Open shlokanegi opened 6 months ago
Attaching the config.yaml
file here -
CPGISLANDLOC: "resources/positions"
# path to named cpg region file
CPGREGIONS : "resources/named.cpgIslands.hg38.sorted.bed"
#paths to rust executables
RUSTANNOTATE : "workflow/scripts/./intervalAssign"
# default region file
DEFAULTREGION : "resources/allChrom.bed"
#Files and paths needed for annotation
NAMEDCPGS : "resources/cpgIslands.sorted.named.core.tsv"
NAMEDGENES : "resources/all.sorted.targets.intervals.tsv"
single_target : "Nothing"
LC_ALL : C
samples: config/blood_5mc_bam_files.tsv
targetfile: config/targets.txt
control_metadata: config/blood_5mc_control_metadata.csv
metadata: config/test_metadata.csv
minimum_control_CpGs: 4000000
methylation_type: "5mc" # 5mc, 5hmc5mc_ignore, 5hmc5mc_bayes
Hi,
I am trying to run something similar and I am getting the same error. Were you able to find what the problem was?
Thank you
Hello, I'm experiencing the same issue, even when I try to do a dry run with the example config files. Any help would be much appreciated! Thanks, Madeline
Hi. I don't have experience running Snakemake, so forgive me if it's a rookie mistake on my end.
I am trying to run MeOW on a set of patient samples, sequenced with nanopore. My sample IDs are of the format "M11AB, M11CD, etc..." So, I made changes to the Snakefile to match the pattern -
SAMPLE="M\d{2}[A-Z]{2}"
. I followed all steps mentioned in the README. Below is the screenshot of the "blood_5mc_bam_files.tsv" file, consisting of bamfile paths.This is what I run -
snakemake --use-conda --cores 32
Error message
Please let me know if you need any other information. Appreciate any help! Thank You!!