[2018-02-05 13:00:58,616] multiqc [DEBUG ] No MultiQC config found: /home/shared/anaconda3/lib/python3.6/site-packages/multiqc-1.5.dev0-py3.6.egg/multiqc_config.yaml [2018-02-05 13:00:58,616] multiqc [DEBUG ] No MultiQC config found: /home/sam/.multiqc_config.yaml [2018-02-05 13:00:58,616] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2018-02-05 13:00:58,616] multiqc [DEBUG ] Command used: /home/shared/anaconda3/bin/multiqc /home/sam/data/geoduck_illumina/trimmed/20180205_trimmed_fastqc_02/ [2018-02-05 13:00:59,328] multiqc [DEBUG ] Latest MultiQC version is v1.4 [2018-02-05 13:00:59,328] multiqc [INFO ] This is MultiQC v1.5.dev0 [2018-02-05 13:00:59,328] multiqc [DEBUG ] Command : /home/shared/anaconda3/bin/multiqc /home/sam/data/geoduck_illumina/trimmed/20180205_trimmed_fastqc_02/ [2018-02-05 13:00:59,328] multiqc [DEBUG ] Working dir : /home/sam/data/geoduck_illumina/trimmed/20180205_trimmed_fastqc_02 [2018-02-05 13:00:59,328] multiqc [INFO ] Template : default [2018-02-05 13:00:59,329] multiqc [INFO ] Searching '/home/sam/data/geoduck_illumina/trimmed/20180205_trimmed_fastqc_02/' [2018-02-05 13:00:59,329] 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 [2018-02-05 13:00:59,330] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmp4fof8wib [2018-02-05 13:00:59,379] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR005_S4_L001_R1_001_val_1_val_1_fastqc.html [2018-02-05 13:00:59,379] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR013_AD013_S2_L002_R1_001_val_1_val_1_fastqc.html [2018-02-05 13:00:59,379] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR012_S1_L001_R2_001_val_2_val_2_fastqc.html [2018-02-05 13:00:59,379] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR005_S4_L002_R1_001_val_1_val_1_fastqc.html [2018-02-05 13:00:59,379] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR021_S8_L001_R2_001_val_2_val_2_fastqc.html [2018-02-05 13:00:59,380] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR013_AD013_S2_L001_R1_001_val_1_val_1_fastqc.html [2018-02-05 13:00:59,380] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: AD002_S9_L001_R2_001_val_2_val_2_fastqc.html [2018-02-05 13:00:59,396] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR006_S3_L001_R1_001_val_1_val_1_fastqc.html [2018-02-05 13:00:59,396] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR006_S3_L001_R2_001_val_2_val_2_fastqc.html [2018-02-05 13:00:59,396] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR019_S7_L002_R2_001_val_2_val_2_fastqc.html [2018-02-05 13:00:59,396] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR012_S1_L001_R1_001_val_1_val_1_fastqc.html [2018-02-05 13:00:59,397] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR021_S8_L002_R1_001_val_1_val_1_fastqc.html [2018-02-05 13:00:59,397] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR019_S7_L001_R2_001_val_2_val_2_fastqc.html [2018-02-05 13:00:59,397] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR021_S8_L001_R1_001_val_1_val_1_fastqc.html [2018-02-05 13:00:59,400] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR019_S7_L001_R1_001_val_1_val_1_fastqc.html [2018-02-05 13:00:59,402] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR014_AD014_S5_L002_R1_001_val_1_val_1_fastqc.html [2018-02-05 13:00:59,402] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR019_S7_L002_R1_001_val_1_val_1_fastqc.html [2018-02-05 13:00:59,403] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: AD002_S9_L001_R1_001_val_1_val_1_fastqc.html [2018-02-05 13:00:59,403] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR015_AD015_S6_L002_R2_001_val_2_val_2_fastqc.html [2018-02-05 