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专业背景:计算机科学 研究方向与兴趣: JavaEE-Web软件开发, 生物信息学, 数据挖掘与机器学习, 智能信息系统 目前工作: 基因组, 转录组, NGS高通量数据分析, 生物数据挖掘, 植物系统发育和比较进化基因组学

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amos-3.1.0的安装和使用  

2015-05-11 21:28:32|  分类: 生信分析软件 |  标签: |举报 |字号 订阅

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AMOS的安装需要先安装mummer,Qt 和BLAT。其中,QT为可选。

$ wget http://jaist.dl.sourceforge.net/project/mummer/mummer/3.23/MUMmer3.23.tar.gz
$ tar zxf MUMmer3.23.tar.gz
$ cd MUMmer3.23/
$ make check
$ make install
$ echo PATH=$PWD/:'$PATH' >> ~/.bashrc
如果运行时出现下面错误,请重新编译:

出现如下错误:可能是reference 的数据格式不对,可能是fasta格式的数据标题过长
如:
>标题过长,所以要修改一下标题
postnuc: tigrinc.cc:337: int Read_String(FILE*, char*&, long int&, char*,
int): Assertion `Len > 0 && Line [Len - 1] == '\n'' failed.
sh: line 1: 16222 Aborted

这可能是query数据格式不对,同时序列中不能含有 "N"
prenuc: tigrinc.cc:337: int Read_String(FILE*, char*&, long int&, char*,
> int): Assertion `Len > 0 && Line [Len - 1] == '\n'' failed.


I reported the following error when I tried to compare whole genomes of hg19 and Chinese using mummer. Is there a way by which I can increase the maximum limit of textlen?

./mummer -mum -b -c /Users/ Hg19/WholeGenome_Hg19.fa /Users/Chinese/chinese_whole_genome.fa > hg19_chinese_whole.mums
# reading input file " /Users/ Hg19/WholeGenome_Hg19.fa" of length 3095694007
# construct suffix tree for sequence of length 3095694007
# (maximum reference length is 536870908)
# (maximum query length is 4294967295)
# process 30956940 characters per dot
./mummer: suffix tree construction failed: textlen=3095694007 larger than maximal textlen=536870908

Regards,
Vishnu


Hi Vishnu,
In the MUMmer base directory, type:

> make clean
> make CPPFLAGS="-O3 -DSIXTYFOURBITS"

That should recompile MUMmer in 64-bit mode so it will be able to construct
very large trees.


http://sourceforge.net/p/mummer/mailman/mummer-help/thread/AANLkTik555sFkzTEvIONovJt1_0yYuuQzoalzrF6-wHt@mail.gmail.com/
http://sourceforge.net/p/mummer/mailman/message/22416185/


 $ wget http://download.qt-project.org/official_releases/qt/4.8/4.8.5/qt-everywhere-opensource-src-4.8.5.tar.gz $ tar zxf qt-everywhere-opensource-src-4.8.5.tar.gz $ cd qt-everywhere-opensource-src-4.8.5 $ ./configure --prefix= your path $ sudo yum install gstreamer-plugins-base-devel* $ gmake -j 8 $ sudo gmake install $ echo 'PTAH=/usr/local/Trolltech/Qt-4.8.5/bin:$PATH' >> ~/.bashrc $ wget http://nchc.dl.sourceforge.net/project/amos/amos/3.1.0/amos-3.1.0.tar.gz $ tar zxf amos-3.1.0.tar.gz $ cd amos-3.1.0 $ ./configure --prefix=/home/zhaolei/software/amos-3.1.0 --with-Boost-dir=/home/zhaolei/software/boost-1.58/include $ make -j 8 然后报错(find-tandem.cc
find-tandem.cc: In function ‘int main(int, char**)’:
find-tandem.cc:243:3: error: ‘optarg’ was not declared in this scope
find-tandem.cc:245:63: error: ‘getopt’ was not declared in this scope
find-tandem.cc:258:55: error: ‘optopt’ was not declared in this scope
make[3]: *** [find-tandem.o] Error 1
make[3]: Leaving directory `/usr/local/amos-3.1.0/src/Align'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/usr/local/amos-3.1.0/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/usr/local/amos-3.1.0'
make: *** [all] Error 2) 解决办法:Add this in the front group of src/Align/find-tandem.cc file, yes,
this is a hack, but a sensible one.
#include <getopt.h>
http://seqanswers.com/forums/archive/index.php/t-17802.html

 $ make -j 8 $ make install
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