[2020-11-10 11:25:12,241] multiqc [DEBUG ] No MultiQC config found: /gscratch/srlab/programs/anaconda3/lib/python3.7/site-packages/multiqc_config.yaml [2020-11-10 11:25:12,301] multiqc [DEBUG ] Loading config settings from: /usr/lusers/samwhite/.multiqc_config.yaml [2020-11-10 11:25:12,301] multiqc [DEBUG ] Added to filename patterns: {'fastp': {'fn': '*report.json'}} [2020-11-10 11:25:12,302] multiqc [DEBUG ] New config 'hisat2': {'contents': 'HISAT2 summary stats:', 'shared': True} [2020-11-10 11:25:12,302] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2020-11-10 11:25:12,302] multiqc [DEBUG ] Command used: /gscratch/srlab/programs/anaconda3/bin/multiqc . [2020-11-10 11:25:17,607] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2020-11-10 11:25:17,607] multiqc [INFO ] This is MultiQC v1.8 [2020-11-10 11:25:17,609] multiqc [DEBUG ] Command : /gscratch/srlab/programs/anaconda3/bin/multiqc . [2020-11-10 11:25:17,609] multiqc [DEBUG ] Working dir : /gscratch/scrubbed/samwhite/outputs/20201110_cgig_fastqc_ronit-ploidy-wgbs [2020-11-10 11:25:17,609] multiqc [INFO ] Template : default [2020-11-10 11:25:17,610] multiqc [DEBUG ] Running Python 3.7.3 (default, Mar 27 2019, 22:11:17) [GCC 7.3.0] [2020-11-10 11:25:17,610] multiqc [INFO ] Searching : /gscratch/scrubbed/samwhite/outputs/20201110_cgig_fastqc_ronit-ploidy-wgbs [2020-11-10 11:25:17,611] 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 [2020-11-10 11:25:17,611] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpeguriw4z [2020-11-10 11:25:18,341] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_2_R2_fastqc.html [2020-11-10 11:25:18,365] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 20201110_cgig_fastqc_ronit-ploidy-wgbs.sh [2020-11-10 11:25:18,376] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_8_R1_fastqc.html [2020-11-10 11:25:18,376] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_6_R1_fastqc.html [2020-11-10 11:25:18,376] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_1_R2_fastqc.html [2020-11-10 11:25:18,376] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_2_R1_fastqc.html [2020-11-10 11:25:18,376] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_3_R1_fastqc.html [2020-11-10 11:25:18,376] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_7_R1_fastqc.html [2020-11-10 11:25:18,377] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_8_R2_fastqc.html [2020-11-10 11:25:18,377] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_10_R1_fastqc.html [2020-11-10 11:25:18,377] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_10_R2_fastqc.html [2020-11-10 11:25:18,377] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_9_R2_fastqc.html [2020-11-10 11:25:18,378] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_5_R1_fastqc.html [2020-11-10 11:25:18,382] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: slurm-453885.out [2020-11-10 11:25:18,383] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: slurm-453885.out [2020-11-10 11:25:18,394] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_3_R2_fastqc.html [2020-11-10 11:25:18,394] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_5_R2_fastqc.html [2020-11-10 11:25:18,394] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_7_R2_fastqc.html [2020-11-10 11:25:18,394] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_6_R2_fastqc.html [2020-11-10 11:25:18,394] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_4_R1_fastqc.html [2020-11-10 11:25:18,394] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_4_R2_fastqc.html [2020-11-10 11:25:18,395] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: