[2020-03-23 10:53:17,966] multiqc [DEBUG ] No MultiQC config found: /gscratch/srlab/programs/anaconda3/lib/python3.7/site-packages/multiqc_config.yaml [2020-03-23 10:53:17,967] multiqc [DEBUG ] No MultiQC config found: /usr/lusers/sr320/.multiqc_config.yaml [2020-03-23 10:53:17,967] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2020-03-23 10:53:17,967] multiqc [DEBUG ] Command used: /gscratch/srlab/programs/anaconda3/bin/multiqc -o Pact-multiqc /gscratch/scrubbed/sr320/031520-TG-100g/Pact_tg/ [2020-03-23 10:53:22,976] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2020-03-23 10:53:22,976] multiqc [INFO ] This is MultiQC v1.8 [2020-03-23 10:53:22,976] multiqc [DEBUG ] Command : /gscratch/srlab/programs/anaconda3/bin/multiqc -o Pact-multiqc /gscratch/scrubbed/sr320/031520-TG-100g/Pact_tg/ [2020-03-23 10:53:22,976] multiqc [DEBUG ] Working dir : /gscratch/scrubbed/sr320/032320-mqc [2020-03-23 10:53:22,976] multiqc [INFO ] Template : default [2020-03-23 10:53:22,977] multiqc [DEBUG ] Running Python 3.7.3 (default, Mar 27 2019, 22:11:17) [GCC 7.3.0] [2020-03-23 10:53:22,977] multiqc [INFO ] Searching : /gscratch/scrubbed/sr320/031520-TG-100g/Pact_tg [2020-03-23 10:53:22,978] 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 [2020-03-23 10:53:22,978] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpuz9niicp [2020-03-23 10:53:23,114] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth7_R1_001_val_1_bismark_bt2_pe.bam [2020-03-23 10:53:23,125] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth8_R1_001_val_1_bismark_bt2_pe.bam [2020-03-23 10:53:23,126] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth9_R1_001_val_1_bismark_bt2_pe.bam [2020-03-23 10:53:23,126] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth6_R1_001_val_1_bismark_bt2_pe.bam [2020-03-23 10:53:23,126] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth5_R1_001_val_1_bismark_bt2_pe.bam [2020-03-23 10:53:23,127] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth4_R1_001_val_1_bismark_bt2_pe.bam [2020-03-23 10:53:23,128] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth2_R1_001_val_1_bismark_bt2_pe.bam [2020-03-23 10:53:23,128] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth3_R1_001_val_1_bismark_bt2_pe.bam [2020-03-23 10:53:23,128] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth1_R1_001_val_1_bismark_bt2_pe.bam [2020-03-23 10:53:23,159] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth4_R1_001_val_1_bismark_bt2_pe.sorted.bam.bai [2020-03-23 10:53:23,159] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth6_R1_001_val_1_bismark_bt2_pe.sorted.bam [2020-03-23 10:53:23,159] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth5_R1_001_val_1_bismark_bt2_pe.sorted.bam.bai [2020-03-23 10:53:23,160] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth5_R1_001_val_1_bismark_bt2_pe.sorted.bam [2020-03-23 10:53:23,161] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth6_R1_001_val_1_bismark_bt2_pe.bam [2020-03-23 10:53:23,166] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth5_R1_001_val_1_bismark_bt2_pe.bam [2020-03-23 10:53:23,166] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth4_R1_001_val_1_bismark_bt2_pe.bam [2020-03-23 10:53:23,166] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth4_R1_001_val_1_bismark_bt2_pe.sorted.bam [2020-03-23 10:53:23,167] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth6_R1_001_val_1_bismark_bt2_pe.sorted.bam.bai [2020-03-23 10:53:23,171] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth2_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam.bai [2020-03-23 10:53:23,174] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth7_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam.bai [2020-03-23 10:53:23,176] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth2_R1_001_val_1_bismark_bt2_pe.deduplicated.bam [2020-03-23 10:53:23,178] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth9_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam [2020-03-23 10:53:23,180] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth7_R1_001_val_1_bismark_bt2_pe.bam [2020-03-23 10:53:23,183] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth3_R1_001_val_1_bismark_bt2_pe.deduplicated.bam [2020-03-23 10:53:23,184] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth8_R1_001_val_1_bismark_bt2_pe.bam [2020-03-23 10:53:23,185] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth9_R1_001_val_1_bismark_bt2_pe.bam [2020-03-23 10:53:23,186] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth1_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam.bai [2020-03-23 