[2020-04-14 04:44:42,043] multiqc [DEBUG ] No MultiQC config found: /home/sam/.local/lib/python3.5/site-packages/multiqc-1.8-py3.5.egg/multiqc_config.yaml [2020-04-14 04:44:42,044] multiqc [DEBUG ] No MultiQC config found: /home/sam/.multiqc_config.yaml [2020-04-14 04:44:42,044] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2020-04-14 04:44:42,044] multiqc [DEBUG ] Command used: /usr/local/bin/multiqc . [2020-04-14 04:44:43,202] multiqc [DEBUG ] Latest MultiQC version is v1.8 [2020-04-14 04:44:43,202] multiqc [INFO ] This is MultiQC v1.8 [2020-04-14 04:44:43,202] multiqc [DEBUG ] Command : /usr/local/bin/multiqc . [2020-04-14 04:44:43,202] multiqc [DEBUG ] Working dir : /home/sam/analyses/20200414_cbai_RNAseq_fastqc_multiqc [2020-04-14 04:44:43,202] multiqc [INFO ] Template : default [2020-04-14 04:44:43,202] multiqc [DEBUG ] Running Python 3.5.2 (default, Oct 8 2019, 13:06:37) [GCC 5.4.0 20160609] [2020-04-14 04:44:43,202] multiqc [INFO ] Searching : /home/sam/analyses/20200414_cbai_RNAseq_fastqc_multiqc [2020-04-14 04:44:43,203] 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 [2020-04-14 04:44:43,203] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmp5fs8i3ud [2020-04-14 04:44:43,303] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380825_S6_L001_R2_001_fastqc.html [2020-04-14 04:44:43,303] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380821_S2_L002_R1_001_fastqc.html [2020-04-14 04:44:43,362] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380820_S1_L001_R2_001_fastqc.html [2020-04-14 04:44:43,363] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380821_S2_L001_R1_001_fastqc.html [2020-04-14 04:44:43,365] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380822_S3_L002_R2_001_fastqc.html [2020-04-14 04:44:43,367] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380820_S1_L001_R1_001_fastqc.html [2020-04-14 04:44:43,367] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380824_S5_L001_R1_001_fastqc.html [2020-04-14 04:44:43,368] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380822_S3_L002_R1_001_fastqc.html [2020-04-14 04:44:43,369] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380822_S3_L001_R2_001_fastqc.html [2020-04-14 04:44:43,369] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380823_S4_L001_R1_001_fastqc.html [2020-04-14 04:44:43,371] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380823_S4_L002_R2_001_fastqc.html [2020-04-14 04:44:43,371] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380821_S2_L002_R2_001_fastqc.html [2020-04-14 04:44:43,372] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380821_S2_L001_R2_001_fastqc.html [2020-04-14 04:44:43,372] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380823_S4_L001_R2_001_fastqc.html [2020-04-14 04:44:43,377] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380825_S6_L001_R1_001_fastqc.html [2020-04-14 04:44:43,377] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380820_S1_L002_R2_001_fastqc.html [2020-04-14 04:44:43,381] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380825_S6_L002_R1_001_fastqc.html [2020-04-14 04:44:43,383] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380824_S5_L002_R1_001_fastqc.html [2020-04-14 04:44:43,385] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380822_S3_L001_R1_001_fastqc.html [2020-04-14 04:44:43,385] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380824_S5_L002_R2_001_fastqc.html [2020-04-14 04:44:43,387] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380823_S4_L002_R1_001_fastqc.html [2020-04-14 