突然想到,曾经遇到过相似的问题。于是查看之前的实验记录:
sort -k1,1V -k2,2n CosmicCodingMuts.hg19.vcf >CosmicCodingMuts.hg19_sorted.vcf
最后,成功。
grep -o -E "^\w+([-+.]\w+)*" CosmicCodingMuts.hg19_sorted.vcf |uniq
chr1
chr2
chr3
chr4
chr5
……
是我们想要的结果。
所以,我们需要对我们在处理的过程中,“遇到问题-解决问题”的经验给有效的整理出来,这样在下次遇到的时候,可以提高我们解决问题的效率。
这个问题,卡住了我一个下午和一个晚上。现在想想,是非常蠢笨的。最本质的原因,还是自己对于Linux的指令掌握的并不是非常的熟悉。但是,sort -k1,1V
这个指令并不是经常使用的。所以,还是需要对过去的经验进行有效的整理。
(今天有时间的话,要把如何在染色体号前添加chr,以及按照染色体号排序这个经验整理出来)
这个问题就解决了。
我们来看一下,运行那个指令之后,是否会报错?
补充: 如何按照gtf文档,提取exon的首尾位置,并将其转换为bed文件的过程?
参考链接:https://www.cnblogs.com/leezx/p/8642723.html
cat hg19.gtf | grep exon | cut -f1,4,5,9 | cut -f1 -d";" | awk '{print $1, $2, $3, $5}' | sed -e 's/ /\t/g' | sed -e 's/\"//g' > hg19.fa.exon.bed
chr1 11869 12227 “ENSG00000223972”
chr1 11872 12227 “ENSG00000223972”
chr1 11874 12227 “ENSG00000223972”
chr1 12010 12057 “ENSG00000223972”
chr1 12179 12227 “ENSG00000223972”
chr1 12595 12721 “ENSG00000223972”
chr1 12613 12697 “ENSG00000223972”
chr1 12613 12721 “ENSG00000223972”
chr1 12613 12721 “ENSG00000223972”
chr1 12975 13052 “ENSG00000223972”
不知道这个文件,是否是运行这个程序所需要的?
解决了这个问题之后,我们还剩下了最后的一个问题——speedseq的安装的问题。
我决定重新安装speedseq。
切换到Linux平台上,看一下使用我的热点,是否可以把speedseq的那个安装包下载下来。
参考链接:https://cloud.tencent.com/developer/article/1556036
https://github.com/hall-lab/speedseq
http://blog.sciencenet.cn/blog-2970729-1083082.html
git clone --recursive https://github.com/hall-lab/speedseq
cd speedseq
make
现在,我们使用数据尝试是否能够下载下来(下载下来之后,再在新的平台上重新进行编译)。
出现错误:
fatal: unable to access ‘https://github.com/hall-lab/speedseq/’: gnutls_handshake() failed: The TLS connection was non-properly terminated.
错误解决:
git clone --recursive git://github.com/hall-lab/speedseq
fatal: unable to access ‘https://github.com/abyzovlab/CNVnator/’: gnutls_handshake() failed: Error in the pull function.
fatal: clone of ‘https://github.com/abyzovlab/CNVnator’ into submodule path ‘/home/zxx/speedseq/src/CNVnator’ failed
Failed to clone ‘src/CNVnator’. Retry scheduled
Cloning into ‘/home/zxx/speedseq/src/bamkit’…
fatal: unable to access ‘https://github.com/cc2qe/bamkit.git/’: gnutls_handshake() failed: The TLS connection was non-properly terminated.
fatal: clone of ‘https://github.com/cc2qe/bamkit.git’ into submodule path ‘/home/zxx/speedseq/src/bamkit’ failed
Failed to clone ‘src/bamkit’. Retry scheduled
Cloning into ‘/home/zxx/speedseq/src/bwa’…
fatal: unable to access ‘https://github.com/lh3/bwa.git/’: gnutls_handshake() failed: Error in the pull function.
fatal: clone of ‘https://github.com/lh3/bwa.git’ into submodule path ‘/home/zxx/speedseq/src/bwa’ failed
Failed to clone ‘src/bwa’. Retry scheduled
Cloning into ‘/home/zxx/speedseq/src/freebayes’…
fatal: unable to access ‘https://github.com/ekg/freebayes.git/’: gnutls_handshake() failed: Error in the pull function.
fatal: clone of ‘https://github.com/ekg/freebayes.git’ into submodule path ‘/home/zxx/speedseq/src/freebayes’ failed
Failed to clone ‘src/freebayes’. Retry scheduled
Cloning into ‘/home/zxx/speedseq/src/tabix’…
fatal: unable to access ‘https://github.com/samtools/tabix.git/’: gnutls_handshake() failed: Error in the pull function.
fatal: clone of ‘https://github.com/samtools/tabix.git’ into submodule path ‘/home/zxx/speedseq/src/tabix’ failed
Failed to clone ‘src/tabix’. Retry scheduled
Cloning into ‘/home/zxx/speedseq/src/vawk’…
fatal: unable to access ‘https://github.com/cc2qe/vawk.git/’: gnutls_handshake() failed: Error in the pull function.
fatal: clone of ‘https://github.com/cc2qe/vawk.git’ into submodule path ‘/home/zxx/speedseq/src/vawk’ failed
Failed to clone ‘src/vawk’. Retry scheduled
Cloning into ‘/home/zxx/speedseq/src/CNVnator’…
fatal: unable to access ‘https://github.com/abyzovlab/CNVnator/’: gnutls_handshake() failed: Error in the pull function.
fatal: clone of ‘https://github.com/abyzovlab/CNVnator’ into submodule path ‘/home/zxx/speedseq/src/CNVnator’ failed
Failed to clone ‘src/CNVnator’ a second time, aborting
(子模块没有下载完全)
参考链接:https://www.it610.com/article/1293776155517722624.htm
问题描述:git clone子模块没有下载完全