13:00:59,403] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR014_AD014_S5_L002_R2_001_val_2_val_2_fastqc.html [2018-02-05 13:00:59,403] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR006_S3_L002_R2_001_val_2_val_2_fastqc.html [2018-02-05 13:00:59,404] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR006_S3_L002_R1_001_val_1_val_1_fastqc.html [2018-02-05 13:00:59,404] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR015_AD015_S6_L002_R1_001_val_1_val_1_fastqc.html [2018-02-05 13:00:59,405] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR014_AD014_S5_L001_R2_001_val_2_val_2_fastqc.html [2018-02-05 13:00:59,405] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: AD002_S9_L002_R1_001_val_1_val_1_fastqc.html [2018-02-05 13:00:59,406] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR014_AD014_S5_L001_R1_001_val_1_val_1_fastqc.html [2018-02-05 13:00:59,406] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR013_AD013_S2_L002_R2_001_val_2_val_2_fastqc.html [2018-02-05 13:00:59,407] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR005_S4_L001_R2_001_val_2_val_2_fastqc.html [2018-02-05 13:00:59,407] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR005_S4_L002_R2_001_val_2_val_2_fastqc.html [2018-02-05 13:00:59,407] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR012_S1_L002_R2_001_val_2_val_2_fastqc.html [2018-02-05 13:00:59,408] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR021_S8_L002_R2_001_val_2_val_2_fastqc.html [2018-02-05 13:00:59,408] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR012_S1_L002_R1_001_val_1_val_1_fastqc.html [2018-02-05 13:00:59,408] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR015_AD015_S6_L001_R2_001_val_2_val_2_fastqc.html [2018-02-05 13:00:59,409] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR013_AD013_S2_L001_R2_001_val_2_val_2_fastqc.html [2018-02-05 13:00:59,409] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR015_AD015_S6_L001_R1_001_val_1_val_1_fastqc.html [2018-02-05 13:00:59,409] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: AD002_S9_L002_R2_001_val_2_val_2_fastqc.html [2018-02-05 13:01:00,260] multiqc [DEBUG ] No samples found: afterqc [2018-02-05 13:01:00,303] multiqc [DEBUG ] No samples found: custom_content [2018-02-05 13:01:00,313] multiqc [DEBUG ] No samples found: conpair [2018-02-05 13:01:00,324] multiqc [DEBUG ] No samples found: peddy [2018-02-05 13:01:00,340] multiqc [DEBUG ] No samples found: methylQA [2018-02-05 13:01:00,356] multiqc [DEBUG ] No samples found: qualimap [2018-02-05 13:01:00,370] multiqc [DEBUG ] No samples found: preseq [2018-02-05 13:01:00,375] multiqc [DEBUG ] No samples found: quast [2018-02-05 13:01:00,381] multiqc [DEBUG ] No samples found: qorts [2018-02-05 13:01:00,386] multiqc [DEBUG ] No samples found: rna_seqc [2018-02-05 13:01:00,392] multiqc [DEBUG ] No samples found: rsem [2018-02-05 13:01:00,402] multiqc [DEBUG ] No samples found: rseqc [2018-02-05 13:01:00,415] multiqc [DEBUG ] No samples found: busco [2018-02-05 13:01:00,432] multiqc [DEBUG ] No samples found: goleft_indexcov [2018-02-05 13:01:00,453] multiqc [DEBUG ] No samples found: disambiguate [2018-02-05 13:01:00,470] multiqc [DEBUG ] No samples found: supernova [2018-02-05 13:01:00,489] multiqc [DEBUG ] No samples found: deeptools [2018-02-05 13:01:00,505] multiqc [DEBUG ] No samples found: sargasso [2018-02-05 13:01:00,510] multiqc [DEBUG ] No samples found: verifybamid [2018-02-05 13:01:00,536] multiqc [DEBUG ] No samples found: homer [2018-02-05 13:01:00,542] multiqc [DEBUG ] No samples found: macs2 [2018-02-05 13:01:00,547] multiqc [DEBUG ] No samples found: theta2 [2018-02-05 