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mikewolfe / ChIPseq_pipeline

A general ChIP-seq pipeline to reproducibly process many samples at once.
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Multiqc report is not linking files for each sample together very well #10

Closed mikewolfe closed 3 years ago

mikewolfe commented 3 years ago

Warning messages:

Activating conda environment: /mnt/scratch/hustmyer/ChIPseq_pipeline/.snakemake/conda/31d4d5e3
[INFO   ]         multiqc : This is MultiQC v1.9 (7e91591)
[INFO   ]         multiqc : Template    : default
[INFO   ]         multiqc : Searching   : /mnt/scratch/hustmyer/ChIPseq_pipeline/results
Searching 855 files..  [####################################]  100%
[INFO   ]         bowtie2 : Found 20 reports
[WARNING]    plotCoverage : Replacing duplicate sample r2_wt_inputA.
[WARNING]    plotCoverage : Replacing duplicate sample r2_wt_stpA.
[WARNING]    plotCoverage : Replacing duplicate sample r2_wt_rfaH.
[WARNING]    plotCoverage : Replacing duplicate sample r2_dr_inputA.
[WARNING]    plotCoverage : Replacing duplicate sample r2_dr_inputG.
[WARNING]    plotCoverage : Replacing duplicate sample r2_dr_hns.
[WARNING]    plotCoverage : Replacing duplicate sample r2_dr_stpA.
[WARNING]    plotCoverage : Replacing duplicate sample r2_dr_rfaH.
[WARNING]    plotCoverage : Replacing duplicate sample r2_dr_beta.
[WARNING]    plotCoverage : Replacing duplicate sample r2_dr_sigma.
[WARNING]    plotCoverage : Replacing duplicate sample r2_2x_inputA.
[WARNING]    plotCoverage : Replacing duplicate sample r2_2x_inputG.
[WARNING]    plotCoverage : Replacing duplicate sample r2_2x_hns.
[WARNING]    plotCoverage : Replacing duplicate sample r2_2x_stpA.
[WARNING]    plotCoverage : Replacing duplicate sample r2_2x_rfaH.
[WARNING]    plotCoverage : Replacing duplicate sample r2_2x_beta.
[WARNING]    plotCoverage : Replacing duplicate sample r2_2x_sigma.
[WARNING]    plotCoverage : Replacing duplicate sample r2_3x_inputG.
[WARNING]    plotCoverage : Replacing duplicate sample r2_3x_beta.
[WARNING]    plotCoverage : Replacing duplicate sample r2_3x_sigma.
[WARNING]    plotCoverage : Replacing duplicate sample r2_wt_inputA.
[WARNING]    plotCoverage : Replacing duplicate sample r2_wt_stpA.
[WARNING]    plotCoverage : Replacing duplicate sample r2_wt_rfaH.
[WARNING]    plotCoverage : Replacing duplicate sample r2_dr_inputA.
[WARNING]    plotCoverage : Replacing duplicate sample r2_dr_inputG.
[WARNING]    plotCoverage : Replacing duplicate sample r2_dr_hns.
[WARNING]    plotCoverage : Replacing duplicate sample r2_dr_stpA.
[WARNING]    plotCoverage : Replacing duplicate sample r2_dr_rfaH.
[WARNING]    plotCoverage : Replacing duplicate sample r2_dr_beta.
[WARNING]    plotCoverage : Replacing duplicate sample r2_dr_sigma.
[WARNING]    plotCoverage : Replacing duplicate sample r2_2x_inputA.
[WARNING]    plotCoverage : Replacing duplicate sample r2_2x_inputG.
[WARNING]    plotCoverage : Replacing duplicate sample r2_2x_hns.
[WARNING]    plotCoverage : Replacing duplicate sample r2_2x_stpA.
[WARNING]    plotCoverage : Replacing duplicate sample r2_2x_rfaH.
[WARNING]    plotCoverage : Replacing duplicate sample r2_2x_beta.
[WARNING]    plotCoverage : Replacing duplicate sample r2_2x_sigma.
[WARNING]    plotCoverage : Replacing duplicate sample r2_3x_inputG.
[WARNING]    plotCoverage : Replacing duplicate sample r2_3x_beta.
[WARNING]    plotCoverage : Replacing duplicate sample r2_3x_sigma.
[INFO   ]       deeptools : Found 160 total deepTools samples
[INFO   ]           macs2 : Found 14 logs
[INFO   ]          fastqc : Found 40 reports
[INFO   ]     trimmomatic : Found 20 logs
[INFO   ]        cutadapt : Found 20 reports
[INFO   ]          fastqc : Found 40 reports
[INFO   ]         multiqc : Compressing plot data
[INFO   ]         multiqc : Report      : results/quality_control/multiqc_report.html
[INFO   ]         multiqc : Data        : results/quality_control/multiqc_data
[INFO   ]         multiqc : MultiQC complete

Reworking of config files will be needed to clean up report output.