10:53:23,186] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth9_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam.bai [2020-03-23 10:53:23,189] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth1_R1_001_val_1_bismark_bt2_pe.deduplicated.bam [2020-03-23 10:53:23,192] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth8_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam [2020-03-23 10:53:23,193] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth7_R1_001_val_1_bismark_bt2_pe.deduplicated.bam [2020-03-23 10:53:23,195] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth8_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam.bai [2020-03-23 10:53:23,196] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth3_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam [2020-03-23 10:53:23,196] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth7_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam [2020-03-23 10:53:23,196] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth1_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam [2020-03-23 10:53:23,197] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth9_R1_001_val_1_bismark_bt2_pe.deduplicated.bam [2020-03-23 10:53:23,197] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth2_R1_001_val_1_bismark_bt2_pe.bam [2020-03-23 10:53:23,197] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth3_R1_001_val_1_bismark_bt2_pe.bam [2020-03-23 10:53:23,199] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth3_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam.bai [2020-03-23 10:53:23,200] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth1_R1_001_val_1_bismark_bt2_pe.bam [2020-03-23 10:53:23,201] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth8_R1_001_val_1_bismark_bt2_pe.deduplicated.bam [2020-03-23 10:53:23,201] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth2_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam [2020-03-23 10:53:23,444] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 2.2.4 [2020-03-23 10:53:23,445] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 2.2.4 [2020-03-23 10:53:23,446] multiqc [DEBUG ] No samples found: custom_content [2020-03-23 10:53:23,449] multiqc [DEBUG ] No samples found: conpair [2020-03-23 10:53:23,452] multiqc [DEBUG ] No samples found: peddy [2020-03-23 10:53:23,458] multiqc [DEBUG ] No samples found: methylQA [2020-03-23 10:53:23,463] multiqc [DEBUG ] No samples found: phantompeakqualtools [2020-03-23 10:53:23,470] multiqc [DEBUG ] No samples found: qualimap [2020-03-23 10:53:23,473] multiqc [DEBUG ] No samples found: preseq [2020-03-23 10:53:23,477] multiqc [DEBUG ] No samples found: quast [2020-03-23 10:53:23,480] multiqc [DEBUG ] No samples found: qorts [2020-03-23 10:53:23,483] multiqc [DEBUG ] No samples found: rna_seqc [2020-03-23 10:53:23,485] multiqc [DEBUG ] No samples found: rsem [2020-03-23 10:53:23,489] multiqc [DEBUG ] No samples found: rseqc [2020-03-23 10:53:23,494] multiqc [DEBUG ] No samples found: busco [2020-03-23 10:53:23,498] multiqc [DEBUG ] No samples found: goleft_indexcov [2020-03-23 10:53:23,502] multiqc [DEBUG ] No samples found: disambiguate [2020-03-23 10:53:23,504] multiqc [DEBUG ] No samples found: supernova [2020-03-23 10:53:23,508] multiqc [DEBUG ] No samples found: deeptools [2020-03-23 10:53:23,511] multiqc [DEBUG ] No samples found: sargasso [2020-03-23 10:53:23,514] multiqc [DEBUG ] No samples found: verifybamid [2020-03-23 10:53:23,517] multiqc [DEBUG ] No samples found: mirtrace [2020-03-23 10:53:23,521] multiqc [DEBUG ] No samples found: happy [2020-03-23 10:53:23,528] multiqc [DEBUG ] No samples found: homer [2020-03-23 10:53:23,530] multiqc [DEBUG ] No samples found: macs2 [2020-03-23 10:53:23,532] multiqc [DEBUG ] No samples found: theta2 [2020-03-23 10:53:23,536] multiqc [DEBUG ] No samples found: snpeff [2020-03-23 10:53:23,544] multiqc [DEBUG ] No samples found: gatk [2020-03-23 10:53:23,550] multiqc [DEBUG ] No samples found: htseq [2020-03-23 10:53:23,552] multiqc [DEBUG ] No samples found: bcftools [2020-03-23 10:53:23,555] multiqc [DEBUG ] No samples found: featureCounts [2020-03-23 10:53:23,557] multiqc [DEBUG ] No samples found: fgbio [2020-03-23 10:53:23,560] multiqc [DEBUG ] No samples found: dedup [2020-03-23 10:53:23,564] multiqc [DEBUG ] No samples found: damageprofiler [2020-03-23 10:53:23,570] multiqc [DEBUG ] No samples found: biobambam2 [2020-03-23 10:53:23,574] multiqc [DEBUG ] No samples found: mtnucratio [2020-03-23 10:53:23,576] multiqc [DEBUG ] No samples found: picard [2020-03-23 10:53:23,578] multiqc [DEBUG ] No samples