[2018-09-11 14:37:08,429] multiqc [DEBUG ] No MultiQC config found: /home/shared/anaconda3/lib/python3.6/site-packages/multiqc-1.5.dev0-py3.6.egg/multiqc_config.yaml [2018-09-11 14:37:08,429] multiqc [DEBUG ] No MultiQC config found: /home/sam/.multiqc_config.yaml [2018-09-11 14:37:08,429] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2018-09-11 14:37:08,429] multiqc [DEBUG ] Command used: /home/shared/anaconda3/bin/multiqc . [2018-09-11 14:37:09,245] multiqc [WARNING] MultiQC Version v1.6 now available! [2018-09-11 14:37:09,245] multiqc [INFO ] This is MultiQC v1.5.dev0 [2018-09-11 14:37:09,245] multiqc [DEBUG ] Command : /home/shared/anaconda3/bin/multiqc . [2018-09-11 14:37:09,245] multiqc [DEBUG ] Working dir : /home/sam/analyses/20180911_virginica_oil_trimgalore_01 [2018-09-11 14:37:09,245] multiqc [INFO ] Template : default [2018-09-11 14:37:09,245] multiqc [INFO ] Searching '.' [2018-09-11 14:37:09,246] multiqc [DEBUG ] Analysing modules: afterqc, custom_content, conpair, peddy, methylQA, qualimap, preseq, quast, qorts, rna_seqc, rsem, rseqc, busco, goleft_indexcov, disambiguate, supernova, deeptools, sargasso, verifybamid, homer, macs2, theta2, snpeff, gatk, htseq, bcftools, featureCounts, picard, prokka, samblaster, samtools, bamtools, jellyfish, vcftools, bbmap, bismark, hicexplorer, hicup, salmon, kallisto, slamdunk, star, hisat2, tophat, bowtie2, bowtie1, leehom, adapterRemoval, cutadapt, flexbar, trimmomatic, skewer, sortmerna, biobloomtools, fastq_screen, fastqc, clusterflow, bcl2fastq, interop [2018-09-11 14:37:09,246] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpe6e5js1r [2018-09-11 14:37:09,283] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 2112_lane1_TTAGGC_trimmed.fq.gz [2018-09-11 14:37:09,338] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 2112_lane1_ATCACG_trimmed.fq.gz [2018-09-11 14:37:09,383] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 2112_lane1_GCCAAT_trimmed.fq.gz [2018-09-11 14:37:09,415] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 2112_lane1_CAGATC_trimmed.fq.gz [2018-09-11 14:37:09,415] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 2112_lane1_ACAGTG_trimmed.fq.gz [2018-09-11 14:37:09,448] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 2112_lane1_TGACCA_trimmed.fq.gz [2018-09-11 14:37:09,448] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 2112_lane1_ACAGTG_trimmed_fastqc.html [2018-09-11 14:37:09,449] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 2112_lane1_TTAGGC_trimmed_fastqc.html [2018-09-11 14:37:09,449] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 2112_lane1_GCCAAT_trimmed_fastqc.html [2018-09-11 14:37:09,449] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 2112_lane1_ATCACG_trimmed_fastqc.html [2018-09-11 14:37:09,450] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 2112_lane1_CAGATC_trimmed_fastqc.html [2018-09-11 14:37:09,450] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 2112_lane1_TGACCA_trimmed_fastqc.html [2018-09-11 14:37:10,281] multiqc [DEBUG ] No samples found: afterqc [2018-09-11 14:37:10,315] multiqc [DEBUG ] No samples found: custom_content [2018-09-11 14:37:10,326] multiqc [DEBUG ] No samples found: conpair [2018-09-11 14:37:10,336] multiqc [DEBUG ] No samples found: peddy [2018-09-11 14:37:10,352] multiqc [DEBUG ] No samples found: methylQA [2018-09-11 14:37:10,370] multiqc [DEBUG ] No samples found: qualimap [2018-09-11 14:37:10,382] multiqc [DEBUG ] No samples found: preseq [2018-09-11 14:37:10,387] multiqc [DEBUG ] No samples found: quast [2018-09-11 14:37:10,393] multiqc [DEBUG ] No samples found: qorts [2018-09-11 14:37:10,399] multiqc [DEBUG ] No samples found: rna_seqc [2018-09-11 14:37:10,404] multiqc [DEBUG ] No samples found: rsem [2018-09-11 14:37:10,414] multiqc [DEBUG ] No samples found: rseqc [2018-09-11 14:37:10,427] multiqc [DEBUG ] No samples found: busco [2018-09-11 14:37:10,444] multiqc [DEBUG ] No samples found: goleft_indexcov [2018-09-11 14:37:10,465] multiqc [DEBUG ] No samples found: disambiguate [2018-09-11 14:37:10,483] multiqc [DEBUG ] No samples found: supernova [2018-09-11 14:37:10,501] multiqc [DEBUG ] No samples found: deeptools [2018-09-11 14:37:10,517] multiqc [DEBUG ] No samples found: sargasso [2018-09-11 14:37:10,522] multiqc [DEBUG ] No samples found: verifybamid [2018-09-11 14:37:10,548] multiqc [DEBUG ] No samples found: homer [2018-09-11 14:37:10,554] multiqc [DEBUG ] No samples found: macs2 [2018-09-11 