[2018-01-29 07:24:58,304] multiqc [DEBUG ] No MultiQC config found: /home/shared/anaconda3/lib/python3.6/site-packages/multiqc-1.5.dev0-py3.6.egg/multiqc_config.yaml [2018-01-29 07:24:58,305] multiqc [DEBUG ] No MultiQC config found: /home/sam/.multiqc_config.yaml [2018-01-29 07:24:58,305] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2018-01-29 07:24:58,305] multiqc [DEBUG ] Command used: /home/shared/anaconda3/bin/multiqc /home/sam/data/geoduck_illumina/trimmed/ [2018-01-29 07:24:58,877] multiqc [DEBUG ] Latest MultiQC version is v1.4 [2018-01-29 07:24:58,878] multiqc [INFO ] This is MultiQC v1.5.dev0 [2018-01-29 07:24:58,878] multiqc [DEBUG ] Command : /home/shared/anaconda3/bin/multiqc /home/sam/data/geoduck_illumina/trimmed/ [2018-01-29 07:24:58,878] multiqc [DEBUG ] Working dir : /home/sam/gitrepos/LabDocs/jupyter_nbs/sam [2018-01-29 07:24:58,878] multiqc [INFO ] Template : default [2018-01-29 07:24:58,878] multiqc [INFO ] Searching '/home/sam/data/geoduck_illumina/trimmed/' [2018-01-29 07:24:58,879] 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 [2018-01-29 07:24:58,887] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmp3yxvkja6 [2018-01-29 07:24:59,032] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR012_S1_L001_R2_001_val_2.fq.gz [2018-01-29 07:24:59,032] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR014_AD014_S5_L002_R2_001_val_2.fq.gz [2018-01-29 07:24:59,032] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR005_S4_L001_R1_001_val_1.fq.gz [2018-01-29 07:24:59,094] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: AD002_S9_L002_R1_001_val_1.fq.gz [2018-01-29 07:24:59,208] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR015_AD015_S6_L001_R1_001_val_1.fq.gz [2018-01-29 07:24:59,238] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR005_S4_L002_R2_001_val_2.fq.gz [2018-01-29 07:24:59,238] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR013_AD013_S2_L001_R1_001_val_1.fq.gz [2018-01-29 07:24:59,250] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR021_S8_L002_R2_001_val_2.fq.gz [2018-01-29 07:24:59,250] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR015_AD015_S6_L001_R2_001_val_2.fq.gz [2018-01-29 07:24:59,250] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR006_S3_L001_R1_001_val_1.fq.gz [2018-01-29 07:24:59,263] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR005_S4_L002_R1_001_val_1.fq.gz [2018-01-29 07:24:59,263] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR014_AD014_S5_L001_R1_001_val_1.fq.gz [2018-01-29 07:24:59,317] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR012_S1_L002_R1_001_val_1.fq.gz [2018-01-29 07:24:59,317] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR012_S1_L002_R2_001_val_2.fq.gz [2018-01-29 07:24:59,317] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR006_S3_L002_R1_001_val_1.fq.gz [2018-01-29 07:24:59,317] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR013_AD013_S2_L002_R2_001_val_2.fq.gz [2018-01-29 07:24:59,342] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR012_S1_L001_R1_001_val_1.fq.gz [2018-01-29 07:24:59,456] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR015_AD015_S6_L002_R2_001_val_2.fq.gz [2018-01-29 07:24:59,490] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR015_AD015_S6_L002_R1_001_val_1.fq.gz [2018-01-29 07:24:59,490] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR019_S7_L001_R1_001_val_1.fq.gz [2018-01-29 