13:01:00,566] multiqc [DEBUG ] No samples found: snpeff [2018-02-05 13:01:00,589] multiqc [DEBUG ] No samples found: gatk [2018-02-05 13:01:00,598] multiqc [DEBUG ] No samples found: htseq [2018-02-05 13:01:00,622] multiqc [DEBUG ] No samples found: bcftools [2018-02-05 13:01:00,633] multiqc [DEBUG ] No samples found: featureCounts [2018-02-05 13:01:00,649] multiqc [DEBUG ] No samples found: picard [2018-02-05 13:01:00,654] multiqc [DEBUG ] No samples found: prokka [2018-02-05 13:01:00,663] multiqc [DEBUG ] No samples found: samblaster [2018-02-05 13:01:00,670] multiqc [DEBUG ] No samples found: samtools [2018-02-05 13:01:00,693] multiqc [DEBUG ] No samples found: bamtools [2018-02-05 13:01:00,698] multiqc [DEBUG ] No samples found: jellyfish [2018-02-05 13:01:00,706] multiqc [DEBUG ] No samples found: vcftools [2018-02-05 13:01:00,727] multiqc [DEBUG ] No samples found: bbmap [2018-02-05 13:01:00,739] multiqc [DEBUG ] No samples found: bismark [2018-02-05 13:01:00,750] multiqc [DEBUG ] No samples found: hicexplorer [2018-02-05 13:01:00,755] multiqc [DEBUG ] No samples found: hicup [2018-02-05 13:01:00,760] multiqc [DEBUG ] No samples found: salmon [2018-02-05 13:01:00,766] multiqc [DEBUG ] No samples found: kallisto [2018-02-05 13:01:00,775] multiqc [DEBUG ] No samples found: slamdunk [2018-02-05 13:01:00,780] multiqc [DEBUG ] No samples found: star [2018-02-05 13:01:00,789] multiqc [DEBUG ] No samples found: hisat2 [2018-02-05 13:01:00,804] multiqc [DEBUG ] No samples found: tophat [2018-02-05 13:01:00,820] multiqc [DEBUG ] No samples found: bowtie2 [2018-02-05 13:01:00,830] multiqc [DEBUG ] No samples found: bowtie1 [2018-02-05 13:01:00,845] multiqc [DEBUG ] No samples found: leehom [2018-02-05 13:01:00,858] multiqc [DEBUG ] No samples found: adapterRemoval [2018-02-05 13:01:00,871] multiqc [DEBUG ] No samples found: cutadapt [2018-02-05 13:01:00,886] multiqc [DEBUG ] No samples found: flexbar [2018-02-05 13:01:00,892] multiqc [DEBUG ] No samples found: trimmomatic [2018-02-05 13:01:00,908] multiqc [DEBUG ] No samples found: skewer [2018-02-05 13:01:00,913] multiqc [DEBUG ] No samples found: sortmerna [2018-02-05 13:01:00,925] multiqc [DEBUG ] No samples found: biobloomtools [2018-02-05 13:01:00,942] multiqc [DEBUG ] No samples found: fastq_screen [2018-02-05 13:01:07,857] multiqc.modules.fastqc.fastqc [INFO ] Found 36 reports [2018-02-05 13:01:08,530] multiqc [DEBUG ] No samples found: clusterflow [2018-02-05 13:01:08,544] multiqc [DEBUG ] No samples found: bcl2fastq [2018-02-05 13:01:08,558] multiqc [DEBUG ] No samples found: interop [2018-02-05 13:01:08,629] multiqc [INFO ] Compressing plot data [2018-02-05 13:01:09,454] multiqc [INFO ] Report : multiqc_report.html [2018-02-05 13:01:09,454] multiqc [INFO ] Data : multiqc_data [2018-02-05 13:01:09,454] multiqc [DEBUG ] Moving data file from '/tmp/tmp4fof8wib/multiqc_data/multiqc_general_stats.txt' to '/home/sam/data/geoduck_illumina/trimmed/20180205_trimmed_fastqc_02/multiqc_data' [2018-02-05 13:01:09,454] multiqc [DEBUG ] Moving data file from '/tmp/tmp4fof8wib/multiqc_data/multiqc_fastqc.txt' to '/home/sam/data/geoduck_illumina/trimmed/20180205_trimmed_fastqc_02/multiqc_data' [2018-02-05 13:01:09,454] multiqc [DEBUG ] Moving data file from '/tmp/tmp4fof8wib/multiqc_data/multiqc_data.json' to '/home/sam/data/geoduck_illumina/trimmed/20180205_trimmed_fastqc_02/multiqc_data' [2018-02-05 13:01:09,454] multiqc [DEBUG ] Moving data file from '/tmp/tmp4fof8wib/multiqc_data/multiqc_sources.txt' to '/home/sam/data/geoduck_illumina/trimmed/20180205_trimmed_fastqc_02/multiqc_data' [2018-02-05 13:01:09,693] multiqc [INFO ] MultiQC complete