found: prokka [2020-03-23 10:53:23,580] multiqc [DEBUG ] No samples found: samblaster [2020-03-23 10:53:23,582] multiqc [DEBUG ] No samples found: samtools [2020-03-23 10:53:23,584] multiqc [DEBUG ] No samples found: sexdeterrmine [2020-03-23 10:53:23,588] multiqc [DEBUG ] No samples found: bamtools [2020-03-23 10:53:23,591] multiqc [DEBUG ] No samples found: jellyfish [2020-03-23 10:53:23,597] multiqc [DEBUG ] No samples found: vcftools [2020-03-23 10:53:23,600] multiqc [DEBUG ] No samples found: longranger [2020-03-23 10:53:23,603] multiqc [DEBUG ] No samples found: stacks [2020-03-23 10:53:23,607] multiqc [DEBUG ] No samples found: bbmap [2020-03-23 10:53:23,881] multiqc.modules.bismark.bismark [INFO ] Found 9 bismark alignment reports [2020-03-23 10:53:23,889] multiqc.modules.bismark.bismark [INFO ] Found 6 bismark dedup reports [2020-03-23 10:53:23,890] multiqc.modules.bismark.bismark [INFO ] Found 9 bismark methextract reports [2020-03-23 10:53:23,911] multiqc [DEBUG ] No samples found: biscuit [2020-03-23 10:53:23,919] multiqc [DEBUG ] No samples found: hicexplorer [2020-03-23 10:53:23,924] multiqc [DEBUG ] No samples found: hicup [2020-03-23 10:53:23,927] multiqc [DEBUG ] No samples found: hicpro [2020-03-23 10:53:23,930] multiqc [DEBUG ] No samples found: salmon [2020-03-23 10:53:23,934] multiqc [DEBUG ] No samples found: kallisto [2020-03-23 10:53:23,936] multiqc [DEBUG ] No samples found: slamdunk [2020-03-23 10:53:23,940] multiqc [DEBUG ] No samples found: star [2020-03-23 10:53:23,942] multiqc [DEBUG ] No samples found: hisat2 [2020-03-23 10:53:23,945] multiqc [DEBUG ] No samples found: tophat [2020-03-23 10:53:23,947] multiqc [DEBUG ] No samples found: bowtie2 [2020-03-23 10:53:23,952] multiqc [DEBUG ] No samples found: bowtie1 [2020-03-23 10:53:23,956] multiqc [DEBUG ] No samples found: kat [2020-03-23 10:53:23,959] multiqc [DEBUG ] No samples found: leehom [2020-03-23 10:53:23,961] multiqc [DEBUG ] No samples found: adapterRemoval [2020-03-23 10:53:23,963] multiqc [DEBUG ] No samples found: clipandmerge [2020-03-23 10:53:23,966] multiqc [DEBUG ] No samples found: cutadapt [2020-03-23 10:53:23,969] multiqc [DEBUG ] No samples found: flexbar [2020-03-23 10:53:23,973] multiqc [DEBUG ] No samples found: trimmomatic [2020-03-23 10:53:23,975] multiqc [DEBUG ] No samples found: skewer [2020-03-23 10:53:23,978] multiqc [DEBUG ] No samples found: sortmerna [2020-03-23 10:53:23,983] multiqc [DEBUG ] No samples found: biobloomtools [2020-03-23 10:53:23,985] multiqc [DEBUG ] No samples found: fastq_screen [2020-03-23 10:53:23,987] multiqc [DEBUG ] No samples found: afterqc [2020-03-23 10:53:23,990] multiqc [DEBUG ] No samples found: fastp [2020-03-23 10:53:23,993] multiqc [DEBUG ] No samples found: fastqc [2020-03-23 10:53:23,996] multiqc [DEBUG ] No samples found: minionqc [2020-03-23 10:53:23,998] multiqc [DEBUG ] No samples found: mosdepth [2020-03-23 10:53:24,003] multiqc [DEBUG ] No samples found: clusterflow [2020-03-23 10:53:24,007] multiqc [DEBUG ] No samples found: bcl2fastq [2020-03-23 10:53:24,013] multiqc [DEBUG ] No samples found: interop [2020-03-23 10:53:24,016] multiqc [DEBUG ] No samples found: flash [2020-03-23 10:53:24,018] multiqc [DEBUG ] No samples found: seqyclean [2020-03-23 10:53:24,029] multiqc [INFO ] Compressing plot data [2020-03-23 10:53:24,127] multiqc [INFO ] Report : Pact-multiqc/multiqc_report.html [2020-03-23 10:53:24,127] multiqc [INFO ] Data : Pact-multiqc/multiqc_data [2020-03-23 10:53:24,127] multiqc [DEBUG ] Moving data file from '/tmp/tmpuz9niicp/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to 'Pact-multiqc/multiqc_data' [2020-03-23 10:53:24,128] multiqc [DEBUG ] Moving data file from '/tmp/tmpuz9niicp/multiqc_data/multiqc_bismark_alignment.txt' to 'Pact-multiqc/multiqc_data' [2020-03-23 10:53:24,129] multiqc [DEBUG ] Moving data file from '/tmp/tmpuz9niicp/multiqc_data/multiqc_bismark_dedup.txt' to 'Pact-multiqc/multiqc_data' [2020-03-23 10:53:24,130] multiqc [DEBUG ] Moving data file from '/tmp/tmpuz9niicp/multiqc_data/multiqc_bismark_methextract.txt' to 'Pact-multiqc/multiqc_data' [2020-03-23 10:53:24,131] multiqc [DEBUG ] Moving data file from '/tmp/tmpuz9niicp/multiqc_data/multiqc_general_stats.txt' to 'Pact-multiqc/multiqc_data' [2020-03-23 10:53:24,132] multiqc [DEBUG ] Moving data file from '/tmp/tmpuz9niicp/multiqc_data/multiqc_sources.txt' to 'Pact-multiqc/multiqc_data' [2020-03-23 10:53:24,133] multiqc [DEBUG ] Moving data file from '/tmp/tmpuz9niicp/multiqc_data/multiqc_data.json' to 'Pact-multiqc/multiqc_data' [2020-03-23 10:53:24,203] multiqc [INFO ] MultiQC complete