[2025-03-15 13:15:26,067] multiqc [DEBUG ] This is MultiQC v1.12 [2025-03-15 13:15:26,067] multiqc [DEBUG ] No MultiQC config found: /opt/anaconda/anaconda3/lib/python3.9/site-packages/multiqc_config.yaml [2025-03-15 13:15:26,067] multiqc [DEBUG ] No MultiQC config found: /home/sr320/.multiqc_config.yaml [2025-03-15 13:15:26,067] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2025-03-15 13:15:26,067] multiqc [DEBUG ] Command used: /opt/anaconda/anaconda3/bin/multiqc . [2025-03-15 13:15:26,821] multiqc [WARNING] MultiQC Version v1.27.1 now available! [2025-03-15 13:15:26,822] multiqc [DEBUG ] Command : /opt/anaconda/anaconda3/bin/multiqc . [2025-03-15 13:15:26,822] multiqc [DEBUG ] Working dir : /home/shared/16TB_HDD_01/sr320/github/project-oyster-oa/analyses/Haws-14 [2025-03-15 13:15:26,822] multiqc [DEBUG ] Template : default [2025-03-15 13:15:26,822] multiqc [DEBUG ] Running Python 3.9.7 (default, Sep 16 2021, 13:09:58) [GCC 7.5.0] [2025-03-15 13:15:26,823] multiqc [DEBUG ] Analysing modules: custom_content, ccs, ngsderive, purple, conpair, lima, peddy, somalier, methylQA, mosdepth, phantompeakqualtools, qualimap, preseq, quast, qorts, rna_seqc, rockhopper, rsem, rseqc, busco, bustools, goleft_indexcov, gffcompare, disambiguate, supernova, deeptools, sargasso, verifybamid, mirtrace, happy, mirtop, sambamba, homer, hops, macs2, theta2, snpeff, gatk, htseq, bcftools, featureCounts, fgbio, dragen, dedup, pbmarkdup, damageprofiler, biobambam2, jcvi, mtnucratio, picard, vep, sentieon, prokka, qc3C, nanostat, samblaster, samtools, sexdeterrmine, eigenstratdatabasetools, bamtools, jellyfish, vcftools, longranger, stacks, varscan2, snippy, bbmap, bismark, biscuit, hicexplorer, hicup, hicpro, salmon, kallisto, slamdunk, star, hisat2, tophat, bowtie2, bowtie1, snpsplit, odgi, pangolin, kat, leehom, adapterRemoval, clipandmerge, cutadapt, flexbar, kaiju, kraken, malt, trimmomatic, sickle, skewer, sortmerna, biobloomtools, fastq_screen, afterqc, fastp, fastqc, pychopper, pycoqc, minionqc, multivcfanalyzer, clusterflow, checkqc, bcl2fastq, bclconvert, interop, ivar, flash, seqyclean, optitype, whatshap [2025-03-15 13:15:26,823] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmp1_zagpex [2025-03-15 13:15:26,910] multiqc [INFO ] Search path : /home/shared/16TB_HDD_01/sr320/github/project-oyster-oa/analyses/Haws-14 [2025-03-15 13:15:26,923] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_4_pe.deduplicated.bam [2025-03-15 13:15:26,924] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_15_pe.deduplicated.bam [2025-03-15 13:15:27,001] multiqc [DEBUG ] File ignored by ccs/v4 because it exceeded search pattern filesize limit: zr3644_2.cytosine_context_summary.txt [2025-03-15 13:15:27,004] multiqc [DEBUG ] File ignored by lima/summary because it exceeded search pattern filesize limit: zr3644_2.cytosine_context_summary.txt [2025-03-15 13:15:27,027] multiqc [DEBUG ] File ignored by ccs/v4 because it exceeded search pattern filesize limit: zr3644_19.cytosine_context_summary.txt [2025-03-15 13:15:27,028] multiqc [DEBUG ] File ignored by lima/summary because it exceeded search pattern filesize limit: zr3644_19.cytosine_context_summary.txt [2025-03-15 13:15:27,034] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_8_pe.deduplicated.bam [2025-03-15 13:15:27,090] multiqc [DEBUG ] File ignored by ccs/v4 because it exceeded search pattern filesize limit: zr3644_13.cytosine_context_summary.txt [2025-03-15 13:15:27,092] multiqc [DEBUG ] File ignored by lima/summary because it exceeded search pattern filesize limit: zr3644_13.cytosine_context_summary.txt [2025-03-15 13:15:27,102] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_7_pe.deduplicated.bam [2025-03-15 13:15:27,156] multiqc [DEBUG ] File ignored by ccs/v4 because it exceeded search pattern filesize limit: zr3644_14.cytosine_context_summary.txt [2025-03-15 13:15:27,157] multiqc [DEBUG ] File ignored by lima/summary because it exceeded search pattern filesize limit: zr3644_14.cytosine_context_summary.txt [2025-03-15 13:15:27,168] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_3_pe.deduplicated.bam [2025-03-15 13:15:27,169] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_6_pe.deduplicated.bam [2025-03-15 13:15:27,173] multiqc [DEBUG ] File ignored by ccs/v4 because it exceeded search pattern filesize limit: zr3644_22.cytosine_context_summary.txt [2025-03-15 