Snakemake snakefile error.
0
2
Entering edit mode
13 months ago
BM ▴ 70

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

RNA-Seq Snakemake Snakefile GitHub • 929 views
ADD COMMENT
0
Entering edit mode

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.
code_formatting

ADD REPLY
0
Entering edit mode

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

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1191 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6