[2019-10-25 07:57:08,199] multiqc [DEBUG ] No MultiQC config found: /home/sam/.local/lib/python3.5/site-packages/multiqc-1.6-py3.5.egg/multiqc_config.yaml [2019-10-25 07:57:08,200] multiqc [DEBUG ] No MultiQC config found: /home/sam/.multiqc_config.yaml [2019-10-25 07:57:08,200] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2019-10-25 07:57:08,200] multiqc [DEBUG ] Command used: /usr/local/bin/multiqc . [2019-10-25 07:57:09,206] multiqc [WARNING] MultiQC Version v1.7 now available! [2019-10-25 07:57:09,206] multiqc [INFO ] This is MultiQC v1.6 [2019-10-25 07:57:09,206] multiqc [DEBUG ] Command : /usr/local/bin/multiqc . [2019-10-25 07:57:09,206] multiqc [DEBUG ] Working dir : /home/sam/analyses/20191024_cbai_fastqc_multiqc [2019-10-25 07:57:09,206] multiqc [INFO ] Template : default [2019-10-25 07:57:09,206] multiqc [INFO ] Searching '.' [2019-10-25 07:57:09,208] multiqc [DEBUG ] Analysing modules: custom_content, conpair, peddy, methylQA, 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, dedup, picard, prokka, samblaster, samtools, bamtools, jellyfish, vcftools, longranger, bbmap, bismark, 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, clusterflow, bcl2fastq, interop [2019-10-25 07:57:09,208] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpfy2rpdc9 [2019-10-25 07:57:09,266] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329777_S4_L001_R1_001_fastqc.html [2019-10-25 07:57:09,331] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329775_S2_L001_R1_001_fastqc.html [2019-10-25 07:57:09,331] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329775_S2_L001_R2_001_fastqc.html [2019-10-25 07:57:09,333] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329774_S1_L001_R1_001_fastqc.html [2019-10-25 07:57:09,333] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329776_S3_L002_R2_001_fastqc.html [2019-10-25 07:57:09,334] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329774_S1_L002_R1_001_fastqc.html [2019-10-25 07:57:09,334] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329776_S3_L001_R1_001_fastqc.html [2019-10-25 07:57:09,335] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329777_S4_L002_R2_001_fastqc.html [2019-10-25 07:57:09,335] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329775_S2_L002_R1_001_fastqc.html [2019-10-25 07:57:09,335] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329777_S4_L001_R2_001_fastqc.html [2019-10-25 07:57:09,336] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329776_S3_L002_R1_001_fastqc.html [2019-10-25 07:57:09,338] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329774_S1_L002_R2_001_fastqc.html [2019-10-25 07:57:09,340] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329777_S4_L002_R1_001_fastqc.html [2019-10-25 07:57:09,341] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329776_S3_L001_R2_001_fastqc.html [2019-10-25 07:57:09,341] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329774_S1_L001_R2_001_fastqc.html [2019-10-25 07:57:09,341] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329775_S2_L002_R2_001_fastqc.html [2019-10-25 07:57:09,344] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: fastqc_report.html [2019-10-25 07:57:09,379] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: fastqc_report.html [2019-10-25 07:57:09,409] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: fastqc_report.html [2019-10-25 07:57:09,440] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: fastqc_report.html [2019-10-25 07:57:09,471] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: fastqc_report.html [2019-10-25 07:57:09,501] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: fastqc_report.html [2019-10-25 07:57:09,531] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: fastqc_report.html [2019-10-25 07:57:09,562] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: fastqc_report.html [2019-10-25 07:57:09,592] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: fastqc_report.html [2019-10-25 07:57:09,622] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: fastqc_report.html [2019-10-25 07:57:09,653] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: fastqc_report.html [2019-10-25 07:57:09,683] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: fastqc_report.html [2019-10-25 