Comments (2)
mikewolfe
commented on July 27, 2024
Weird. What are the commands you used to generate this? Did you run the pipeline, clean some stuff up, and run it again?
The multiqc error is suggesting that it has already been run and is running again: [WARNING] multiqc : Previous MultiQC output found! Adjusting filenames..
Snakemake is looking for a multiqc_report.html file but for some reason multiqc is outputting a multiqc_report_1.html file. I'm not sure how that is occurring though. Can you walk me through the commands or series of commands that got you here?
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mikewolfe
commented on July 27, 2024
Running the pipeline multiple times without deleting the results allows multiqc to run twice and change the name of the output files. Multiqc probably shouldn't be running again when its output files already exist but closing this issue for now.
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Related Issues (13)
- Make clean commands also clear dependent downstream calculations
- Multiqc report is not linking files for each sample together very well
- Allow for a "masked" region of the genome when performing alignments/coverage calculations
- Add ability to do summaries over regions or at specified locations
- Error in macs2_peakcalling on test HOT 3
- Issue with development pipeline branch, cmartt peak calling HOT 1
- Add bre-seq to automatically run on input samples
- Bug in running coverage and norm post-cleaning coverage and norm core HOT 1
- Allow for the pipeline to run on reference genomes with more than one contig HOT 1
- Allow for normalization based on a specified known background area of the chromosome
- add MOSAiCs peak calling algorithm option HOT 1
- Automatically parse genbanks for features and output into a .gff
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