP6.dna.toplevel.fa genome.fa ``` 5. 执行以下命令建立索引。 ``` bowtie2-build genome.fa genome ``` 6. 执行以下命令运行TopHat2测试。 ``` time -p tophat2 -p 128 genome R1.fq R2.fq ``` -p后面接的是线程数，本文以“128”举例。 算例运行结束后有“Run complete”字样表示运行正常。如果出现“FAILED”则表示出现运行错误。 要查看日志中最后的time命令输出中的“real”数值，单位是时间“x秒”，数值越低性能越优。 输出的结果信息如下所示。 ``` [2024-02-20 20:03:27] Beginning TopHat run (v2.1.1) ----------------------------------------------- [2024-02-20 20:03:27] Checking for Bowtie Bowtie version: 2.3.5.1 [2024-02-20 20:03:27] Checking for Bowtie index files (genome).. [2024-02-20 20:03:27] Checking for reference FASTA file [2024-02-20 20:03:27] Generating SAM header for genome [2024-02-20 20:03:28] Preparing reads left reads: min. length=35, max. length=151, 3748054 kept reads (1946 discarded) right reads: min. length=35, max. length=151, 3748733 kept reads (1267 discarded) [2024-02-20 20:05:47] Mapping left_kept_reads to genome genome with Bowtie2 [2024-02-20 20:09:46] Mapping left_kept_reads_seg1 to genome genome with Bowtie2 (1/6) [2024-02-20 20:10:18] Mapping left_kept_reads_seg2 to genome genome with Bowtie2 (2/6) [2024-02-20 20:10:56] Mapping left_kept_reads_seg3 to genome genome with Bowtie2 (3/6) [2024-02-20 20:11:33] Mapping left_kept_reads_seg4 to genome genome with Bowtie2 (4/6) [2024-02-20 20:12:16] Mapping left_kept_reads_seg5 to genome genome with Bowtie2 (5/6) [2024-02-20 20:13:08] Mapping left_kept_reads_seg6 to genome genome with Bowtie2 (6/6) [2024-02-20 20:14:06] Mapping right_kept_reads to genome genome with Bowtie2 [2024-02-20 20:18:11] Mapping right_kept_reads_seg1 to genome genome with Bowtie2 (1/6) [2024-02-20 20:18:49] Mapping right_kept_reads_seg2 to genome genome with Bowtie2 (2/6) [2024-02-20 20:19:30] Mapping right_kept_reads_seg3 to genome genome with Bowtie2 (3/6) [2024-02-20 20:20:15] Mapping right_kept_reads_seg4 to genome genome with Bowtie2 (4/6) [2024-02-20 20:21:09] Mapping right_kept_reads_seg5 to genome genome with Bowtie2 (5/6) [2024-02-20 20:22:13] Mapping right_kept_reads_seg6 to genome genome with Bowtie2 (6/6) [2024-02-20 20:23:30] Searching for junctions via segment mapping [2024-02-20 20:32:36] Retrieving sequences for splices [2024-02-20 20:32:39] Indexing splices Building a SMALL index [2024-02-20 20:32:39] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/6) [2024-02-20 20:32:53] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/6) [2024-02-20 20:33:08] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/6) [2024-02-20 20:33:24] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/6) [2024-02-20 20:33:40] Mapping left_kept_reads_seg5 to genome segment_juncs with Bowtie2 (5/6) [2024-02-20 20:33:57] Mapping left_kept_reads_seg6 to genome segment_juncs with Bowtie2 (6/6) [2024-02-20 20:34:20] Joining segment hits [2024-02-20 20:37:13] Mapping right_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/6) [2024-02-20 20:37:31] Mapping right_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/6) [2024-02-20 20:37:48] Mapping right_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/6) [2024-02-20 20:38:06] Mapping right_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/6) [2024-02-20 20:38:29] Mapping right_kept_reads_seg5 to genome segment_juncs with Bowtie2 (5/6) [2024-02-20 20:38:54] Mapping right_kept_reads_seg6 to genome segment_juncs with Bowtie2 (6/6) [2024-02-20 20:39:26] Joining segment hits [2024-02-20 20:42:26] Reporting output tracks ----------------------------------------------- [2024-02-20 20:43:35] A summary of the alignment counts can be found in ./tophat_out/align_summary.txt [2024-02-20 20:43:35] Run complete: 00:17:08 elapsed ```