04:44:43,387] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380825_S6_L002_R2_001_fastqc.html [2020-04-14 04:44:43,388] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380820_S1_L002_R1_001_fastqc.html [2020-04-14 04:44:43,390] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380824_S5_L001_R2_001_fastqc.html [2020-04-14 04:44:44,327] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 2.2.5 [2020-04-14 04:44:44,328] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 2.2.5 [2020-04-14 04:44:44,329] multiqc [DEBUG ] No samples found: custom_content [2020-04-14 04:44:44,353] multiqc [DEBUG ] No samples found: conpair [2020-04-14 04:44:44,364] multiqc [DEBUG ] No samples found: peddy [2020-04-14 04:44:44,376] multiqc [DEBUG ] No samples found: methylQA [2020-04-14 04:44:44,381] multiqc [DEBUG ] No samples found: phantompeakqualtools [2020-04-14 04:44:44,396] multiqc [DEBUG ] No samples found: qualimap [2020-04-14 04:44:44,402] multiqc [DEBUG ] No samples found: preseq [2020-04-14 04:44:44,407] multiqc [DEBUG ] No samples found: quast [2020-04-14 04:44:44,412] multiqc [DEBUG ] No samples found: qorts [2020-04-14 04:44:44,416] multiqc [DEBUG ] No samples found: rna_seqc [2020-04-14 04:44:44,427] multiqc [DEBUG ] No samples found: rsem [2020-04-14 04:44:44,444] multiqc [DEBUG ] No samples found: rseqc [2020-04-14 04:44:44,448] multiqc [DEBUG ] No samples found: busco [2020-04-14 04:44:44,453] multiqc [DEBUG ] No samples found: goleft_indexcov [2020-04-14 04:44:44,458] multiqc [DEBUG ] No samples found: disambiguate [2020-04-14 04:44:44,462] multiqc [DEBUG ] No samples found: supernova [2020-04-14 04:44:44,472] multiqc [DEBUG ] No samples found: deeptools [2020-04-14 04:44:44,476] multiqc [DEBUG ] No samples found: sargasso [2020-04-14 04:44:44,481] multiqc [DEBUG ] No samples found: verifybamid [2020-04-14 04:44:44,491] multiqc [DEBUG ] No samples found: mirtrace [2020-04-14 04:44:44,497] multiqc [DEBUG ] No samples found: happy [2020-04-14 04:44:44,503] multiqc [DEBUG ] No samples found: homer [2020-04-14 04:44:44,508] multiqc [DEBUG ] No samples found: macs2 [2020-04-14 04:44:44,512] multiqc [DEBUG ] No samples found: theta2 [2020-04-14 04:44:44,517] multiqc [DEBUG ] No samples found: snpeff [2020-04-14 04:44:44,523] multiqc [DEBUG ] No samples found: gatk [2020-04-14 04:44:44,538] multiqc [DEBUG ] No samples found: htseq [2020-04-14 04:44:44,544] multiqc [DEBUG ] No samples found: bcftools [2020-04-14 04:44:44,548] multiqc [DEBUG ] No samples found: featureCounts [2020-04-14 04:44:44,553] multiqc [DEBUG ] No samples found: fgbio [2020-04-14 04:44:44,558] multiqc [DEBUG ] No samples found: dedup [2020-04-14 04:44:44,562] multiqc [DEBUG ] No samples found: damageprofiler [2020-04-14 04:44:44,581] multiqc [DEBUG ] No samples found: biobambam2 [2020-04-14 04:44:44,586] multiqc [DEBUG ] No samples found: mtnucratio [2020-04-14 04:44:44,590] multiqc [DEBUG ] No samples found: picard [2020-04-14 04:44:44,594] multiqc [DEBUG ] No samples found: prokka [2020-04-14 04:44:44,599] multiqc [DEBUG ] No samples found: samblaster [2020-04-14 04:44:44,605] multiqc [DEBUG ] No samples found: samtools [2020-04-14 04:44:44,610] multiqc [DEBUG ] No samples found: sexdeterrmine [2020-04-14 04:44:44,615] multiqc [DEBUG ] No samples found: bamtools [2020-04-14 04:44:44,620] multiqc [DEBUG ] No samples found: jellyfish [2020-04-14 04:44:44,626] multiqc [DEBUG ] No samples found: vcftools [2020-04-14 04:44:44,642] multiqc [DEBUG ] No samples found: longranger [2020-04-14 04:44:44,647] multiqc [DEBUG ] No samples found: stacks [2020-04-14 04:44:44,657] multiqc [DEBUG ] No samples found: bbmap [2020-04-14 04:44:44,662] multiqc [DEBUG ] No samples found: bismark [2020-04-14 04:44:44,668] multiqc [DEBUG ] No samples found: biscuit [2020-04-14 04:44:44,673] multiqc [DEBUG ] No samples found: hicexplorer [2020-04-14 04:44:44,678] multiqc [DEBUG ] No samples found: hicup [2020-04-14 04:44:44,682] multiqc [DEBUG ] No samples found: hicpro [2020-04-14 04:44:44,687] multiqc [DEBUG ] No samples found: salmon [2020-04-14 04:44:44,692] multiqc [DEBUG ] No samples found: kallisto [2020-04-14 04:44:44,697] multiqc [DEBUG ] No samples found: slamdunk [2020-04-14 04:44:44,702] multiqc [DEBUG ] No samples found: star [2020-04-14 04:44:44,707] multiqc [DEBUG ] No samples found: hisat2 [2020-04-14 04:44:44,712] multiqc [DEBUG ] No samples found: tophat [2020-04-14 04:44:44,716] multiqc [DEBUG ] No samples found: bowtie2 [2020-04-14 04:44:44,721] multiqc [DEBUG ] No samples found: bowtie1 [2020-04-14 04:44:44,730] multiqc [DEBUG ] No samples found: kat [2020-04-14 04:44:44,735] multiqc [DEBUG ] No samples found: leehom [2020-04-14 04:44:44,739] multiqc [DEBUG ] No samples found: adapterRemoval [2020-04-14 04:44:44,744] multiqc [DEBUG ] No samples found: clipandmerge [2020-04-14 04:44:44,749] multiqc [DEBUG ] No samples found: cutadapt [2020-04-14 04:44:44,754] multiqc [DEBUG ] No samples found: flexbar [2020-04-14 04:44:44,758] multiqc [DEBUG ] No samples found: trimmomatic [2020-04-14 04:44:44,763] multiqc [DEBUG ] No samples found: skewer [2020-04-14 04:44:44,768] multiqc [DEBUG ] No samples found: sortmerna [2020-04-14 04:44:44,773] multiqc [DEBUG ] No samples found: biobloomtools [2020-04-14 04:44:44,777] multiqc [DEBUG ] No samples found: fastq_screen [2020-04-14 04:44:44,782] multiqc [DEBUG ] No samples found: afterqc [2020-04-14 04:44:44,787] multiqc [DEBUG ] No samples found: fastp [2020-04-14 04:44:46,180] multiqc.modules.fastqc.fastqc [INFO ] Found 24 reports [2020-04-14 04:44:46,650] multiqc [DEBUG ] No samples found: minionqc [2020-04-14 04:44:46,655] multiqc [DEBUG ] No samples found: mosdepth [2020-04-14 04:44:46,661] multiqc [DEBUG ] No samples found: clusterflow [2020-04-14 04:44:46,666] multiqc [DEBUG ] No samples found: bcl2fastq [2020-04-14 04:44:46,671] multiqc [DEBUG ] No samples found: interop [2020-04-14 04:44:46,676] multiqc [DEBUG ] No samples found: flash [2020-04-14 04:44:46,681] multiqc [DEBUG ] No samples found: seqyclean [2020-04-14 04:44:46,726] multiqc [INFO ] Compressing plot data [2020-04-14 04:44:47,286] multiqc [INFO ] Report : multiqc_report.html [2020-04-14 04:44:47,286] multiqc [INFO ] Data : multiqc_data [2020-04-14 04:44:47,286] multiqc [DEBUG ] Moving data file from '/tmp/tmp5fs8i3ud/multiqc_data/multiqc_general_stats.txt' to '/home/sam/analyses/20200414_cbai_RNAseq_fastqc_multiqc/multiqc_data' [2020-04-14 04:44:47,287] multiqc [DEBUG ] Moving data file from '/tmp/tmp5fs8i3ud/multiqc_data/multiqc_fastqc.txt' to '/home/sam/analyses/20200414_cbai_RNAseq_fastqc_multiqc/multiqc_data' [2020-04-14 04:44:47,287] multiqc [DEBUG ] Moving data file from '/tmp/tmp5fs8i3ud/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/home/sam/analyses/20200414_cbai_RNAseq_fastqc_multiqc/multiqc_data' [2020-04-14 04:44:47,287] multiqc [DEBUG ] Moving data file from '/tmp/tmp5fs8i3ud/multiqc_data/multiqc_sources.txt' to '/home/sam/analyses/20200414_cbai_RNAseq_fastqc_multiqc/multiqc_data' [2020-04-14 04:44:47,287] multiqc [DEBUG ] Moving data file from '/tmp/tmp5fs8i3ud/multiqc_data/multiqc_data.json' to '/home/sam/analyses/20200414_cbai_RNAseq_fastqc_multiqc/multiqc_data' [2020-04-14 04:44:47,643] multiqc [INFO ] MultiQC complete