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simoncchu / REPdenovo

A tool to construct repeats directly from raw reads
MIT License
16 stars 3 forks source link

can't run REPdenovo #9

Open warreg opened 6 years ago

warreg commented 6 years ago

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 commented 6 years ago

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 commented 6 years ago

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