[2023-12-12 15:19:38,806] multiqc [DEBUG ] This is MultiQC v1.12 [2023-12-12 15:19:38,806] multiqc [DEBUG ] No MultiQC config found: /opt/anaconda/anaconda3/lib/python3.9/site-packages/multiqc_config.yaml [2023-12-12 15:19:38,806] multiqc [DEBUG ] No MultiQC config found: /home/shared/8TB_HDD_02/graceleuchtenberger/.multiqc_config.yaml [2023-12-12 15:19:38,806] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-12-12 15:19:38,806] multiqc [DEBUG ] Command used: /opt/anaconda/anaconda3/bin/multiqc . [2023-12-12 15:19:39,067] multiqc [WARNING] MultiQC Version v1.17 now available! [2023-12-12 15:19:39,067] multiqc [DEBUG ] Command : /opt/anaconda/anaconda3/bin/multiqc . [2023-12-12 15:19:39,067] multiqc [DEBUG ] Working dir : /home/shared/8TB_HDD_02/graceleuchtenberger/Github/byssus-exp-analysis/output/fastqc/untrimmed [2023-12-12 15:19:39,067] multiqc [DEBUG ] Template : default [2023-12-12 15:19:39,067] multiqc [DEBUG ] Running Python 3.9.7 (default, Sep 16 2021, 13:09:58) [GCC 7.5.0] [2023-12-12 15:19:39,068] 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 [2023-12-12 15:19:39,068] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpjj5qb__w [2023-12-12 15:19:39,207] multiqc [INFO ] Search path : /home/shared/8TB_HDD_02/graceleuchtenberger/Github/byssus-exp-analysis/output/fastqc/untrimmed [2023-12-12 15:19:39,251] multiqc [DEBUG ] File ignored by ccs/v4 because it exceeded search pattern filesize limit: T007FX_S225_L001_R1_001_fastqc.html [2023-12-12 15:19:39,252] multiqc [DEBUG ] File ignored by hicexplorer because it 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[2023-12-12 15:19:43,807] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: T010G_S121_L001_R1_001_fastqc.html [2023-12-12 15:19:43,807] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: T010G_S121_L001_R1_001_fastqc.html [2023-12-12 15:19:43,807] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: T010G_S121_L001_R1_001_fastqc.html [2023-12-12 15:19:43,807] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: T010G_S121_L001_R1_001_fastqc.html [2023-12-12 15:19:43,807] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: T010G_S121_L001_R1_001_fastqc.html [2023-12-12 15:19:43,854] multiqc [DEBUG ] File ignored by nanostat because it exceeded search pattern filesize limit: T010G_S121_L001_R1_001_fastqc.html [2023-12-12 15:19:43,864] multiqc [DEBUG ] File ignored by ccs/v4 because it exceeded search pattern filesize limit: T026F_S179_L002_R1_001_fastqc.html [2023-12-12 15:19:43,864] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: T026F_S179_L002_R1_001_fastqc.html [2023-12-12 15:19:43,865] multiqc [DEBUG ] File ignored by lima/summary because it exceeded search pattern filesize limit: T026F_S179_L002_R1_001_fastqc.html [2023-12-12 15:19:43,866] multiqc [DEBUG ] File ignored by vep/vep_txt because it exceeded search pattern filesize limit: T026F_S179_L002_R1_001_fastqc.html [2023-12-12 15:19:43,867] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: T026F_S179_L002_R1_001_fastqc.html [2023-12-12 15:19:43,867] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: T026F_S179_L002_R1_001_fastqc.html [2023-12-12 15:19:43,867] multiqc [DEBUG ] File ignored by 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15:19:44,037] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: T005G_S116_L001_R1_001_fastqc.html [2023-12-12 15:19:44,037] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: T005G_S116_L001_R1_001_fastqc.html [2023-12-12 15:19:44,037] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: T005G_S116_L001_R1_001_fastqc.html [2023-12-12 15:19:44,037] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: T005G_S116_L001_R1_001_fastqc.html [2023-12-12 15:19:44,037] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: T005G_S116_L001_R1_001_fastqc.html [2023-12-12 15:19:44,038] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: T005G_S116_L001_R1_001_fastqc.html [2023-12-12 15:19:44,082] multiqc [DEBUG ] File ignored by nanostat because it exceeded search pattern filesize limit: T005G_S116_L001_R1_001_fastqc.html [2023-12-12 15:19:44,089] multiqc [DEBUG ] File ignored by ccs/v4 because it exceeded search pattern filesize limit: T011F_S110_L002_R1_001_fastqc.html [2023-12-12 15:19:44,090] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: T011F_S110_L002_R1_001_fastqc.html [2023-12-12 15:19:44,091] multiqc [DEBUG ] File ignored by lima/summary because it exceeded search pattern filesize limit: T011F_S110_L002_R1_001_fastqc.html [2023-12-12 