AME perl python output issue

[Rdmb]

Hello MEME,

I’ve some issues with the local version of MEME and more precisely AME. 

• By using AME with the following command, the output is similar to the online version but I do not have the tsv files 

module load MEME/4.11.1-foss-2015b

ame --oc ame_out --shuffle-- fasta_file.fa MEME_file

• And  who I’m using this following command, I do have the tsv files, but the results of the analysis is aberrant compare to the online and the other command outputs

module load MEME/5.0.4-foss-2018b-Python-3.6.6

module load Perl/5.20.3-foss-2015b

module load Python/3.6.6-foss-2018b

ame --oc ame_out --shuffle-- fasta_file.fa MEME_file

Do you have any idea why such a thing is happening and how to solve this problem ?

Cheers.

[cegrant]

By using AME with the following command, the output is similar to the online version but I do not have the tsv files 

 

module load MEME/4.11.1-foss-2015b 

The tsv output was added to several commands (including ame) in the 5.0 release of the MEME Suite.

And  who I’m using this following command, I do have the tsv files, but the results of the analysis is aberrant compare to the online and the other command outputs

AME  doesn't use Perl or Python. Other tools in the MEME Suite do, but the paths to perl and python are compiled in when the MEME Suite is built, so the module commands for Perl and Python should have no effect. How different is the output? Some slight difference would be expected because you've asked AME to use a random shuffle of your sequences as the control set, and you wouldn't necessarily expect to get the exact same shuffle on different system . If the differences are significant the best was to diagnose the issue would be to run the tests that are provided with the MEME Suite source code. You may need to talk to the local administrators who created the module and see if they ran the tests after building the software (make check or make smoke).

Charles