[2020-12-06 21:14:09,849] multiqc [DEBUG ] No MultiQC config found: /gscratch/srlab/programs/anaconda3/lib/python3.7/site-packages/multiqc_config.yaml [2020-12-06 21:14:09,866] multiqc [DEBUG ] Loading config settings from: /usr/lusers/samwhite/.multiqc_config.yaml [2020-12-06 21:14:09,866] multiqc [DEBUG ] Added to filename patterns: {'fastp': {'fn': '*report.json'}} [2020-12-06 21:14:09,866] multiqc [DEBUG ] New config 'hisat2': {'contents': 'HISAT2 summary stats:', 'shared': True} [2020-12-06 21:14:09,867] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2020-12-06 21:14:09,867] multiqc [DEBUG ] Command used: /gscratch/srlab/programs/anaconda3/bin/multiqc . [2020-12-06 21:14:15,165] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2020-12-06 21:14:15,165] multiqc [INFO ] This is MultiQC v1.8 [2020-12-06 21:14:15,169] multiqc [DEBUG ] Command : /gscratch/srlab/programs/anaconda3/bin/multiqc . [2020-12-06 21:14:15,169] multiqc [DEBUG ] Working dir : /gscratch/scrubbed/samwhite/outputs/20201206_cgig_fastqc_multiqc_ploidy-pH-wgbs [2020-12-06 21:14:15,169] multiqc [INFO ] Template : default [2020-12-06 21:14:15,169] multiqc [DEBUG ] Running Python 3.7.3 (default, Mar 27 2019, 22:11:17) [GCC 7.3.0] [2020-12-06 21:14:15,169] multiqc [INFO ] Searching : /gscratch/scrubbed/samwhite/outputs/20201206_cgig_fastqc_multiqc_ploidy-pH-wgbs [2020-12-06 21:14:15,170] multiqc [DEBUG ] Analysing modules: custom_content, conpair, peddy, methylQA, phantompeakqualtools, qualimap, preseq, quast, qorts, rna_seqc, rsem, rseqc, busco, goleft_indexcov, disambiguate, supernova, deeptools, sargasso, verifybamid, mirtrace, happy, homer, macs2, theta2, snpeff, gatk, htseq, bcftools, featureCounts, fgbio, dedup, damageprofiler, biobambam2, mtnucratio, picard, prokka, samblaster, samtools, sexdeterrmine, bamtools, jellyfish, vcftools, longranger, stacks, bbmap, bismark, biscuit, hicexplorer, hicup, hicpro, salmon, kallisto, slamdunk, star, hisat2, tophat, bowtie2, bowtie1, kat, leehom, adapterRemoval, clipandmerge, cutadapt, flexbar, trimmomatic, skewer, sortmerna, biobloomtools, fastq_screen, afterqc, fastp, fastqc, minionqc, mosdepth, clusterflow, bcl2fastq, interop, flash, seqyclean [2020-12-06 21:14:15,171] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmphi2c4lr9 [2020-12-06 21:14:15,846] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_18_R1_fastqc.html [2020-12-06 21:14:15,847] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_3_R2_fastqc.html [2020-12-06 21:14:15,847] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_3_R1_fastqc.html [2020-12-06 21:14:15,847] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_17_R2_fastqc.html [2020-12-06 21:14:15,847] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_1_R1_fastqc.html [2020-12-06 21:14:15,858] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_19_R2_fastqc.html [2020-12-06 21:14:15,858] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_8_R1_fastqc.html [2020-12-06 21:14:15,859] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_19_R1_fastqc.html [2020-12-06 21:14:15,859] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_14_R2_fastqc.html [2020-12-06 21:14:15,859] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_2_R1_fastqc.html [2020-12-06 21:14:15,860] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_9_R1_fastqc.html [2020-12-06 21:14:15,860] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_4_R2_fastqc.html [2020-12-06 21:14:15,871] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: slurm-539853.out [2020-12-06 21:14:15,872] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: slurm-539853.out [2020-12-06 21:14:15,899] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_24_R1_fastqc.html [2020-12-06 21:14:15,899] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_24_R2_fastqc.html [2020-12-06 21:14:15,900] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_21_R1_fastqc.html [2020-12-06 21:14:15,900] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_20_R1_fastqc.html [2020-12-06 21:14:15,900] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_16_R2_fastqc.html [2020-12-06 21:14:15,900] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_20_R2_fastqc.html [2020-12-06 21:14:15,900] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_18_R2_fastqc.html [2020-12-06 21:14:15,900] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_10_R2_fastqc.html [2020-12-06 21:14:15,905] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_13_R1_fastqc.html [2020-12-06 21:14:15,905] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_11_R2_fastqc.html [2020-12-06 21:14:15,905] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_5_R1_fastqc.html [2020-12-06 21:14:15,905] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_23_R2_fastqc.html [2020-12-06 21:14:15,905] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_13_R2_fastqc.html [2020-12-06 21:14:15,905] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_6_R2_fastqc.html [2020-12-06 21:14:15,905] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_8_R2_fastqc.html [2020-12-06 21:14:15,905] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_12_R1_fastqc.html [2020-12-06 21:14:15,905] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_10_R1_fastqc.html [2020-12-06 21:14:15,906] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_5_R2_fastqc.html [2020-12-06 21:14:15,906] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_23_R1_fastqc.html [2020-12-06 21:14:15,906] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_16_R1_fastqc.html [2020-12-06 21:14:15,906] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_1_R2_fastqc.html [2020-12-06 21:14:15,907] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_22_R1_fastqc.html [2020-12-06 21:14:15,907] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_12_R2_fastqc.html [2020-12-06 21:14:15,907] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_15_R1_fastqc.html [2020-12-06 21:14:15,907] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_21_R2_fastqc.html [2020-12-06 21:14:15,911] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 20201206_cgig_fastqc_multiqc_ploidy-pH-wgbs.sh [2020-12-06 21:14:15,915] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_17_R1_fastqc.html [2020-12-06 21:14:15,915] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_9_R2_fastqc.html [2020-12-06 21:14:15,915] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_2_R2_fastqc.html [2020-12-06 21:14:15,915] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_7_R2_fastqc.html [2020-12-06 21:14:15,915] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_7_R1_fastqc.html [2020-12-06 21:14:15,916] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: fastq_checksums.md5 [2020-12-06 21:14:15,916] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_15_R2_fastqc.html [2020-12-06 21:14:15,916] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_22_R2_fastqc.html [2020-12-06 21:14:15,917] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_4_R1_fastqc.html [2020-12-06 21:14:15,917] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_14_R1_fastqc.html [2020-12-06 