07:57:09,714] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: fastqc_report.html [2019-10-25 07:57:09,744] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: fastqc_report.html [2019-10-25 07:57:09,775] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: fastqc_report.html [2019-10-25 07:57:09,824] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: fastqc_report.html [2019-10-25 07:57:10,653] multiqc [DEBUG ] No samples found: custom_content [2019-10-25 07:57:10,662] multiqc [DEBUG ] No samples found: conpair [2019-10-25 07:57:10,670] multiqc [DEBUG ] No samples found: peddy [2019-10-25 07:57:10,683] multiqc [DEBUG ] No samples found: methylQA [2019-10-25 07:57:10,688] multiqc [DEBUG ] No samples found: qualimap [2019-10-25 07:57:10,693] multiqc [DEBUG ] No samples found: preseq [2019-10-25 07:57:10,698] multiqc [DEBUG ] No samples found: quast [2019-10-25 07:57:10,702] multiqc [DEBUG ] No samples found: qorts [2019-10-25 07:57:10,707] multiqc [DEBUG ] No samples found: rna_seqc [2019-10-25 07:57:10,712] multiqc [DEBUG ] No samples found: rsem [2019-10-25 07:57:10,730] multiqc [DEBUG ] No samples found: rseqc [2019-10-25 07:57:10,735] multiqc [DEBUG ] No samples found: busco [2019-10-25 07:57:10,740] multiqc [DEBUG ] No samples found: goleft_indexcov [2019-10-25 07:57:10,744] multiqc [DEBUG ] No samples found: disambiguate [2019-10-25 07:57:10,748] multiqc [DEBUG ] No samples found: supernova [2019-10-25 07:57:10,755] multiqc [DEBUG ] No samples found: deeptools [2019-10-25 07:57:10,759] multiqc [DEBUG ] No samples found: sargasso [2019-10-25 07:57:10,763] multiqc [DEBUG ] No samples found: verifybamid [2019-10-25 07:57:10,767] multiqc [DEBUG ] No samples found: mirtrace [2019-10-25 07:57:10,771] multiqc [DEBUG ] No samples found: happy [2019-10-25 07:57:10,776] multiqc [DEBUG ] No samples found: homer [2019-10-25 07:57:10,780] multiqc [DEBUG ] No samples found: macs2 [2019-10-25 07:57:10,785] multiqc [DEBUG ] No samples found: theta2 [2019-10-25 07:57:10,797] multiqc [DEBUG ] No samples found: snpeff [2019-10-25 07:57:10,803] multiqc [DEBUG ] No samples found: gatk [2019-10-25 07:57:10,807] multiqc [DEBUG ] No samples found: htseq [2019-10-25 07:57:10,812] multiqc [DEBUG ] No samples found: bcftools [2019-10-25 07:57:10,818] multiqc [DEBUG ] No samples found: featureCounts [2019-10-25 07:57:10,825] multiqc [DEBUG ] No samples found: dedup [2019-10-25 07:57:10,838] multiqc [DEBUG ] No samples found: picard [2019-10-25 07:57:10,845] multiqc [DEBUG ] No samples found: prokka [2019-10-25 07:57:10,851] multiqc [DEBUG ] No samples found: samblaster [2019-10-25 07:57:10,860] multiqc [DEBUG ] No samples found: samtools [2019-10-25 07:57:10,867] multiqc [DEBUG ] No samples found: bamtools [2019-10-25 07:57:10,873] multiqc [DEBUG ] No samples found: jellyfish [2019-10-25 07:57:10,879] multiqc [DEBUG ] No samples found: vcftools [2019-10-25 07:57:10,884] multiqc [DEBUG ] No samples found: longranger [2019-10-25 07:57:10,892] multiqc [DEBUG ] No samples found: bbmap [2019-10-25 07:57:10,896] multiqc [DEBUG ] No samples found: bismark [2019-10-25 07:57:10,900] multiqc [DEBUG ] No samples found: hicexplorer [2019-10-25 07:57:10,904] multiqc [DEBUG ] No samples found: hicup [2019-10-25 07:57:10,909] multiqc [DEBUG ] No samples found: hicpro [2019-10-25 07:57:10,913] multiqc [DEBUG ] No samples found: salmon [2019-10-25 07:57:10,917] multiqc [DEBUG ] No samples found: kallisto [2019-10-25 07:57:10,921] multiqc [DEBUG ] No samples found: slamdunk [2019-10-25 07:57:10,925] multiqc [DEBUG ] No samples found: star [2019-10-25 07:57:10,929] multiqc [DEBUG ] No samples found: hisat2 [2019-10-25 07:57:10,933] multiqc [DEBUG ] No samples found: tophat [2019-10-25 07:57:10,938] multiqc [DEBUG ] No samples found: bowtie2 [2019-10-25 07:57:10,942] multiqc [DEBUG ] No samples found: bowtie1 [2019-10-25 07:57:10,946] multiqc [DEBUG ] No samples found: kat [2019-10-25 07:57:10,950] multiqc [DEBUG ] No samples found: leehom [2019-10-25 07:57:10,955] multiqc [DEBUG ] No samples found: adapterRemoval [2019-10-25 07:57:10,959] multiqc [DEBUG ] No samples found: clipandmerge [2019-10-25 07:57:10,964] multiqc [DEBUG ] No samples found: cutadapt [2019-10-25 07:57:10,968] multiqc [DEBUG ] No samples found: flexbar [2019-10-25 07:57:10,972] multiqc [DEBUG ] No samples found: trimmomatic [2019-10-25 07:57:10,976] multiqc [DEBUG ] No samples found: skewer [2019-10-25 07:57:10,980] multiqc [DEBUG ] No samples found: sortmerna [2019-10-25 07:57:10,984] multiqc [DEBUG ] No samples found: biobloomtools [2019-10-25 07:57:10,989] multiqc [DEBUG ] No samples found: fastq_screen [2019-10-25 07:57:10,993] multiqc [DEBUG ] No samples found: afterqc [2019-10-25 07:57:10,997] multiqc [DEBUG ] No samples found: fastp [2019-10-25 07:57:14,554] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping '329774_S1_L002_R2_001_fastqc.zip' as already parsed '329774_S1_L002_R2_001' [2019-10-25 07:57:14,555] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping '329776_S3_L002_R2_001_fastqc.zip' as already parsed '329776_S3_L002_R2_001' [2019-10-25 07:57:14,555] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping '329774_S1_L002_R1_001_fastqc.zip' as already parsed '329774_S1_L002_R1_001' [2019-10-25 07:57:14,555] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping '329777_S4_L002_R1_001_fastqc.zip' as already parsed '329777_S4_L002_R1_001' [2019-10-25 07:57:14,555] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping '329777_S4_L001_R1_001_fastqc.zip' as already parsed '329777_S4_L001_R1_001' [2019-10-25 07:57:14,555] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping '329776_S3_L001_R1_001_fastqc.zip' as already parsed '329776_S3_L001_R1_001' [2019-10-25 07:57:14,555] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping '329775_S2_L002_R1_001_fastqc.zip' as already parsed '329775_S2_L002_R1_001' [2019-10-25 07:57:14,556] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping '329777_S4_L002_R2_001_fastqc.zip' as already parsed '329777_S4_L002_R2_001' [2019-10-25 07:57:14,556] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping '329774_S1_L001_R2_001_fastqc.zip' as already parsed '329774_S1_L001_R2_001' [2019-10-25 07:57:14,556] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping '329776_S3_L001_R2_001_fastqc.zip' as already parsed '329776_S3_L001_R2_001' [2019-10-25 07:57:14,556] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping '329775_S2_L002_R2_001_fastqc.zip' as already parsed '329775_S2_L002_R2_001' [2019-10-25 07:57:14,556] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping '329775_S2_L001_R2_001_fastqc.zip' as already parsed '329775_S2_L001_R2_001' [2019-10-25 07:57:14,557] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping '329777_S4_L001_R2_001_fastqc.zip' as already parsed '329777_S4_L001_R2_001' [2019-10-25 07:57:14,557] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping '329776_S3_L002_R1_001_fastqc.zip' as already parsed '329776_S3_L002_R1_001' [2019-10-25 07:57:14,557] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping '329774_S1_L001_R1_001_fastqc.zip' as already parsed '329774_S1_L001_R1_001' [2019-10-25 07:57:14,557] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping '329775_S2_L001_R1_001_fastqc.zip' as already parsed '329775_S2_L001_R1_001' [2019-10-25 07:57:14,557] multiqc.modules.fastqc.fastqc [INFO ] Found 16 reports [2019-10-25 07:57:14,894] multiqc [DEBUG ] No samples found: clusterflow [2019-10-25 07:57:14,898] multiqc [DEBUG ] No samples found: bcl2fastq [2019-10-25 07:57:14,904] multiqc [DEBUG ] No samples found: interop [2019-10-25 07:57:14,935] multiqc [INFO ] Compressing plot data [2019-10-25 07:57:15,305] multiqc [INFO ] Report : multiqc_report.html [2019-10-25 07:57:15,305] multiqc [INFO ] Data : multiqc_data [2019-10-25 07:57:15,305] multiqc [DEBUG ] Moving data file from '/tmp/tmpfy2rpdc9/multiqc_data/multiqc_general_stats.txt' to '/home/sam/analyses/20191024_cbai_fastqc_multiqc/multiqc_data' [2019-10-25 07:57:15,305] multiqc [DEBUG ] Moving data file from '/tmp/tmpfy2rpdc9/multiqc_data/multiqc_fastqc.txt' to '/home/sam/analyses/20191024_cbai_fastqc_multiqc/multiqc_data' [2019-10-25 07:57:15,306] multiqc [DEBUG ] Moving data file from '/tmp/tmpfy2rpdc9/multiqc_data/multiqc_sources.txt' to '/home/sam/analyses/20191024_cbai_fastqc_multiqc/multiqc_data' [2019-10-25 07:57:15,306] multiqc [DEBUG ] Moving data file from '/tmp/tmpfy2rpdc9/multiqc_data/multiqc_data.json' to '/home/sam/analyses/20191024_cbai_fastqc_multiqc/multiqc_data' [2019-10-25 07:57:15,543] multiqc [INFO ] MultiQC complete