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hsigeman / findZX

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Error when skipping read trimming #18

Open rotifergirl opened 2 months ago

rotifergirl commented 2 months ago

I am trying to use findZX on reads that have already been trimmed, but I keep getting an error that only happens when I skip the trimming part of the pipeline.

Is there a way around this? Or should I just run it with trimming turned on?

This is the full message I get when I try and run without trimming Workflow defines that rule genome_faidx is eligible for caching between workflows (use the --cache argument to enable this). Workflow defines that rule bwa_index is eligible for caching between workflows (use the --cache argument to enable this). Building DAG of jobs... AmbiguousRuleException: Rules normalize_cov_mean and gencov_bedtools are ambiguous for the file results/Snapper_wild_to_F1/coverage/gencov.mismatch.0.0.norm.sexAverage.out. Consider starting rule output with a unique prefix, constrain your wildcards, or use the ruleorder directive. Wildcards: normalize_cov_mean: ED=0.0 gencov_bedtools: ED=0.0.norm.sexAverage Expected input files: normalize_cov_mean: results/Snapper_wild_to_F1/coverage/gencov.mismatch.0.0.out gencov_bedtools: results/Snapper_wild_to_F1/coverage/genome_5kb_windows.outExpected output files: normalize_cov_mean: results/Snapper_wild_to_F1/coverage/gencov.mismatch.0.0.norm.sexAverage.out gencov_bedtools: results/Snapper_wild_to_F1/coverage/gencov.mismatch.0.0.norm.sexAverage.out

hsigeman commented 1 month ago

Hi!

I tried to recreate this problem using the test config file (.test/config.yml) but the pipeline finished without issues. Would you mind testing this as well to make sure that the error is not related to the pipeline or the installed software?

In the test config file, I set all these three trimming and subsampling parameters to false: 

# Trimming and subsampling of reads  #

## These three variables control trimming and subsampling of reads
## Set all to "false" to disable trimming and subsampling
## Only one variable is allowed to be "true"

trim_reads: false 
  # Set to true for trimming of reads

trim_and_subsample: false
  # Set to true for trimming and subsampling of reads

subsample_only: false
  # Set to true for subsampling of reads (but not trimming)

And then ran the pipeline like this: snakemake -s workflow/findZX --configfile .test/config.yml --cores 1 -R all --use-conda -k

Another situation when these error messages occur is when snakemake cannot find all the input files. So if the test dataset finishes without errors, could you also doublecheck that the paths to all the input files are correct?

Hope this helps! Hanna