13:15:27,174] multiqc [DEBUG ] File ignored by lima/summary because it exceeded search pattern filesize limit: zr3644_22.cytosine_context_summary.txt [2025-03-15 13:15:27,180] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_9_pe.deduplicated.bam [2025-03-15 13:15:27,182] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_24_pe.deduplicated.bam [2025-03-15 13:15:27,185] multiqc [DEBUG ] File ignored by ccs/v4 because it exceeded search pattern filesize limit: zr3644_24.cytosine_context_summary.txt [2025-03-15 13:15:27,185] multiqc [DEBUG ] File ignored by lima/summary because it exceeded search pattern filesize limit: zr3644_24.cytosine_context_summary.txt [2025-03-15 13:15:27,192] multiqc [DEBUG ] File ignored by ccs/v4 because it exceeded search pattern filesize limit: zr3644_18.cytosine_context_summary.txt [2025-03-15 13:15:27,192] multiqc [DEBUG ] File ignored by lima/summary because it exceeded search pattern filesize limit: zr3644_18.cytosine_context_summary.txt [2025-03-15 13:15:27,195] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_20_pe.deduplicated.bam [2025-03-15 13:15:27,195] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_13_pe.deduplicated.bam [2025-03-15 13:15:27,197] multiqc [DEBUG ] File ignored by ccs/v4 because it exceeded search pattern filesize limit: zr3644_5.cytosine_context_summary.txt [2025-03-15 13:15:27,197] multiqc [DEBUG ] File ignored by lima/summary because it exceeded search pattern filesize limit: zr3644_5.cytosine_context_summary.txt [2025-03-15 13:15:27,200] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_19_pe.deduplicated.bam [2025-03-15 13:15:27,201] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_10_pe.deduplicated.bam [2025-03-15 13:15:27,201] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_14_pe.deduplicated.bam [2025-03-15 13:15:27,201] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_18_pe.deduplicated.bam [2025-03-15 13:15:27,202] multiqc [DEBUG ] File ignored by ccs/v4 because it exceeded search pattern filesize limit: zr3644_23.cytosine_context_summary.txt [2025-03-15 13:15:27,203] multiqc [DEBUG ] File ignored by lima/summary because it exceeded search pattern filesize limit: zr3644_23.cytosine_context_summary.txt [2025-03-15 13:15:27,206] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_21_pe.deduplicated.bam [2025-03-15 13:15:27,208] multiqc [DEBUG ] File ignored by ccs/v4 because it exceeded search pattern filesize limit: zr3644_4.cytosine_context_summary.txt [2025-03-15 13:15:27,209] multiqc [DEBUG ] File ignored by lima/summary because it exceeded search pattern filesize limit: zr3644_4.cytosine_context_summary.txt [2025-03-15 13:15:27,213] multiqc [DEBUG ] File ignored by ccs/v4 because it exceeded search pattern filesize limit: zr3644_20.cytosine_context_summary.txt [2025-03-15 13:15:27,213] multiqc [DEBUG ] File ignored by lima/summary because it exceeded search pattern filesize limit: zr3644_20.cytosine_context_summary.txt [2025-03-15 13:15:27,218] multiqc [DEBUG ] File ignored by ccs/v4 because it exceeded search pattern filesize limit: zr3644_17.cytosine_context_summary.txt [2025-03-15 13:15:27,219] multiqc [DEBUG ] File ignored by lima/summary because it exceeded search pattern filesize limit: zr3644_17.cytosine_context_summary.txt [2025-03-15 13:15:27,221] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_12_pe.deduplicated.bam [2025-03-15 13:15:27,223] multiqc [DEBUG ] File ignored by ccs/v4 because it exceeded search pattern filesize limit: zr3644_10.cytosine_context_summary.txt [2025-03-15 13:15:27,223] multiqc [DEBUG ] File ignored by lima/summary because it exceeded search pattern filesize limit: zr3644_10.cytosine_context_summary.txt [2025-03-15 13:15:27,233] multiqc [DEBUG ] File ignored by ccs/v4 because it exceeded search pattern filesize limit: zr3644_6.cytosine_context_summary.txt [2025-03-15 13:15:27,233] multiqc [DEBUG ] File ignored by lima/summary because it exceeded search pattern filesize limit: zr3644_6.cytosine_context_summary.txt [2025-03-15 13:15:27,237] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_17_pe.deduplicated.bam [2025-03-15 13:15:27,239] multiqc [DEBUG ] File ignored by ccs/v4 because it exceeded search pattern filesize limit: zr3644_7.cytosine_context_summary.txt [2025-03-15 13:15:27,239] multiqc [DEBUG ] File ignored by lima/summary because it exceeded search pattern filesize limit: zr3644_7.cytosine_context_summary.txt [2025-03-15 13:15:27,244] multiqc [DEBUG ] File ignored by ccs/v4 because it exceeded search pattern filesize limit: zr3644_12.cytosine_context_summary.txt [2025-03-15 13:15:27,245] multiqc [DEBUG ] File ignored by lima/summary because it exceeded search pattern filesize limit: zr3644_12.cytosine_context_summary.txt [2025-03-15 13:15:27,249] multiqc [DEBUG ] File ignored by ccs/v4 because it exceeded search pattern filesize limit: zr3644_16.cytosine_context_summary.txt [2025-03-15 13:15:27,249] multiqc [DEBUG ] File ignored by lima/summary because it exceeded search pattern filesize limit: zr3644_16.cytosine_context_summary.txt [2025-03-15 13:15:27,253] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_5_pe.deduplicated.bam [2025-03-15 13:15:27,253] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_1_pe.deduplicated.bam [2025-03-15 13:15:27,254] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_16_pe.deduplicated.bam [2025-03-15 13:15:27,256] multiqc [DEBUG ] File ignored by ccs/v4 because it exceeded search pattern filesize limit: zr3644_8.cytosine_context_summary.txt [2025-03-15 13:15:27,256] multiqc [DEBUG ] File ignored by lima/summary because it exceeded search pattern filesize limit: zr3644_8.cytosine_context_summary.txt [2025-03-15 13:15:27,260] multiqc [DEBUG ] File ignored by ccs/v4 because it exceeded search pattern filesize limit: zr3644_9.cytosine_context_summary.txt [2025-03-15 13:15:27,261] multiqc [DEBUG ] File ignored by lima/summary because it exceeded search pattern filesize limit: zr3644_9.cytosine_context_summary.txt [2025-03-15 13:15:27,264] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_23_pe.deduplicated.bam [2025-03-15 13:15:27,265] multiqc [DEBUG ] File ignored by ccs/v4 because it exceeded search pattern filesize limit: zr3644_15.cytosine_context_summary.txt [2025-03-15 13:15:27,266] multiqc [DEBUG ] File ignored by lima/summary because it exceeded search pattern filesize limit: zr3644_15.cytosine_context_summary.txt [2025-03-15 13:15:27,270] multiqc [DEBUG ] File ignored by ccs/v4 because it exceeded search pattern filesize limit: zr3644_11.cytosine_context_summary.txt [2025-03-15 13:15:27,270] multiqc [DEBUG ] File ignored by lima/summary because it exceeded search pattern filesize limit: zr3644_11.cytosine_context_summary.txt [2025-03-15 13:15:27,273] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_2_pe.deduplicated.bam [2025-03-15 13:15:27,275] multiqc [DEBUG ] File ignored by ccs/v4 because it exceeded search pattern filesize limit: zr3644_21.cytosine_context_summary.txt [2025-03-15 13:15:27,275] multiqc [DEBUG ] File ignored by lima/summary because it exceeded search pattern filesize limit: zr3644_21.cytosine_context_summary.txt [2025-03-15 13:15:27,278] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_11_pe.deduplicated.bam [2025-03-15 13:15:27,278] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_22_pe.deduplicated.bam [2025-03-15 13:15:27,280] multiqc [DEBUG ] File ignored by ccs/v4 because it exceeded search pattern filesize limit: zr3644_1.cytosine_context_summary.txt [2025-03-15 13:15:27,280] multiqc [DEBUG ] File ignored by lima/summary because it exceeded search pattern filesize limit: zr3644_1.cytosine_context_summary.txt [2025-03-15 13:15:27,284] multiqc [DEBUG ] File ignored by ccs/v4 because it exceeded search pattern filesize limit: zr3644_3.cytosine_context_summary.txt [2025-03-15 13:15:27,285] multiqc [DEBUG ] File ignored by lima/summary because it exceeded search pattern filesize limit: zr3644_3.cytosine_context_summary.txt [2025-03-15 13:15:27,466] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.4.3 [2025-03-15 13:15:27,467] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.4.3 [2025-03-15 13:15:27,695] multiqc.modules.bismark.bismark [INFO ] Found 24 dedup reports [2025-03-15 13:15:27,698] multiqc.modules.bismark.bismark [INFO ] Found 24 methextract reports [2025-03-15 13:15:27,738] multiqc [INFO ] Compressing plot data [2025-03-15 13:15:27,927] multiqc [INFO ] Report : multiqc_report.html [2025-03-15 13:15:27,927] multiqc [INFO ] Data : multiqc_data [2025-03-15 13:15:27,927] multiqc [DEBUG ] Moving data file from '/tmp/tmp1_zagpex/multiqc_data' to '/home/shared/16TB_HDD_01/sr320/github/project-oyster-oa/analyses/Haws-14/multiqc_data' [2025-03-15 13:15:27,984] multiqc [INFO ] MultiQC complete