07:24:59,490] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR013_AD013_S2_L001_R2_001_val_2.fq.gz [2018-01-29 07:24:59,490] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR014_AD014_S5_L002_R1_001_val_1.fq.gz [2018-01-29 07:24:59,504] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR019_S7_L002_R1_001_val_1.fq.gz [2018-01-29 07:24:59,561] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR021_S8_L001_R2_001_val_2.fq.gz [2018-01-29 07:24:59,573] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR006_S3_L001_R2_001_val_2.fq.gz [2018-01-29 07:24:59,638] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR019_S7_L002_R2_001_val_2.fq.gz [2018-01-29 07:24:59,665] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR014_AD014_S5_L001_R2_001_val_2.fq.gz [2018-01-29 07:24:59,665] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: AD002_S9_L001_R1_001_val_1.fq.gz [2018-01-29 07:24:59,665] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: AD002_S9_L002_R2_001_val_2.fq.gz [2018-01-29 07:24:59,718] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR005_S4_L001_R2_001_val_2.fq.gz [2018-01-29 07:24:59,781] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: AD002_S9_L001_R2_001_val_2.fq.gz [2018-01-29 07:24:59,781] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR013_AD013_S2_L002_R1_001_val_1.fq.gz [2018-01-29 07:24:59,781] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR019_S7_L001_R2_001_val_2.fq.gz [2018-01-29 07:24:59,781] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR021_S8_L002_R1_001_val_1.fq.gz [2018-01-29 07:24:59,781] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR006_S3_L002_R2_001_val_2.fq.gz [2018-01-29 07:24:59,782] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR021_S8_L001_R1_001_val_1.fq.gz [2018-01-29 07:25:34,206] multiqc [DEBUG ] No samples found: afterqc [2018-01-29 07:25:34,249] multiqc [DEBUG ] No samples found: custom_content [2018-01-29 07:25:34,259] multiqc [DEBUG ] No samples found: conpair [2018-01-29 07:25:34,270] multiqc [DEBUG ] No samples found: peddy [2018-01-29 07:25:34,286] multiqc [DEBUG ] No samples found: methylQA [2018-01-29 07:25:34,302] multiqc [DEBUG ] No samples found: qualimap [2018-01-29 07:25:34,316] multiqc [DEBUG ] No samples found: preseq [2018-01-29 07:25:34,321] multiqc [DEBUG ] No samples found: quast [2018-01-29 07:25:34,326] multiqc [DEBUG ] No samples found: qorts [2018-01-29 07:25:34,332] multiqc [DEBUG ] No samples found: rna_seqc [2018-01-29 07:25:34,338] multiqc [DEBUG ] No samples found: rsem [2018-01-29 07:25:34,349] multiqc [DEBUG ] No samples found: rseqc [2018-01-29 07:25:34,361] multiqc [DEBUG ] No samples found: busco [2018-01-29 07:25:34,378] multiqc [DEBUG ] No samples found: goleft_indexcov [2018-01-29 07:25:34,399] multiqc [DEBUG ] No samples found: disambiguate [2018-01-29 07:25:34,416] multiqc [DEBUG ] No samples found: supernova [2018-01-29 07:25:34,435] multiqc [DEBUG ] No samples found: deeptools [2018-01-29 07:25:34,451] multiqc [DEBUG ] No samples found: sargasso [2018-01-29 07:25:34,456] multiqc [DEBUG ] No samples found: verifybamid [2018-01-29 07:25:34,490] multiqc [DEBUG ] No samples found: homer [2018-01-29 07:25:34,496] multiqc [DEBUG ] No samples found: macs2 [2018-01-29 07:25:34,501] multiqc [DEBUG ] No samples found: theta2 [2018-01-29 07:25:34,512] multiqc [DEBUG ] No samples found: snpeff [2018-01-29 07:25:34,535] multiqc [DEBUG ] No samples found: gatk [2018-01-29 07:25:34,544] multiqc [DEBUG ] No samples found: htseq [2018-01-29 07:25:34,568] multiqc [DEBUG ] No samples found: bcftools [2018-01-29 07:25:34,578] multiqc [DEBUG ] No samples found: featureCounts [2018-01-29 07:25:34,595] multiqc [DEBUG ] No samples found: picard [2018-01-29 07:25:34,600] multiqc [DEBUG ] No samples found: prokka [2018-01-29 07:25:34,609] multiqc [DEBUG ] No samples found: samblaster [2018-01-29 07:25:34,616] multiqc [DEBUG ] No samples found: samtools [2018-01-29 07:25:34,639] multiqc [DEBUG ] No samples found: bamtools [2018-01-29 07:25:34,644] multiqc [DEBUG ] No samples found: jellyfish [2018-01-29 07:25:34,652] multiqc [DEBUG ] No samples found: vcftools [2018-01-29 07:25:34,674] multiqc [DEBUG ] No samples found: bbmap [2018-01-29 07:25:34,685] multiqc [DEBUG ] No samples found: bismark [2018-01-29 07:25:34,696] multiqc [DEBUG ] No samples found: hicexplorer [2018-01-29 07:25:34,701] multiqc [DEBUG ] No samples found: hicup [2018-01-29 07:25:34,707] multiqc [DEBUG ] No samples found: salmon [2018-01-29 07:25:34,712] multiqc [DEBUG ] No samples found: kallisto [2018-01-29 07:25:34,729] multiqc [DEBUG ] No samples found: slamdunk [2018-01-29 07:25:34,734] multiqc [DEBUG ] No samples found: star [2018-01-29 07:25:34,743] multiqc [DEBUG ] No samples found: hisat2 [2018-01-29 07:25:34,758] multiqc [DEBUG ] No samples found: tophat [2018-01-29 07:25:34,774] multiqc [DEBUG ] No samples found: bowtie2 [2018-01-29 07:25:34,784] multiqc [DEBUG ] No samples found: bowtie1 [2018-01-29 07:25:34,800] multiqc [DEBUG ] No samples found: leehom [2018-01-29 07:25:34,813] multiqc [DEBUG ] No samples found: adapterRemoval [2018-01-29 07:25:34,902] multiqc.modules.cutadapt.cutadapt [INFO ] Found 36 reports [2018-01-29 07:25:34,999] multiqc [DEBUG ] No samples found: flexbar [2018-01-29 07:25:35,004] multiqc [DEBUG ] No samples found: trimmomatic [2018-01-29 07:25:35,021] multiqc [DEBUG ] No samples found: skewer [2018-01-29 07:25:35,026] multiqc [DEBUG ] No samples found: sortmerna [2018-01-29 07:25:35,037] multiqc [DEBUG ] No samples found: biobloomtools [2018-01-29 07:25:35,054] multiqc [DEBUG ] No samples found: fastq_screen [2018-01-29 07:25:35,071] multiqc [DEBUG ] No samples found: fastqc [2018-01-29 07:25:35,083] multiqc [DEBUG ] No samples found: clusterflow [2018-01-29 07:25:35,097] multiqc [DEBUG ] No samples found: bcl2fastq [2018-01-29 07:25:35,103] multiqc [DEBUG ] No samples found: interop [2018-01-29 07:25:35,120] multiqc [INFO ] Compressing plot data [2018-01-29 07:25:35,587] multiqc [INFO ] Report : multiqc_report.html [2018-01-29 07:25:35,587] multiqc [INFO ] Data : multiqc_data [2018-01-29 07:25:35,587] multiqc [DEBUG ] Moving data file from '/tmp/tmp3yxvkja6/multiqc_data/multiqc_general_stats.txt' to '/home/sam/gitrepos/LabDocs/jupyter_nbs/sam/multiqc_data' [2018-01-29 07:25:35,588] multiqc [DEBUG ] Moving data file from '/tmp/tmp3yxvkja6/multiqc_data/multiqc_data.json' to '/home/sam/gitrepos/LabDocs/jupyter_nbs/sam/multiqc_data' [2018-01-29 07:25:35,588] multiqc [DEBUG ] Moving data file from '/tmp/tmp3yxvkja6/multiqc_data/multiqc_cutadapt.txt' to '/home/sam/gitrepos/LabDocs/jupyter_nbs/sam/multiqc_data' [2018-01-29 07:25:35,588] multiqc [DEBUG ] Moving data file from '/tmp/tmp3yxvkja6/multiqc_data/multiqc_sources.txt' to '/home/sam/gitrepos/LabDocs/jupyter_nbs/sam/multiqc_data' [2018-01-29 07:25:35,874] multiqc [INFO ] MultiQC complete