Snakemake snakefile error.

Question

[BM]

I am using code from a GitHub Snakemake repository to perform RNA-seq anlaysis on a cluster computer.

The following error is giving after submission to the error:

"KeyError in line 7 of /rna_seq_snakemake-master/rna_seq_snakemake-master/rna_seq.snakefile:
'species'
  File "/rna_seq_snakemake-master/rna_seq_snakemake-master/rna_seq.snakefile", line 7, in <module>

The code for the rna_seq.snakefile:

import pandas as pd
import os
import subprocess

configfile: "config/config.yaml"
include: "rules/helpers.py"
SPECIES_VERSION = get_species_version(config['species'])

The code for the config.yaml file where species is indicated:
# end_type: pe
# readLen: 50
# # #mouse or human
# species: "mouse"
# feature_counts_strand_info: "-s 2"

Can anyone advise please?

Thanks in advance

[Ram]

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.

[cschu181]

You don't have a "species" entry in your config file.

edit: d'oh. didn't read the commented lines.

[cschu181]

Or are the lines from the config file actually commented out?