Impossible to run psp-gen and MEME

[wang jenny]

I installed MEME like this

tar zxf meme_4.10.1.tar.gz 

cd meme_4.10.1 ./configure --prefix=$HOME/meme --with-url=http://meme-suite.org --enable-build-libxml2 --enable-build-libxslt 

make 

make test 

make install

1. When i run

• Starting psp-gen
  psp-gen -pos W9_IP.fasta -neg W9_IP_control.fasta -alpha dna -minw 6 -maxw 10

it shows errors like:

Can't locate PriorUtils.pm in @INC (@INC contains: /clusterdata/hiseq_apps/bin/freeze001/meme/meme_4.10.1/bin /clusterdata/uqywan30/meme/lib/perl . /clusterdata/uqqzhao/perl_module/lib64/perl5 /clusterdata/uqqzhao/perl_module /opt/perl/lib/site_perl/5.14.2/x86_64-linux-thread-multi /opt/perl/lib/site_perl/5.14.2 /opt/perl/lib/5.14.2/x86_64-linux-thread-multi /opt/perl/lib/5.14.2) at /clusterdata/hiseq_apps/bin/freeze001/meme/meme_4.10.1/bin/psp-gen line 37.

2. When i ran 

• Starting meme
  meme W9_IP.fasta -dna -oc . -nostatus -time 18000 -maxsize 60000 -mod zoops -nmotifs 10 -minw 6 -maxw 10 -revcomp -psp priors.psp

it shows errors like:

Can't locate PriorUtils.pm in @INC (@INC contains: /clusterdata/hiseq_apps/bin/freeze001/meme/meme_4.10.1/bin /clusterdata/uqywan30/meme/lib/perl /opt/perl/lib/site_perl/5.14.2/x86_64-linux-thread-multi /opt/perl/lib/site_perl/5.14.2 /opt/perl/lib/5.14.2/x86_64-linux-thread-multi /opt/perl/lib/5.14.2 .) at /clusterdata/hiseq_apps/bin/freeze001/meme/meme_4.10.1/bin/psp-gen line 37.

[James Johnson]

The error "Can't locate PriorUtils.pm" comes from Perl. All your install steps look correct but can you confirm that "PriorUtils.pm" exists in "$HOME/meme/lib/perl"?

From the paths it looks like you have 2 copies of the MEME Suite in the path at "/clusterdata/hiseq_apps/bin/freeze001/meme/meme_4.10.1" and "/clusterdata/uqywan30/meme". This should be fine but something has gotten messed up. For example you seem to be running "/clusterdata/hiseq_apps/bin/freeze001/meme/meme_4.10.1/bin/psp-gen" and so I would expect it to look for the Perl libraries in "/clusterdata/hiseq_apps/bin/freeze001/meme/meme_4.10.1/lib/perl" but instead it is looking in "/clusterdata/uqywan30/meme/lib/perl" and I'm not really sure why.

Did you move the install from "/clusterdata/uqywan30/meme"? If that is the case then the paths compiled into the program will be wrong and might explain the errors.