VIRUSBreakend Debug

https://github.com/PapenfussLab/gridss
https://github.com/PapenfussLab/gridss/blob/master/VIRUSBreakend_Readme.md

build it from source.

To build gridsstools from source run the following:

git clone http://github.com/PapenfussLab/gridss/ cd gridss git
submodule init
git submodule update
cd src/main/c/gridsstools/htslib/
autoheader
autoconf
./configure && make
cd …
autoheader
autoconf
./configure && make all

autoheader command not found
m4 not found
…
手动安装出错 m4，autoconf
yum install gcc
yum install m4
yum install gcc-c++
yum install autoconf
yum install automake

依然报错，试图的source编译未走通，undefined reference to ‘libdeflate_crc32’，conda issue没解决

直接用下载好的gridss-2.12.0.tar.gz，解压后直接配置环境变量

nohup virusbreakend-build --jar /home/hjb_usr04/anaconda3/share/gridss-2.1.0-0/gridss.jar virusbreakenddb >log 2>&1 &

rysnc报错，安装

wget https://download.samba.org/pub/rsync/src/rsync-3.0.6.tar.gz
tar -zxvf rsync-3.0.6.tar.gz
./configure --prefix=~/local/rsync
make
make install

Downloading nucleotide est accession to taxon map...rsync: link_stat "/taxonomy/accession2taxid/nucl_est.accession2taxid.gz" (in pub) failed: No such file or directory (2)
rsync error: some files/attrs were not transferred (see previous errors) (code 23) at main.c(1659) [Receiver=3.1.3]

官网
Source (99 KB): Kraken2’s source code and README. The current official version of Kraken 2 is v2.0.8-beta (released April 25th, 2019). However, additional fixes/changes are in the newest github version.

The source code for the current release and the newest version are both available at the Kraken 2 GitHub repository.

导致我安装的conda版本出错，安装github版本

kraken安装

sh install_kraken2.sh ~/kraken2

继续报错

unable to find dustmasker in path, can’t mask low-complexity sequences

virusbreakend-build requires:

An internet connection
GRIDSS
samtools
Kraken2
dustmasker (part of the NCBI BLAST+ package)
EDirect utilities

要安装ncbi-blast+

ncbi-blast+

https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.11.0±x64-linux.tar.gz

error log:

~/gridss-2.12.0/scripts/virusbreakend-build: line 107: esearch: co
mmand not found
~/gridss-2.12.0/scripts/virusbreakend-build: line 108: efetch: com
mand not found

install

ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/edirect.zip
一直报错，从新安装edrict

官方安装（https://dataguide.nlm.nih.gov/edirect/install.html）

0608:
rsync install: https://rsync.samba.org/

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• gridss.jar
  conda自动安装的版本是最初版本，会报错。最好安装最新2.12.0 但是环境依赖出了问题。安装2.8.0暂时不报错 conda install -c bioconda gridss=2.8.0
• 由于gridsstools需要源码编译，上面之前遇到的问题再次面临undefined reference to 'libdeflate_crc32'，然后解决方法是，退出conda环境，安装相关环境配置。

conda deactivate
yum install -y zlib zlib-devel
yum install bzip2-devel
yum install xz-devel
yum install curl-devel
yum install openssl-devel

• 环境配置时分别配置了

PATH=$PATH:/home/hjb_usr04/gridss/scripts/
PATH=$PATH:/home/hjb_usr04/anaconda3/share/gridss-2.8.0-0/
PATH=$PATH:/home/hjb_usr04/gridss/src/main/c/gridsstools/

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下载了fna文件后 ，出现的错误。[E::fai_build_core] Different line length in sequence ‘kraken:taxid|436|NZ_CP062147.1‘