can't run REPdenovo

[warreg]

Hi,
I'm student in intership in a Lab in France.
So i rread many times your review while my bibliography project.
So now i'm testing your tool and i get some problem.
Please find the output error
output_error.txt

my config file
config_file.txt

and the readfile
read_file_1.txt

Thanks you

[simoncchu]

Change this:

SAMTOOLS_PATH GLOBAL /usr/bin/samtools
JELLYFISH_PATH GLOBAL /usr/bin/jellyfish
VELVET_PATH GLOBAL /usr/bin/

to:

SAMTOOLS_PATH /usr/bin/samtools
JELLYFISH_PATH /usr/bin/jellyfish
VELVET_PATH /usr/bin/

Also, please check whether your python is properly installed. And you can try step by step like:

python ./main.py -c Assembly -g configuration-file-name -r raw-reads-file-name

[warreg]

hi,

i changed config_file like this:
config_file.txt

here the new output error:
output_error.txt

and i get 3 new files in my REPdenovo_output file:
-contigs.fa (empty)
-dumped_30mers.txt (also empty)
and
-reads_coverage.txt
reads_coverage.txt

Ps: i've checked my python version, it's looks good to me and my jellyfish version is 2.2.4

Thank you