fastq_checksums.md5 [2020-11-10 11:25:18,395] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_1_R1_fastqc.html [2020-11-10 11:25:18,395] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_9_R1_fastqc.html [2020-11-10 11:25:24,262] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 2.2.4 [2020-11-10 11:25:24,278] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 2.2.4 [2020-11-10 11:25:24,312] multiqc [DEBUG ] No samples found: custom_content [2020-11-10 11:25:24,417] multiqc [DEBUG ] No samples found: conpair [2020-11-10 11:25:24,561] multiqc [DEBUG ] No samples found: peddy [2020-11-10 11:25:24,646] multiqc [DEBUG ] No samples found: methylQA [2020-11-10 11:25:24,687] multiqc [DEBUG ] No samples found: phantompeakqualtools [2020-11-10 11:25:24,808] multiqc [DEBUG ] No samples found: qualimap [2020-11-10 11:25:24,844] multiqc [DEBUG ] No samples found: preseq [2020-11-10 11:25:24,892] multiqc [DEBUG ] No samples found: quast [2020-11-10 11:25:24,915] multiqc [DEBUG ] No samples found: qorts [2020-11-10 11:25:24,996] multiqc [DEBUG ] No samples found: rna_seqc [2020-11-10 11:25:25,043] multiqc [DEBUG ] No samples found: rsem [2020-11-10 11:25:25,194] multiqc [DEBUG ] No samples found: rseqc [2020-11-10 11:25:25,239] multiqc [DEBUG ] No samples found: busco [2020-11-10 11:25:25,296] multiqc [DEBUG ] No samples found: goleft_indexcov [2020-11-10 11:25:25,310] multiqc [DEBUG ] No samples found: disambiguate [2020-11-10 11:25:25,348] multiqc [DEBUG ] No samples found: supernova [2020-11-10 11:25:25,494] multiqc [DEBUG ] No samples found: deeptools [2020-11-10 11:25:25,574] multiqc [DEBUG ] No samples found: sargasso [2020-11-10 11:25:25,616] multiqc [DEBUG ] No samples found: verifybamid [2020-11-10 11:25:25,638] multiqc [DEBUG ] No samples found: mirtrace [2020-11-10 11:25:25,661] multiqc [DEBUG ] No samples found: happy [2020-11-10 11:25:25,744] multiqc [DEBUG ] No samples found: homer [2020-11-10 11:25:25,771] multiqc [DEBUG ] No samples found: macs2 [2020-11-10 11:25:25,797] multiqc [DEBUG ] No samples found: theta2 [2020-11-10 11:25:25,827] multiqc [DEBUG ] No samples found: snpeff [2020-11-10 11:25:25,896] multiqc [DEBUG ] No samples found: gatk [2020-11-10 11:25:25,922] multiqc [DEBUG ] No samples found: htseq [2020-11-10 11:25:25,970] multiqc [DEBUG ] No samples found: bcftools [2020-11-10 11:25:25,983] multiqc [DEBUG ] No samples found: featureCounts [2020-11-10 11:25:25,993] multiqc [DEBUG ] No samples found: fgbio [2020-11-10 11:25:26,002] multiqc [DEBUG ] No samples found: dedup [2020-11-10 11:25:26,053] multiqc [DEBUG ] No samples found: damageprofiler [2020-11-10 11:25:26,324] multiqc [DEBUG ] No samples found: biobambam2 [2020-11-10 11:25:26,346] multiqc [DEBUG ] No samples found: mtnucratio [2020-11-10 11:25:26,353] multiqc [DEBUG ] No samples found: picard [2020-11-10 11:25:26,409] multiqc [DEBUG ] No samples found: prokka [2020-11-10 11:25:26,422] multiqc [DEBUG ] No samples found: samblaster [2020-11-10 11:25:26,503] multiqc [DEBUG ] No samples found: samtools [2020-11-10 11:25:26,547] multiqc [DEBUG ] No samples found: sexdeterrmine [2020-11-10 11:25:26,577] multiqc [DEBUG ] No samples found: bamtools [2020-11-10 11:25:26,590] multiqc [DEBUG ] No samples found: jellyfish [2020-11-10 11:25:26,621] multiqc [DEBUG ] No samples found: vcftools [2020-11-10 11:25:26,644] multiqc [DEBUG ] No samples found: longranger [2020-11-10 11:25:26,706] multiqc [DEBUG ] No samples found: stacks [2020-11-10 11:25:26,814] multiqc [DEBUG ] No samples found: bbmap [2020-11-10 11:25:26,862] multiqc [DEBUG ] No samples found: bismark [2020-11-10 