美文网首页
第一步-hisat2-得到.sam文件

第一步-hisat2-得到.sam文件

作者: MissL_78e0 | 来源:发表于2019-07-10 13:46 被阅读0次
    /mnt/d/AAA-台式机-LY-WorkSpace$ hisat2 -t -x grch38/genome -1 CRC/10samples/108TRA/108TRA_1.fq.gz -2 CRC/10samples/108TRA/108TRA_2.fq.gz -S aligned/108TRA/108TRA.sam

    hisat2 -t --dta -x grch38/genome -1 CRC/10samples/105TRA/105TRA_1.fq.gz -2 CRC/10samples/105TRA/105TRA_2.fq.gz -S aligned/105TRA/105TRA.sam

    hisat2 -t --dta -x grch38/genome -1 CRC/10samples/108TRA/108TRA_1.fq.gz -2 CRC/10samples/108TRA/108TRA_2.fq.gz -S aligned/108TRA/108TRA.sam

    hisat2 -t --dta -x grch38/genome -1 CRC/10samples/112A/112A_1.fq.gz -2 CRC/10samples/112A/112A_2.fq.gz -S aligned/112A/112A.sam

    hisat2 -t --dta -x grch38/genome -1 CRC/10samples/113A/113A_1.fq.gz -2 CRC/10samples/113A/113A_2.fq.gz -S aligned/113A/113A.sam

    hisat2 -t --dta -x grch38/genome -1 CRC/10samples/114A/114A_1.fq.gz -2 CRC/10samples/114A/114A_2.fq.gz -S aligned/114A/114A.sam

    hisat2 -t --dta -x grch38/genome -1 CRC/10samples/122A/122A_1.fq.gz -2 CRC/10samples/122A/122A_2.fq.gz -S aligned/122A/122A.sam

    hisat2 -t --dta -x grch38/genome -1 CRC/10samples/124A/124A_1.fq.gz -2 CRC/10samples/124A/124A_2.fq.gz -S aligned/124A/124A.sam

    hisat2 -t --dta -x grch38/genome -1 CRC/10samples/126A/126A_1.fq.gz -2 CRC/10samples/126A/126A_2.fq.gz -S aligned/126A/126A.sam

    hisat2 -t --dta -x grch38/genome -1 CRC/10samples/127A/127A_1.fq.gz -2 CRC/10samples/127A/127A_2.fq.gz -S aligned/127A/127A.sam

    hisat2 -t --dta -x grch38/genome -1 CRC/10samples/130A/130A_1.fq.gz -2 CRC/10samples/130A/130A_2.fq.gz -S aligned/130A/130A.sam

    忘记了创建114A的文件夹，导致该命令报错，下次记得检查一下！！！！

    最后一条命令在控制台中没有运行，下次应在后面随便添加一条命令！！！！

    比上图多了--dta
    /mnt/d/AAA-台式机-LY-WorkSpace$ hisat2 -t -p 12 --dta -x grch38/genome -1 CRC/10samples/130A/130A_1.fq.gz -2 CRC/10samples/130A/130A_2.fq.gz -S aligned/130A/130A.sam

    -p 设置线程数

    此电脑

    所以线程数最高可设置12

    与单线程相比时间是之前的1/5

    但是在后续stringtie处理过程中报错

    网上查原因可能是基因命名方式不同（？）

    所以又在Hisat网站上重新下载注释基因，第一次下载的是红色的，这次下载黄色方框试一试看（貌似没报错）

    hisat2 index页面

    Align the RNA-seq reads to the genome

    第一步:Map the reads for each sample to the reference genome

    (base) luoyang@DESKTOP-AO2ICCR:/mnt/d/AAA-台式机-LY-WorkSpace$ hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/10samples/130A/130A_1.fq.gz -2 CRC/10samples/130A/130A_2.fq.gz -S aligned/130A/130A.sam

    Time loading forward index: 00:00:38

    Time loading reference: 00:00:07

    Multiseed full-index search: 00:12:35

    32196598 reads; of these:

      32196598 (100.00%) were paired; of these:

        2022163 (6.28%) aligned concordantly 0 times

        28316980 (87.95%) aligned concordantly exactly 1 time

        1857455 (5.77%) aligned concordantly >1 times

        ----

        2022163 pairs aligned concordantly 0 times; of these:

          250312 (12.38%) aligned discordantly 1 time

        ----

        1771851 pairs aligned 0 times concordantly or discordantly; of these:

          3543702 mates make up the pairs; of these:

            1847559 (52.14%) aligned 0 times

            1402980 (39.59%) aligned exactly 1 time

            293163 (8.27%) aligned >1 times

    97.13% overall alignment rate

    Time searching: 00:12:43

    Overall time: 00:13:22

    最后生成105TRA.sam文件

    新命令：（10samples）

    hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/10samples/105TRA/105TRA_1.fq.gz -2 CRC/10samples/105TRA/105TRA_2.fq.gz -S aligned/105TRA/105TRA.sam

    hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/10samples/108TRA/108TRA_1.fq.gz -2 CRC/10samples/108TRA/108TRA_2.fq.gz -S aligned/108TRA/108TRA.sam

    hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/10samples/112A/112A_1.fq.gz -2 CRC/10samples/112A/112A_2.fq.gz -S aligned/112A/112A.sam

    hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/10samples/113A/113A_1.fq.gz -2 CRC/10samples/113A/113A_2.fq.gz -S aligned/113A/113A.sam

    hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/10samples/114A/114A_1.fq.gz -2 CRC/10samples/114A/114A_2.fq.gz -S aligned/114A/114A.sam

    hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/10samples/122A/122A_1.fq.gz -2 CRC/10samples/122A/122A_2.fq.gz -S aligned/122A/122A.sam

    hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/10samples/124A/124A_1.fq.gz -2 CRC/10samples/124A/124A_2.fq.gz -S aligned/124A/124A.sam

    hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/10samples/126A/126A_1.fq.gz -2 CRC/10samples/126A/126A_2.fq.gz -S aligned/126A/126A.sam

    hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/10samples/127A/127A_1.fq.gz -2 CRC/10samples/127A/127A_2.fq.gz -S aligned/127A/127A.sam

    hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/10samples/130A/130A_1.fq.gz -2 CRC/10samples/130A/130A_2.fq.gz -S aligned/130A/130A.sam

    16samples：

    hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/16samples/17F24T/17F24T_1.fq.gz -2 CRC/16samples/17F24T/17F24T_2.fq.gz -S aligned-16/17F24T/17F24T.sam

    hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/16samples/105TRA/105TRA_1.fq.gz -2 CRC/16samples/105TRA/105TRA_2.fq.gz -S aligned-16/105TRA/105TRA.sam

    hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/16samples/109TRA/109TRA_1.fq.gz -2 CRC/16samples/109TRA/109TRA_2.fq.gz -S aligned-16/109TRA/109TRA.sam

    hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/16samples/110A/110A_1.fq.gz -2 CRC/16samples/110A/110A_2.fq.gz -S aligned-16/110A/110A.sam

    hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/16samples/113A/113A_1.fq.gz -2 CRC/16samples/113A/113A_2.fq.gz -S aligned-16/113A/113A.sam

    hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/16samples/114A/114A_1.fq.gz -2 CRC/16samples/114A/114A_2.fq.gz -S aligned-16/114A/114A.sam

    hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/16samples/120A/120A_1.fq.gz -2 CRC/16samples/120A/120A_2.fq.gz -S aligned-16/120A/120A.sam

    hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/16samples/121A/121A_1.fq.gz -2 CRC/16samples/121A/121A_2.fq.gz -S aligned-16/121A/121A.sam

    hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/16samples/122A/122A_1.fq.gz -2 CRC/16samples/122A/122A_2.fq.gz -S aligned-16/122A/122A.sam

    hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/16samples/124A/124A_1.fq.gz -2 CRC/16samples/124A/124A_2.fq.gz -S aligned-16/124A/124A.sam

    hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/16samples/126A/126A_1.fq.gz -2 CRC/16samples/126A/126A_2.fq.gz -S aligned-16/126A/126A.sam

    hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/16samples/136A/136A_1.fq.gz -2 CRC/16samples/136A/136A_2.fq.gz -S aligned-16/136A/136A.sam

    hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/16samples/140A/140A_1.fq.gz -2 CRC/16samples/140A/140A_2.fq.gz -S aligned-16/140A/140A.sam

    hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/16samples/143A/143A_1.fq.gz -2 CRC/16samples/143A/143A_2.fq.gz -S aligned-16/143A/143A.sam

    hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/16samples/153A/153A_1.fq.gz -2 CRC/16samples/153A/153A_2.fq.gz -S aligned-16/153A/153A.sam

    hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/16samples/154A/154A_1.fq.gz -2 CRC/16samples/154A/154A_2.fq.gz -S aligned-16/154A/154A.sam

    其中121A报错：后来发现是该文件夹中没有121A_2.fq.gz，加上后就正常了

    (base) luoyang@DESKTOP-AO2ICCR:/mnt/d/AAA-台式机-LY-WorkSpace$ hisat2 -t -p 12 --dta -x hg38/genome -1 CRC/16samples/121A/121A_1.fq.gz -2 CRC/16samples/121A/121A_2.fq.gz -S aligned-16/121A/121A.sam

    gzip: CRC/16samples/121A/121A_2.fq.gz: No such file or directory

    Time loading forward index: 00:00:38

    Time loading reference: 00:00:07

    Error, fewer reads in file specified with -2 than in file specified with -1

    terminate called after throwing an instance of 'int'

    Aborted (core dumped)

    (ERR): hisat2-align exited with value 134

    相关文章

      网友评论

          本文标题：第一步-hisat2-得到.sam文件

          本文链接：https://www.haomeiwen.com/subject/laxhkctx.html

          延伸阅读

          深度阅读

          • 您也可以注册成为美文阅读网的作者，发表您的原创作品、分享您的心情！

          栏目导航

          热点阅读

          关于我们|服务条款|联系我们|第一步-hisat2-得到.sam文件|投稿指南|网站地图|RSS订阅|排版工具|手机版

          提供经典美文摘抄,优美散文欣赏,现代诗歌精选,短篇小说,心情随笔,表白情书范文,故事会在线阅读欣赏

          Copyright © 2014-2023 Haomeiwen.com All Rights Reserved. 好美文阅读网 版权所有

          备案信息：桂公网安备 45052102000051号 · 桂ICP备13007215号-3

          本站所收录作品、热点评论等信息部分来源互联网，目的只是为了系统归纳学习和传递资讯

          所有作品版权归原创作者所有，与本站立场无关，如不慎侵犯了你的权益，请联系我们告知，我们将做删除处理！