15:19:44,092] multiqc [DEBUG ] File ignored by vep/vep_txt because it exceeded search pattern filesize limit: T011F_S110_L002_R1_001_fastqc.html [2023-12-12 15:19:44,093] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: T011F_S110_L002_R1_001_fastqc.html [2023-12-12 15:19:44,093] multiqc [DEBUG ] File ignored by 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[2023-12-12 15:19:44,266] multiqc [DEBUG ] File ignored by vep/vep_txt because it exceeded search pattern filesize limit: T017G_S186_L001_R1_001_fastqc.html [2023-12-12 15:19:44,266] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: T017G_S186_L001_R1_001_fastqc.html [2023-12-12 15:19:44,266] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: T017G_S186_L001_R1_001_fastqc.html [2023-12-12 15:19:44,266] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: T017G_S186_L001_R1_001_fastqc.html [2023-12-12 15:19:44,266] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: T017G_S186_L001_R1_001_fastqc.html [2023-12-12 15:19:44,266] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: T017G_S186_L001_R1_001_fastqc.html [2023-12-12 15:19:44,267] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: T017G_S186_L001_R1_001_fastqc.html [2023-12-12 15:19:44,314] multiqc [DEBUG ] File ignored by nanostat because it exceeded search pattern filesize limit: T017G_S186_L001_R1_001_fastqc.html [2023-12-12 15:19:44,320] multiqc [DEBUG ] File ignored by ccs/v4 because it exceeded search pattern filesize limit: T003FX_S221_L002_R1_001_fastqc.html [2023-12-12 15:19:44,321] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: T003FX_S221_L002_R1_001_fastqc.html [2023-12-12 15:19:44,321] multiqc [DEBUG ] File ignored by lima/summary because it exceeded search pattern filesize limit: T003FX_S221_L002_R1_001_fastqc.html [2023-12-12 15:19:44,323] multiqc [DEBUG ] File ignored by vep/vep_txt because it exceeded search pattern filesize limit: T003FX_S221_L002_R1_001_fastqc.html [2023-12-12 15:19:44,323] multiqc [DEBUG ] File ignored by 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filesize limit: T134F_S132_L001_R1_001_fastqc.html [2023-12-12 15:19:47,055] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: T134F_S132_L001_R1_001_fastqc.html [2023-12-12 15:19:47,055] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: T134F_S132_L001_R1_001_fastqc.html [2023-12-12 15:19:47,103] multiqc [DEBUG ] File ignored by nanostat because it exceeded search pattern filesize limit: T134F_S132_L001_R1_001_fastqc.html [2023-12-12 15:19:47,110] multiqc [DEBUG ] File ignored by ccs/v4 because it exceeded search pattern filesize limit: T014F_S171_L002_R1_001_fastqc.html [2023-12-12 15:19:47,111] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: T014F_S171_L002_R1_001_fastqc.html [2023-12-12 15:19:47,111] multiqc [DEBUG ] File ignored by lima/summary because it exceeded search pattern filesize limit: T014F_S171_L002_R1_001_fastqc.html [2023-12-12 15:19:47,113] multiqc [DEBUG ] File ignored by vep/vep_txt because it exceeded search pattern filesize limit: T014F_S171_L002_R1_001_fastqc.html [2023-12-12 15:19:47,113] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: T014F_S171_L002_R1_001_fastqc.html [2023-12-12 15:19:47,113] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: T014F_S171_L002_R1_001_fastqc.html [2023-12-12 15:19:47,113] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: T014F_S171_L002_R1_001_fastqc.html [2023-12-12 15:19:47,113] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: T014F_S171_L002_R1_001_fastqc.html [2023-12-12 15:19:47,113] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: T014F_S171_L002_R1_001_fastqc.html [2023-12-12 15:19:47,113] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: T014F_S171_L002_R1_001_fastqc.html [2023-12-12 15:19:47,162] multiqc [DEBUG ] File ignored by nanostat because it exceeded search pattern filesize limit: T014F_S171_L002_R1_001_fastqc.html [2023-12-12 15:19:47,169] multiqc [DEBUG ] File ignored by ccs/v4 because it exceeded search pattern filesize limit: T007G_S118_L001_R1_001_fastqc.html [2023-12-12 15:19:47,170] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: T007G_S118_L001_R1_001_fastqc.html [2023-12-12 15:19:47,170] multiqc [DEBUG ] File ignored by lima/summary because it exceeded search pattern filesize limit: T007G_S118_L001_R1_001_fastqc.html [2023-12-12 15:19:47,172] multiqc [DEBUG ] File ignored by vep/vep_txt because it exceeded search pattern filesize limit: T007G_S118_L001_R1_001_fastqc.html [2023-12-12 15:19:47,172] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: T007G_S118_L001_R1_001_fastqc.html [2023-12-12 15:19:47,172] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: T007G_S118_L001_R1_001_fastqc.html [2023-12-12 15:19:47,172] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: T007G_S118_L001_R1_001_fastqc.html [2023-12-12 15:19:47,172] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: T007G_S118_L001_R1_001_fastqc.html [2023-12-12 15:19:47,172] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: T007G_S118_L001_R1_001_fastqc.html [2023-12-12 15:19:47,172] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: T007G_S118_L001_R1_001_fastqc.html [2023-12-12 15:19:47,218] multiqc [DEBUG ] File ignored by nanostat because it exceeded search pattern filesize limit: T007G_S118_L001_R1_001_fastqc.html [2023-12-12 15:19:47,225] multiqc [DEBUG ] File ignored by ccs/v4 because it exceeded search pattern filesize limit: T005FX_S223_L001_R1_001_fastqc.html [2023-12-12 15:19:47,226] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: T005FX_S223_L001_R1_001_fastqc.html [2023-12-12 15:19:47,226] multiqc [DEBUG ] File ignored by lima/summary because it exceeded search pattern filesize limit: T005FX_S223_L001_R1_001_fastqc.html [2023-12-12 15:19:47,228] multiqc [DEBUG ] File ignored by vep/vep_txt because it exceeded search pattern filesize limit: T005FX_S223_L001_R1_001_fastqc.html [2023-12-12 15:19:47,228] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: T005FX_S223_L001_R1_001_fastqc.html [2023-12-12 15:19:47,228] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: T005FX_S223_L001_R1_001_fastqc.html [2023-12-12 15:19:47,228] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: T005FX_S223_L001_R1_001_fastqc.html [2023-12-12 15:19:47,228] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: T005FX_S223_L001_R1_001_fastqc.html [2023-12-12 15:19:47,228] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: T005FX_S223_L001_R1_001_fastqc.html [2023-12-12 15:19:47,228] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: T005FX_S223_L001_R1_001_fastqc.html [2023-12-12 15:19:47,276] multiqc [DEBUG ] File ignored by nanostat because it exceeded search pattern filesize limit: T005FX_S223_L001_R1_001_fastqc.html [2023-12-12 15:19:47,286] multiqc [DEBUG ] File ignored by ccs/v4 because it exceeded search pattern filesize limit: T001F_S100_L002_R1_001_fastqc.html [2023-12-12 15:19:47,287] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: T001F_S100_L002_R1_001_fastqc.html [2023-12-12 15:19:47,287] multiqc [DEBUG ] File ignored by lima/summary because it exceeded search pattern filesize limit: T001F_S100_L002_R1_001_fastqc.html [2023-12-12 15:19:47,289] multiqc [DEBUG ] File ignored by vep/vep_txt because it exceeded search pattern filesize limit: T001F_S100_L002_R1_001_fastqc.html [2023-12-12 15:19:47,289] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: T001F_S100_L002_R1_001_fastqc.html [2023-12-12 15:19:47,289] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: T001F_S100_L002_R1_001_fastqc.html [2023-12-12 15:19:47,289] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: T001F_S100_L002_R1_001_fastqc.html [2023-12-12 15:19:47,289] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: T001F_S100_L002_R1_001_fastqc.html [2023-12-12 15:19:47,289] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: T001F_S100_L002_R1_001_fastqc.html [2023-12-12 15:19:47,289] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: T001F_S100_L002_R1_001_fastqc.html [2023-12-12 15:19:47,337] multiqc [DEBUG ] File ignored by nanostat because it exceeded search pattern filesize limit: T001F_S100_L002_R1_001_fastqc.html [2023-12-12 15:19:48,627] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.4.3 [2023-12-12 15:19:48,634] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.4.3 [2023-12-12 15:20:00,916] multiqc.modules.fastqc.fastqc [INFO ] Found 145 reports [2023-12-12 15:20:16,227] multiqc [INFO ] Compressing plot data [2023-12-12 15:20:16,294] multiqc [INFO ] Report : multiqc_report.html [2023-12-12 15:20:16,294] multiqc [INFO ] Data : multiqc_data [2023-12-12 15:20:16,294] multiqc [DEBUG ] Moving data file from '/tmp/tmpjj5qb__w/multiqc_data' to '/home/shared/8TB_HDD_02/graceleuchtenberger/Github/byssus-exp-analysis/output/fastqc/untrimmed/multiqc_data' [2023-12-12 15:20:16,530] multiqc [INFO ] MultiQC complete [2023-12-12 15:20:16,530] multiqc [WARNING] 7 flat-image plots used in the report due to large sample numbers