11:25:26,896] multiqc [DEBUG ] No samples found: biscuit [2020-11-10 11:25:26,926] multiqc [DEBUG ] No samples found: hicexplorer [2020-11-10 11:25:27,011] multiqc [DEBUG ] No samples found: hicup [2020-11-10 11:25:27,086] multiqc [DEBUG ] No samples found: hicpro [2020-11-10 11:25:27,099] multiqc [DEBUG ] No samples found: salmon [2020-11-10 11:25:27,164] multiqc [DEBUG ] No samples found: kallisto [2020-11-10 11:25:27,186] multiqc [DEBUG ] No samples found: slamdunk [2020-11-10 11:25:27,213] multiqc [DEBUG ] No samples found: star [2020-11-10 11:25:27,231] multiqc [DEBUG ] No samples found: hisat2 [2020-11-10 11:25:27,288] multiqc [DEBUG ] No samples found: tophat [2020-11-10 11:25:27,313] multiqc [DEBUG ] No samples found: bowtie2 [2020-11-10 11:25:27,341] multiqc [DEBUG ] No samples found: bowtie1 [2020-11-10 11:25:27,354] multiqc [DEBUG ] No samples found: kat [2020-11-10 11:25:27,362] multiqc [DEBUG ] No samples found: leehom [2020-11-10 11:25:27,420] multiqc [DEBUG ] No samples found: adapterRemoval [2020-11-10 11:25:27,433] multiqc [DEBUG ] No samples found: clipandmerge [2020-11-10 11:25:27,465] multiqc [DEBUG ] No samples found: cutadapt [2020-11-10 11:25:27,479] multiqc [DEBUG ] No samples found: flexbar [2020-11-10 11:25:27,516] multiqc [DEBUG ] No samples found: trimmomatic [2020-11-10 11:25:27,548] multiqc [DEBUG ] No samples found: skewer [2020-11-10 11:25:27,561] multiqc [DEBUG ] No samples found: sortmerna [2020-11-10 11:25:27,585] multiqc [DEBUG ] No samples found: biobloomtools [2020-11-10 11:25:27,624] multiqc [DEBUG ] No samples found: fastq_screen [2020-11-10 11:25:27,662] multiqc [DEBUG ] No samples found: afterqc [2020-11-10 11:25:27,705] multiqc [DEBUG ] No samples found: fastp [2020-11-10 11:25:30,978] multiqc.modules.fastqc.fastqc [INFO ] Found 20 reports [2020-11-10 11:25:31,338] multiqc [DEBUG ] No samples found: minionqc [2020-11-10 11:25:31,388] multiqc [DEBUG ] No samples found: mosdepth [2020-11-10 11:25:31,421] multiqc [DEBUG ] No samples found: clusterflow [2020-11-10 11:25:31,466] multiqc [DEBUG ] No samples found: bcl2fastq [2020-11-10 11:25:31,497] multiqc [DEBUG ] No samples found: interop [2020-11-10 11:25:31,525] multiqc [DEBUG ] No samples found: flash [2020-11-10 11:25:31,551] multiqc [DEBUG ] No samples found: seqyclean [2020-11-10 11:25:31,582] multiqc [INFO ] Compressing plot data [2020-11-10 11:25:31,793] multiqc [INFO ] Report : multiqc_report.html [2020-11-10 11:25:31,795] multiqc [INFO ] Data : multiqc_data [2020-11-10 11:25:31,797] multiqc [DEBUG ] Moving data file from '/tmp/tmpeguriw4z/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/gscratch/scrubbed/samwhite/outputs/20201110_cgig_fastqc_ronit-ploidy-wgbs/multiqc_data' [2020-11-10 11:25:31,798] multiqc [DEBUG ] Moving data file from '/tmp/tmpeguriw4z/multiqc_data/multiqc_fastqc.txt' to '/gscratch/scrubbed/samwhite/outputs/20201110_cgig_fastqc_ronit-ploidy-wgbs/multiqc_data' [2020-11-10 11:25:31,799] multiqc [DEBUG ] Moving data file from '/tmp/tmpeguriw4z/multiqc_data/multiqc_general_stats.txt' to '/gscratch/scrubbed/samwhite/outputs/20201110_cgig_fastqc_ronit-ploidy-wgbs/multiqc_data' [2020-11-10 11:25:31,800] multiqc [DEBUG ] Moving data file from '/tmp/tmpeguriw4z/multiqc_data/multiqc_sources.txt' to '/gscratch/scrubbed/samwhite/outputs/20201110_cgig_fastqc_ronit-ploidy-wgbs/multiqc_data' [2020-11-10 11:25:31,800] multiqc [DEBUG ] Moving data file from '/tmp/tmpeguriw4z/multiqc_data/multiqc_data.json' to '/gscratch/scrubbed/samwhite/outputs/20201110_cgig_fastqc_ronit-ploidy-wgbs/multiqc_data' [2020-11-10 11:25:32,929] multiqc [INFO ] MultiQC complete