14:37:10,559] multiqc [DEBUG ] No samples found: theta2 [2018-09-11 14:37:10,579] multiqc [DEBUG ] No samples found: snpeff [2018-09-11 14:37:10,602] multiqc [DEBUG ] No samples found: gatk [2018-09-11 14:37:10,610] multiqc [DEBUG ] No samples found: htseq [2018-09-11 14:37:10,634] multiqc [DEBUG ] No samples found: bcftools [2018-09-11 14:37:10,645] multiqc [DEBUG ] No samples found: featureCounts [2018-09-11 14:37:10,661] multiqc [DEBUG ] No samples found: picard [2018-09-11 14:37:10,666] multiqc [DEBUG ] No samples found: prokka [2018-09-11 14:37:10,675] multiqc [DEBUG ] No samples found: samblaster [2018-09-11 14:37:10,682] multiqc [DEBUG ] No samples found: samtools [2018-09-11 14:37:10,704] multiqc [DEBUG ] No samples found: bamtools [2018-09-11 14:37:10,710] multiqc [DEBUG ] No samples found: jellyfish [2018-09-11 14:37:10,718] multiqc [DEBUG ] No samples found: vcftools [2018-09-11 14:37:10,740] multiqc [DEBUG ] No samples found: bbmap [2018-09-11 14:37:10,751] multiqc [DEBUG ] No samples found: bismark [2018-09-11 14:37:10,762] multiqc [DEBUG ] No samples found: hicexplorer [2018-09-11 14:37:10,768] multiqc [DEBUG ] No samples found: hicup [2018-09-11 14:37:10,773] multiqc [DEBUG ] No samples found: salmon [2018-09-11 14:37:10,778] multiqc [DEBUG ] No samples found: kallisto [2018-09-11 14:37:10,795] multiqc [DEBUG ] No samples found: slamdunk [2018-09-11 14:37:10,800] multiqc [DEBUG ] No samples found: star [2018-09-11 14:37:10,810] multiqc [DEBUG ] No samples found: hisat2 [2018-09-11 14:37:10,824] multiqc [DEBUG ] No samples found: tophat [2018-09-11 14:37:10,841] multiqc [DEBUG ] No samples found: bowtie2 [2018-09-11 14:37:10,851] multiqc [DEBUG ] No samples found: bowtie1 [2018-09-11 14:37:10,866] multiqc [DEBUG ] No samples found: leehom [2018-09-11 14:37:10,879] multiqc [DEBUG ] No samples found: adapterRemoval [2018-09-11 14:37:10,901] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: 2112_lane1_ATCACG [2018-09-11 14:37:10,910] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: 2112_lane1_TGACCA [2018-09-11 14:37:10,916] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: 2112_lane1_TTAGGC [2018-09-11 14:37:10,918] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: 2112_lane1_ACAGTG [2018-09-11 14:37:10,920] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: 2112_lane1_GCCAAT [2018-09-11 14:37:10,922] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: 2112_lane1_CAGATC [2018-09-11 14:37:10,924] multiqc.modules.cutadapt.cutadapt [INFO ] Found 6 reports [2018-09-11 14:37:10,957] multiqc [DEBUG ] No samples found: flexbar [2018-09-11 14:37:10,962] multiqc [DEBUG ] No samples found: trimmomatic [2018-09-11 14:37:10,978] multiqc [DEBUG ] No samples found: skewer [2018-09-11 14:37:10,983] multiqc [DEBUG ] No samples found: sortmerna [2018-09-11 14:37:10,995] multiqc [DEBUG ] No samples found: biobloomtools [2018-09-11 14:37:11,013] multiqc [DEBUG ] No samples found: fastq_screen [2018-09-11 14:37:11,316] multiqc.modules.fastqc.fastqc [INFO ] Found 6 reports [2018-09-11 14:37:11,474] multiqc [DEBUG ] No samples found: clusterflow [2018-09-11 14:37:11,489] multiqc [DEBUG ] No samples found: bcl2fastq [2018-09-11 14:37:11,494] multiqc [DEBUG ] No samples found: interop [2018-09-11 14:37:11,510] multiqc [INFO ] Compressing plot data [2018-09-11 14:37:11,750] multiqc [INFO ] Report : multiqc_report.html [2018-09-11 14:37:11,751] multiqc [INFO ] Data : multiqc_data [2018-09-11 14:37:11,751] multiqc [DEBUG ] Moving data file from '/tmp/tmpe6e5js1r/multiqc_data/multiqc_general_stats.txt' to '/home/sam/analyses/20180911_virginica_oil_trimgalore_01/multiqc_data' [2018-09-11 14:37:11,751] multiqc [DEBUG ] Moving data file from '/tmp/tmpe6e5js1r/multiqc_data/multiqc_fastqc.txt' to '/home/sam/analyses/20180911_virginica_oil_trimgalore_01/multiqc_data' [2018-09-11 14:37:11,751] multiqc [DEBUG ] Moving data file from '/tmp/tmpe6e5js1r/multiqc_data/multiqc_data.json' to '/home/sam/analyses/20180911_virginica_oil_trimgalore_01/multiqc_data' [2018-09-11 14:37:11,751] multiqc [DEBUG ] Moving data file from '/tmp/tmpe6e5js1r/multiqc_data/multiqc_cutadapt.txt' to '/home/sam/analyses/20180911_virginica_oil_trimgalore_01/multiqc_data' [2018-09-11 14:37:11,751] multiqc [DEBUG ] Moving data file from '/tmp/tmpe6e5js1r/multiqc_data/multiqc_sources.txt' to '/home/sam/analyses/20180911_virginica_oil_trimgalore_01/multiqc_data' [2018-09-11 14:37:11,988] multiqc [INFO ] MultiQC complete