[2020-04-26 14:32:57,280] multiqc [DEBUG ] No MultiQC config found: /home/sam/.local/lib/python3.5/site-packages/multiqc-1.8-py3.5.egg/multiqc_config.yaml [2020-04-26 14:32:57,280] multiqc [DEBUG ] No MultiQC config found: /home/sam/.multiqc_config.yaml [2020-04-26 14:32:57,280] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2020-04-26 14:32:57,280] multiqc [DEBUG ] Command used: /usr/local/bin/multiqc . [2020-04-26 14:32:58,500] multiqc [DEBUG ] Latest MultiQC version is v1.8 [2020-04-26 14:32:58,500] multiqc [INFO ] This is MultiQC v1.8 [2020-04-26 14:32:58,501] multiqc [DEBUG ] Command : /usr/local/bin/multiqc . [2020-04-26 14:32:58,501] multiqc [DEBUG ] Working dir : /home/sam/analyses/20200426_olur_fastqc_quantseq [2020-04-26 14:32:58,501] multiqc [INFO ] Template : default [2020-04-26 14:32:58,501] multiqc [DEBUG ] Running Python 3.5.2 (default, Oct 8 2019, 13:06:37) [GCC 5.4.0 20160609] [2020-04-26 14:32:58,501] multiqc [INFO ] Searching : /home/sam/analyses/20200426_olur_fastqc_quantseq [2020-04-26 14:32:58,501] 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 [2020-04-26 14:32:58,502] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpm3qcxaok [2020-04-26 14:32:58,614] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 529_S53_L002_R1_001_fastqc.html [2020-04-26 14:32:58,615] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 431b_S8_L002_R1_001_fastqc.html [2020-04-26 14:32:58,618] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 292_S32_L001_R1_001_fastqc.html [2020-04-26 14:32:58,618] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 562_S77_L002_R1_001_fastqc.html [2020-04-26 14:32:58,621] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 168_S67_L001_R1_001_fastqc.html [2020-04-26 14:32:58,621] multiqc [DEBUG ] Ignoring file as 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525_S18_L002_R1_001_fastqc.html [2020-04-26 14:32:58,627] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 492_S40_L002_R1_001_fastqc.html [2020-04-26 14:32:58,630] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 411_S9_L002_R1_001_fastqc.html [2020-04-26 14:32:58,631] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 413_S38_L002_R1_001_fastqc.html [2020-04-26 14:32:58,631] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 315_S26_L001_R1_001_fastqc.html [2020-04-26 14:32:58,632] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 471b_S51_L002_R1_001_fastqc.html [2020-04-26 14:32:58,632] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 295_S41_L001_R1_001_fastqc.html [2020-04-26 14:32:58,633] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 553_S23_L002_R1_001_fastqc.html [2020-04-26 14:32:58,634] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 461b_S31_L002_R1_001_fastqc.html [2020-04-26 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14:32:58,646] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 46_S66_L002_R1_001_fastqc.html [2020-04-26 14:32:58,646] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 441_S73_L002_R1_001_fastqc.html [2020-04-26 14:32:58,647] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 328_S12_L001_R1_001_fastqc.html [2020-04-26 14:32:58,649] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 331_S53_L001_R1_001_fastqc.html [2020-04-26 14:32:58,649] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 171_S58_L001_R1_001_fastqc.html [2020-04-26 14:32:58,650] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 462b_S64_L002_R1_001_fastqc.html [2020-04-26 14:32:58,651] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 341_S19_L001_R1_001_fastqc.html [2020-04-26 14:32:58,651] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 309_S20_L001_R1_001_fastqc.html [2020-04-26 14:32:58,652] multiqc [DEBUG ] Ignoring file as 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matched an ignore pattern: 311_S2_L001_R1_001_fastqc.html [2020-04-26 14:32:58,681] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 45_S63_L002_R1_001_fastqc.html [2020-04-26 14:32:58,685] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 156_S66_L001_R1_001_fastqc.html [2020-04-26 14:32:58,685] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 339_S10_L001_R1_001_fastqc.html [2020-04-26 14:32:58,686] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 307_S45_L001_R1_001_fastqc.html [2020-04-26 14:32:58,686] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 326_S38_L001_R1_001_fastqc.html [2020-04-26 14:32:58,686] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 344_S27_L001_R1_001_fastqc.html [2020-04-26 14:32:58,686] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 526_S15_L002_R1_001_fastqc.html [2020-04-26 14:32:58,686] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 452b_S2_L002_R1_001_fastqc.html [2020-04-26 14:32:58,686] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 347_S43_L001_R1_001_fastqc.html [2020-04-26 14:32:58,690] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 476_S17_L002_R1_001_fastqc.html [2020-04-26 14:32:58,690] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 338_S4_L001_R1_001_fastqc.html [2020-04-26 14:32:58,690] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 561_S69_L002_R1_001_fastqc.html [2020-04-26 14:32:58,690] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 162_S62_L001_R1_001_fastqc.html [2020-04-26 14:32:58,690] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 169_S65_L001_R1_001_fastqc.html [2020-04-26 14:32:58,691] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 490_S19_L002_R1_001_fastqc.html [2020-04-26 14:32:59,707] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 2.2.5 [2020-04-26 14:32:59,708] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 2.2.5 [2020-04-26 14:32:59,710] multiqc [DEBUG ] No samples found: custom_content [2020-04-26 14:32:59,732] multiqc [DEBUG ] No samples found: conpair [2020-04-26 14:32:59,752] multiqc [DEBUG ] No samples found: peddy [2020-04-26 14:32:59,765] multiqc [DEBUG ] No samples found: methylQA [2020-04-26 14:32:59,770] multiqc [DEBUG ] No samples found: phantompeakqualtools [2020-04-26 14:32:59,775] multiqc [DEBUG ] No samples found: qualimap [2020-04-26 14:32:59,780] multiqc [DEBUG ] No samples found: preseq [2020-04-26 14:32:59,785] multiqc [DEBUG ] No samples found: quast [2020-04-26 14:32:59,790] multiqc [DEBUG ] No samples found: qorts [2020-04-26 14:32:59,795] multiqc [DEBUG ] No samples found: rna_seqc [2020-04-26 14:32:59,808] multiqc [DEBUG ] No samples found: rsem [2020-04-26 14:32:59,824] multiqc [DEBUG ] No samples found: rseqc [2020-04-26 14:32:59,829] multiqc [DEBUG ] No samples found: busco [2020-04-26 14:32:59,834] multiqc [DEBUG ] No samples found: goleft_indexcov [2020-04-26 14:32:59,839] multiqc [DEBUG ] No samples found: disambiguate [2020-04-26 14:32:59,844] multiqc [DEBUG ] No samples found: supernova [2020-04-26 14:32:59,853] multiqc [DEBUG ] No samples found: deeptools [2020-04-26 14:32:59,858] multiqc [DEBUG ] No samples found: sargasso [2020-04-26 14:32:59,863] multiqc [DEBUG ] No samples found: verifybamid [2020-04-26 14:32:59,868] multiqc [DEBUG ] No samples found: mirtrace [2020-04-26 14:32:59,872] multiqc [DEBUG ] No samples found: happy [2020-04-26 14:32:59,878] multiqc [DEBUG ] No samples found: homer [2020-04-26 14:32:59,883] multiqc [DEBUG ] No samples found: macs2 [2020-04-26 14:32:59,887] multiqc [DEBUG ] No samples found: theta2 [2020-04-26 14:32:59,892] multiqc [DEBUG ] No samples found: snpeff [2020-04-26 14:32:59,898] multiqc [DEBUG ] No samples found: gatk [2020-04-26 14:32:59,910] multiqc [DEBUG ] No samples found: htseq [2020-04-26 14:32:59,915] multiqc [DEBUG ] No samples found: bcftools [2020-04-26 14:32:59,920] multiqc [DEBUG ] No samples found: featureCounts [2020-04-26 14:32:59,925] multiqc [DEBUG ] No samples found: fgbio [2020-04-26 14:32:59,930] multiqc [DEBUG ] No samples found: dedup [2020-04-26 14:32:59,935] multiqc [DEBUG ] No samples found: damageprofiler [2020-04-26 14:32:59,954] multiqc [DEBUG ] No samples found: biobambam2 [2020-04-26 14:32:59,958] multiqc [DEBUG ] No samples found: mtnucratio [2020-04-26 14:32:59,962] multiqc [DEBUG ] No samples found: picard [2020-04-26 14:32:59,967] multiqc [DEBUG ] No samples found: prokka [2020-04-26 14:32:59,972] multiqc [DEBUG ] No samples found: samblaster [2020-04-26 14:32:59,979] multiqc [DEBUG ] No samples found: samtools [2020-04-26 14:32:59,984] multiqc [DEBUG ] No samples found: sexdeterrmine [2020-04-26 14:32:59,989] multiqc [DEBUG ] No samples found: bamtools [2020-04-26 14:32:59,994] multiqc [DEBUG ] No samples found: jellyfish [2020-04-26 14:33:00,000] multiqc [DEBUG ] No samples found: vcftools [2020-04-26 14:33:00,014] multiqc [DEBUG ] No samples found: longranger [2020-04-26 14:33:00,019] multiqc [DEBUG ] No samples found: stacks [2020-04-26 14:33:00,029] multiqc [DEBUG ] No samples found: bbmap [2020-04-26 14:33:00,034] multiqc [DEBUG ] No samples found: bismark [2020-04-26 14:33:00,040] multiqc [DEBUG ] No samples found: biscuit [2020-04-26 14:33:00,045] multiqc [DEBUG ] No samples found: hicexplorer [2020-04-26 14:33:00,050] multiqc [DEBUG ] No samples found: hicup [2020-04-26 14:33:00,055] multiqc [DEBUG ] No samples found: hicpro [2020-04-26 14:33:00,060] multiqc [DEBUG ] No samples found: salmon [2020-04-26 14:33:00,065] multiqc [DEBUG ] No samples found: kallisto [2020-04-26 14:33:00,082] multiqc [DEBUG ] No samples found: slamdunk [2020-04-26 14:33:00,087] multiqc [DEBUG ] No samples found: star [2020-04-26 14:33:00,092] multiqc [DEBUG ] No samples found: hisat2 [2020-04-26 14:33:00,097] multiqc [DEBUG ] No samples found: tophat [2020-04-26 14:33:00,102] multiqc [DEBUG ] No samples found: bowtie2 [2020-04-26 14:33:00,107] multiqc [DEBUG ] No samples found: bowtie1 [2020-04-26 14:33:00,112] multiqc [DEBUG ] No samples found: kat [2020-04-26 14:33:00,117] multiqc [DEBUG ] No samples found: leehom [2020-04-26 14:33:00,122] multiqc [DEBUG ] No samples found: adapterRemoval [2020-04-26 14:33:00,127] multiqc [DEBUG ] No samples found: clipandmerge [2020-04-26 14:33:00,133] multiqc [DEBUG ] No samples found: cutadapt [2020-04-26 14:33:00,138] multiqc [DEBUG ] No samples found: flexbar [2020-04-26 14:33:00,143] multiqc [DEBUG ] No samples found: trimmomatic [2020-04-26 14:33:00,148] multiqc [DEBUG ] No samples found: skewer [2020-04-26 14:33:00,154] multiqc [DEBUG ] No samples found: sortmerna [2020-04-26 14:33:00,159] multiqc [DEBUG ] No samples found: biobloomtools [2020-04-26 14:33:00,164] multiqc [DEBUG ] No samples found: fastq_screen [2020-04-26 14:33:00,169] multiqc [DEBUG ] No samples found: afterqc [2020-04-26 14:33:00,174] multiqc [DEBUG ] No samples found: fastp [2020-04-26 14:33:07,467] multiqc.modules.fastqc.fastqc [INFO ] Found 146 