使用MEME-chip进行motif分析时报错,使用代码如下:
meme-chip -db HOCOMOCOv11_full_HUMAN_mono_meme_format.meme -meme-p 4 -dna CTCF_ChIP_motif.fasta
报错显示,没有安装 XML::Simple 模块。
安装XML::Simple 和XML::Parser模块后。
cpan[1]> install XML::Simple
Reading '/home/wuhangrui/.cpan/Metadata'
Database was generated on Thu, 01 Jun 2023 07:17:01 GMT
XML::Simple is up to date (2.25).
cpan[2]> install XML::Parser
XML::Parser is up to date (2.46).
显示成功安装。
但是在MEME文件夹下进行make test,meme-chip依然报错。
报错内容如下:(似乎是找不到XML::Parser::Expat module)
Test meme-chip1 ...
meme-chip -oc results/meme-chip1 -db meme-chip/JASPAR_CORE_2014_vertebrates.meme meme-chip/Klf1.100.fa --meme-p 24 &> log
Can't locate XML/Parser/Expat.pm in @INC (you may need to install the XML::Parser::Expat module) (@INC contains: /home/wuhangrui/meme/lib/meme-5.5.2/perl /home/wuhangrui/meme-5.5.2/scripts /home/wuhangrui/perl5/lib/perl5 /home/wuhangrui/miniconda3/envs/dna/lib/perl5/5.32/site_perl /home/wuhangrui/miniconda3/envs/dna/lib/perl5/site_perl /home/wuhangrui/miniconda3/envs/dna/lib/perl5/5.32/vendor_perl /home/wuhangrui/miniconda3/envs/dna/lib/perl5/vendor_perl /home/wuhangrui/miniconda3/envs/dna/lib/perl5/5.32/core_perl /home/wuhangrui/miniconda3/envs/dna/lib/perl5/core_perl .) at /home/wuhangrui/meme-5.5.2/scripts/CheckingSAX.pm line 12.
BEGIN failed--compilation aborted at /home/wuhangrui/meme-5.5.2/scripts/CheckingSAX.pm line 12.
Compilation failed in require at /home/wuhangrui/miniconda3/envs/dna/lib/perl5/core_perl/base.pm line 137.
...propagated at /home/wuhangrui/miniconda3/envs/dna/lib/perl5/core_perl/base.pm line 159.
BEGIN failed--compilation aborted at /home/wuhangrui/meme-5.5.2/scripts/MemeSAX.pm line 3.
Compilation failed in require at /home/wuhangrui/meme-5.5.2/scripts/MotifInMemeXML.pm line 10.
BEGIN failed--compilation aborted at /home/wuhangrui/meme-5.5.2/scripts/MotifInMemeXML.pm line 10.
Compilation failed in require at /home/wuhangrui/meme-5.5.2/scripts/meme-chip line 133.
BEGIN failed--compilation aborted at /home/wuhangrui/meme-5.5.2/scripts/meme-chip line 133.
-------------------------------------------------------------------------------
meme-chip exited with value 2 indicating failure.
FAILED!
请问可以怎么解决?
感谢
使用MEME-chip进行motif分析时报错,提示没有安装XML::Simple模块。
安装XML::Simple和XML::Parser模块后,在MEME文件夹下进行make test,meme-chip依然报错,提示找不到XML::Parser::Expat模块。
下面是解决方法:
cpan[1]> install XML::Simple
cpan[2]> install XML::Parser
tar zxvf XML-Parser-2.44.tar.gz
cd XML-Parser-2.44
perl Makefile.PL
make
make test
make install
我会注意骑士的疯度