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mikewolfe / ChIPseq_pipeline

A general ChIP-seq pipeline to reproducibly process many samples at once.
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Bug in running coverage and norm post-cleaning coverage and norm core #3

Closed cmhustmyer closed 3 years ago

cmhustmyer commented 3 years ago

Attempting to run a CPM normalization after completing the entire pipeline (with a median normalization).

snakemake clean_coverage_and_norm --use-conda --cores 1 snakemake clean_peak_calling --use-conda --cores 1 snakemake clean_quality_control --use-conda --cores 1 snakemake run_coverage_and_norm --use-conda --cores 1

Error immediately: Building DAG of jobs... MissingInputException in line 18 of /mnt/scratch/hustmyer/ChIPseq_pipeline/workflow/rules/coverage_and_norm.smk: Missing input files for rule run_coverage_and_norm: Then it lists all of the files I'm trying to make with the CPM notation.

I was expecting a new coverage_and_norm directory to be created with the CPM normalized .bw files (similar to what occurred with the median normalization step, but this would be CPM normalized).

config.txt

mikewolfe commented 3 years ago

I was able to reproduce this error using the included test set. Upon running the last snakemake run_coverage_and_norm --use-conda --cores 1 with a config file set similarly to the one above I get the following error:

(ChIPseq_pipeline) mwolfe6@ad.wisc.edu (master *) ChIPseq_pipeline $ snakemake run_coverage_and_norm --use-conda --cores 1
Building DAG of jobs...
MissingInputException in line 18 of /mnt/scratch/mbwolfe/ChIPseq_pipeline/workflow/rules/coverage_and_norm.smk:
Missing input files for rule run_coverage_and_norm:
results/coverage_and_norm/deeptools_log2ratio/genotypeA_rep1_ext_CPM_log2ratio.narrowPeak
results/coverage_and_norm/deeptools_log2ratio/genotypeA_rep2_ext_CPM_log2ratio.narrowPeak
results/coverage_and_norm/deeptools_log2ratio/genotypeB_rep1_ext_CPM_log2ratio.narrowPeak
results/coverage_and_norm/deeptools_log2ratio/genotypeB_rep2_ext_CPM_log2ratio.narrowPeak

The issue appears to be a mis-specification of the file ending for the target output of rule run_coverage_and_norm on line 18 in the file workflow/rules/coverage_and_norm.smk. It specifies a .narrowPeak file when it should be a .bw file.