21:14:15,917] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_6_R1_fastqc.html [2020-12-06 21:14:15,917] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_11_R1_fastqc.html [2020-12-06 21:14:20,567] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 2.2.4 [2020-12-06 21:14:20,582] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 2.2.4 [2020-12-06 21:14:20,674] multiqc [DEBUG ] No samples found: custom_content [2020-12-06 21:14:20,924] multiqc [DEBUG ] No samples found: conpair [2020-12-06 21:14:21,074] multiqc [DEBUG ] No samples found: peddy [2020-12-06 21:14:21,202] multiqc [DEBUG ] No samples found: methylQA [2020-12-06 21:14:21,235] multiqc [DEBUG ] No samples found: phantompeakqualtools [2020-12-06 21:14:21,377] multiqc [DEBUG ] No samples found: qualimap [2020-12-06 21:14:21,434] multiqc [DEBUG ] No samples found: preseq [2020-12-06 21:14:21,460] multiqc [DEBUG ] No samples found: quast [2020-12-06 21:14:21,490] multiqc [DEBUG ] No samples found: qorts [2020-12-06 21:14:21,541] multiqc [DEBUG ] No samples found: rna_seqc [2020-12-06 21:14:21,639] multiqc [DEBUG ] No samples found: rsem [2020-12-06 21:14:21,754] multiqc [DEBUG ] No samples found: rseqc [2020-12-06 21:14:21,781] multiqc [DEBUG ] No samples found: busco [2020-12-06 21:14:21,839] multiqc [DEBUG ] No samples found: goleft_indexcov [2020-12-06 21:14:21,895] multiqc [DEBUG ] No samples found: disambiguate [2020-12-06 21:14:21,943] multiqc [DEBUG ] No samples found: supernova [2020-12-06 21:14:22,143] multiqc [DEBUG ] No samples found: deeptools [2020-12-06 21:14:22,212] multiqc [DEBUG ] No samples found: sargasso [2020-12-06 21:14:22,248] multiqc [DEBUG ] No samples found: verifybamid [2020-12-06 21:14:22,280] multiqc [DEBUG ] No samples found: mirtrace [2020-12-06 21:14:22,357] multiqc [DEBUG ] No samples found: happy [2020-12-06 21:14:22,405] multiqc [DEBUG ] No samples found: homer [2020-12-06 21:14:22,467] multiqc [DEBUG ] No samples found: macs2 [2020-12-06 21:14:22,480] multiqc [DEBUG ] No samples found: theta2 [2020-12-06 21:14:22,505] multiqc [DEBUG ] No samples found: snpeff [2020-12-06 21:14:22,555] multiqc [DEBUG ] No samples found: gatk [2020-12-06 21:14:22,593] multiqc [DEBUG ] No samples found: htseq [2020-12-06 21:14:22,650] multiqc [DEBUG ] No samples found: bcftools [2020-12-06 21:14:22,663] multiqc [DEBUG ] No samples found: featureCounts [2020-12-06 21:14:22,674] multiqc [DEBUG ] No samples found: fgbio [2020-12-06 21:14:22,685] multiqc [DEBUG ] No samples found: dedup [2020-12-06 21:14:22,704] multiqc [DEBUG ] No samples found: damageprofiler [2020-12-06 21:14:22,971] multiqc [DEBUG ] No samples found: biobambam2 [2020-12-06 21:14:23,011] multiqc [DEBUG ] No samples found: mtnucratio [2020-12-06 21:14:23,018] multiqc [DEBUG ] No samples found: picard [2020-12-06 21:14:23,114] multiqc [DEBUG ] No samples found: prokka [2020-12-06 21:14:23,123] multiqc [DEBUG ] No samples found: samblaster [2020-12-06 21:14:23,217] multiqc [DEBUG ] No samples found: samtools [2020-12-06 21:14:23,262] multiqc [DEBUG ] No samples found: sexdeterrmine [2020-12-06 21:14:23,336] multiqc [DEBUG ] No samples found: bamtools [2020-12-06 21:14:23,347] multiqc [DEBUG ] No samples found: jellyfish [2020-12-06 21:14:23,362] multiqc [DEBUG ] No samples found: vcftools [2020-12-06 21:14:23,418] multiqc [DEBUG ] No samples found: longranger [2020-12-06 21:14:23,443] multiqc [DEBUG ] No samples found: stacks [2020-12-06 21:14:23,545] multiqc [DEBUG ] No samples found: bbmap [2020-12-06 21:14:23,574] multiqc [DEBUG ] No samples found: bismark [2020-12-06 21:14:23,600] multiqc [DEBUG ] No samples found: biscuit [2020-12-06 21:14:23,631] multiqc [DEBUG ] No samples found: hicexplorer [2020-12-06 21:14:23,666] multiqc [DEBUG ] No samples found: hicup [2020-12-06 21:14:23,698] multiqc [DEBUG ] No samples found: hicpro [2020-12-06 21:14:23,710] multiqc [DEBUG ] No samples found: salmon [2020-12-06 21:14:23,741] multiqc [DEBUG ] No samples found: kallisto [2020-12-06 21:14:23,766] multiqc [DEBUG ] No samples found: slamdunk [2020-12-06 21:14:23,818] multiqc [DEBUG ] No samples found: star [2020-12-06 21:14:23,866] multiqc [DEBUG ] No samples found: hisat2 [2020-12-06 21:14:23,924] multiqc [DEBUG ] No samples found: tophat [2020-12-06 21:14:23,943] multiqc [DEBUG ] No samples found: bowtie2 [2020-12-06 21:14:23,966] multiqc [DEBUG ] No samples found: bowtie1 [2020-12-06 21:14:23,979] multiqc [DEBUG ] No samples found: kat [2020-12-06 21:14:23,988] multiqc [DEBUG ] No samples found: leehom [2020-12-06 21:14:24,038] multiqc [DEBUG ] No samples found: adapterRemoval [2020-12-06 21:14:24,050] multiqc [DEBUG ] No samples found: clipandmerge [2020-12-06 21:14:24,156] multiqc [DEBUG ] No samples found: cutadapt [2020-12-06 21:14:24,170] multiqc [DEBUG ] No samples found: flexbar [2020-12-06 21:14:24,191] multiqc [DEBUG ] No samples found: trimmomatic [2020-12-06 21:14:24,231] multiqc [DEBUG ] No samples found: skewer [2020-12-06 21:14:24,244] multiqc [DEBUG ] No samples found: sortmerna [2020-12-06 21:14:24,275] multiqc [DEBUG ] No samples found: biobloomtools [2020-12-06 21:14:24,324] multiqc [DEBUG ] No samples found: fastq_screen [2020-12-06 21:14:24,420] multiqc [DEBUG ] No samples found: afterqc [2020-12-06 21:14:24,445] multiqc [DEBUG ] No samples found: fastp [2020-12-06 21:14:34,077] multiqc.modules.fastqc.fastqc [INFO ] Found 48 reports [2020-12-06 21:14:34,852] multiqc [DEBUG ] No samples found: minionqc [2020-12-06 21:14:34,880] multiqc [DEBUG ] No samples found: mosdepth [2020-12-06 21:14:34,902] multiqc [DEBUG ] No samples found: clusterflow [2020-12-06 21:14:34,949] multiqc [DEBUG ] No samples found: bcl2fastq [2020-12-06 21:14:34,977] multiqc [DEBUG ] No samples found: interop [2020-12-06 21:14:35,017] multiqc [DEBUG ] No samples found: flash [2020-12-06 21:14:35,045] multiqc [DEBUG ] No samples found: seqyclean [2020-12-06 21:14:35,099] multiqc [INFO ] Compressing plot data [2020-12-06 21:14:35,581] multiqc [INFO ] Report : multiqc_report.html [2020-12-06 21:14:35,583] multiqc [INFO ] Data : multiqc_data [2020-12-06 21:14:35,585] multiqc [DEBUG ] Moving data file from '/tmp/tmphi2c4lr9/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/gscratch/scrubbed/samwhite/outputs/20201206_cgig_fastqc_multiqc_ploidy-pH-wgbs/multiqc_data' [2020-12-06 21:14:35,586] multiqc [DEBUG ] Moving data file from '/tmp/tmphi2c4lr9/multiqc_data/multiqc_fastqc.txt' to '/gscratch/scrubbed/samwhite/outputs/20201206_cgig_fastqc_multiqc_ploidy-pH-wgbs/multiqc_data' [2020-12-06 21:14:35,587] multiqc [DEBUG ] Moving data file from '/tmp/tmphi2c4lr9/multiqc_data/multiqc_general_stats.txt' to '/gscratch/scrubbed/samwhite/outputs/20201206_cgig_fastqc_multiqc_ploidy-pH-wgbs/multiqc_data' [2020-12-06 21:14:35,588] multiqc [DEBUG ] Moving data file from '/tmp/tmphi2c4lr9/multiqc_data/multiqc_sources.txt' to '/gscratch/scrubbed/samwhite/outputs/20201206_cgig_fastqc_multiqc_ploidy-pH-wgbs/multiqc_data' [2020-12-06 21:14:35,589] multiqc [DEBUG ] Moving data file from '/tmp/tmphi2c4lr9/multiqc_data/multiqc_data.json' to '/gscratch/scrubbed/samwhite/outputs/20201206_cgig_fastqc_multiqc_ploidy-pH-wgbs/multiqc_data' [2020-12-06 21:14:36,599] multiqc [INFO ] MultiQC complete