reports [2020-04-26 14:33:21,524] multiqc [DEBUG ] No samples found: minionqc [2020-04-26 14:33:21,529] multiqc [DEBUG ] No samples found: mosdepth [2020-04-26 14:33:21,534] multiqc [DEBUG ] No samples found: clusterflow [2020-04-26 14:33:21,540] multiqc [DEBUG ] No samples found: bcl2fastq [2020-04-26 14:33:21,545] multiqc [DEBUG ] No samples found: interop [2020-04-26 14:33:21,550] multiqc [DEBUG ] No samples found: flash [2020-04-26 14:33:21,572] multiqc [DEBUG ] No samples found: seqyclean [2020-04-26 14:33:21,843] multiqc [INFO ] Compressing plot data [2020-04-26 14:33:21,908] multiqc [INFO ] Report : multiqc_report.html [2020-04-26 14:33:21,908] multiqc [INFO ] Data : multiqc_data [2020-04-26 14:33:21,908] multiqc [DEBUG ] Moving data file from '/tmp/tmpm3qcxaok/multiqc_data/mqc_fastqc_per_base_n_content_plot_1.txt' to '/home/sam/analyses/20200426_olur_fastqc_quantseq/multiqc_data' [2020-04-26 14:33:21,909] multiqc [DEBUG ] Moving data file from '/tmp/tmpm3qcxaok/multiqc_data/multiqc_general_stats.txt' to '/home/sam/analyses/20200426_olur_fastqc_quantseq/multiqc_data' [2020-04-26 14:33:21,909] multiqc [DEBUG ] Moving data file from '/tmp/tmpm3qcxaok/multiqc_data/multiqc_fastqc.txt' to '/home/sam/analyses/20200426_olur_fastqc_quantseq/multiqc_data' [2020-04-26 14:33:21,909] multiqc [DEBUG ] Moving data file from '/tmp/tmpm3qcxaok/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/home/sam/analyses/20200426_olur_fastqc_quantseq/multiqc_data' [2020-04-26 14:33:21,910] multiqc [DEBUG ] Moving data file from '/tmp/tmpm3qcxaok/multiqc_data/multiqc_sources.txt' to '/home/sam/analyses/20200426_olur_fastqc_quantseq/multiqc_data' [2020-04-26 14:33:21,910] multiqc [DEBUG ] Moving data file from '/tmp/tmpm3qcxaok/multiqc_data/mqc_fastqc_sequence_counts_plot_1.txt' to '/home/sam/analyses/20200426_olur_fastqc_quantseq/multiqc_data' [2020-04-26 14:33:21,910] multiqc [DEBUG ] Moving data file from '/tmp/tmpm3qcxaok/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Counts.txt' to '/home/sam/analyses/20200426_olur_fastqc_quantseq/multiqc_data' [2020-04-26 14:33:21,911] multiqc [DEBUG ] Moving data file from '/tmp/tmpm3qcxaok/multiqc_data/mqc_fastqc_adapter_content_plot_1.txt' to '/home/sam/analyses/20200426_olur_fastqc_quantseq/multiqc_data' [2020-04-26 14:33:21,911] multiqc [DEBUG ] Moving data file from '/tmp/tmpm3qcxaok/multiqc_data/mqc_fastqc_per_sequence_quality_scores_plot_1.txt' to '/home/sam/analyses/20200426_olur_fastqc_quantseq/multiqc_data' [2020-04-26 14:33:21,912] multiqc [DEBUG ] Moving data file from '/tmp/tmpm3qcxaok/multiqc_data/multiqc_data.json' to '/home/sam/analyses/20200426_olur_fastqc_quantseq/multiqc_data' [2020-04-26 14:33:21,912] multiqc [DEBUG ] Moving data file from '/tmp/tmpm3qcxaok/multiqc_data/mqc_fastqc_per_base_sequence_quality_plot_1.txt' to '/home/sam/analyses/20200426_olur_fastqc_quantseq/multiqc_data' [2020-04-26 14:33:21,913] multiqc [DEBUG ] Moving data file from '/tmp/tmpm3qcxaok/multiqc_data/mqc_fastqc_sequence_duplication_levels_plot_1.txt' to '/home/sam/analyses/20200426_olur_fastqc_quantseq/multiqc_data' [2020-04-26 14:33:21,913] multiqc [DEBUG ] Moving data file from '/tmp/tmpm3qcxaok/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Percentages.txt' to '/home/sam/analyses/20200426_olur_fastqc_quantseq/multiqc_data' [2020-04-26 14:33:21,914] multiqc [DEBUG ] Moving data file from '/tmp/tmpm3qcxaok/multiqc_data/mqc_fastqc_overrepresented_sequencesi_plot_1.txt' to '/home/sam/analyses/20200426_olur_fastqc_quantseq/multiqc_data' [2020-04-26 14:33:22,242] multiqc [INFO ] MultiQC complete