[2018-01-29 13:42:13,140] 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 13:42:13,140] multiqc [DEBUG ] No MultiQC config found: /home/sam/.multiqc_config.yaml [2018-01-29 13:42:13,140] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2018-01-29 13:42:13,140] multiqc [DEBUG ] Command used: /home/shared/anaconda3/bin/multiqc /home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_fastqc_01/ [2018-01-29 13:42:13,571] multiqc [DEBUG ] Latest MultiQC version is v1.4 [2018-01-29 13:42:13,571] multiqc [INFO ] This is MultiQC v1.5.dev0 [2018-01-29 13:42:13,572] multiqc [DEBUG ] Command : /home/shared/anaconda3/bin/multiqc /home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_fastqc_01/ [2018-01-29 13:42:13,572] multiqc [DEBUG ] Working dir : /home/sam/data/geoduck_illumina/trimmed [2018-01-29 13:42:13,572] multiqc [INFO ] Template : default [2018-01-29 13:42:13,572] multiqc [INFO ] Searching '/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_fastqc_01/' [2018-01-29 13:42:13,573] 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 13:42:13,573] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmp4x3km9rj [2018-01-29 13:42:13,629] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR021_S8_L001_R1_001_val_1_fastqc.html [2018-01-29 13:42:13,630] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR012_S1_L002_R1_001_val_1_fastqc.html [2018-01-29 13:42:13,630] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR005_S4_L002_R1_001_val_1_fastqc.html [2018-01-29 13:42:13,646] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR012_S1_L001_R2_001_val_2_fastqc.html [2018-01-29 13:42:13,647] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR006_S3_L001_R1_001_val_1_fastqc.html [2018-01-29 13:42:13,647] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR006_S3_L002_R1_001_val_1_fastqc.html [2018-01-29 13:42:13,647] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR006_S3_L002_R2_001_val_2_fastqc.html [2018-01-29 13:42:13,648] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR015_AD015_S6_L001_R1_001_val_1_fastqc.html [2018-01-29 13:42:13,648] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR021_S8_L001_R2_001_val_2_fastqc.html [2018-01-29 13:42:13,649] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR019_S7_L002_R2_001_val_2_fastqc.html [2018-01-29 13:42:13,649] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR005_S4_L001_R2_001_val_2_fastqc.html [2018-01-29 13:42:13,649] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR015_AD015_S6_L001_R2_001_val_2_fastqc.html [2018-01-29 13:42:13,650] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR012_S1_L001_R1_001_val_1_fastqc.html [2018-01-29 13:42:13,651] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR013_AD013_S2_L001_R2_001_val_2_fastqc.html [2018-01-29 13:42:13,652] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR013_AD013_S2_L002_R2_001_val_2_fastqc.html [2018-01-29 13:42:13,652] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR019_S7_L002_R1_001_val_1_fastqc.html [2018-01-29 13:42:13,652] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR014_AD014_S5_L001_R1_001_val_1_fastqc.html [2018-01-29 13:42:13,653] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR019_S7_L001_R2_001_val_2_fastqc.html [2018-01-29 13:42:13,653] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR015_AD015_S6_L002_R2_001_val_2_fastqc.html [2018-01-29 13:42:13,653] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR014_AD014_S5_L002_R1_001_val_1_fastqc.html [2018-01-29 13:42:13,653] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR013_AD013_S2_L002_R1_001_val_1_fastqc.html [2018-01-29 13:42:13,654] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR005_S4_L001_R1_001_val_1_fastqc.html [2018-01-29 13:42:13,655] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: AD002_S9_L001_R2_001_val_2_fastqc.html [2018-01-29 13:42:13,655] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR021_S8_L002_R1_001_val_1_fastqc.html [2018-01-29 13:42:13,656] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR005_S4_L002_R2_001_val_2_fastqc.html [2018-01-29 13:42:13,656] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: AD002_S9_L002_R2_001_val_2_fastqc.html [2018-01-29 13:42:13,656] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR021_S8_L002_R2_001_val_2_fastqc.html [2018-01-29 13:42:13,657] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR014_AD014_S5_L002_R2_001_val_2_fastqc.html [2018-01-29 13:42:13,657] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: AD002_S9_L002_R1_001_val_1_fastqc.html [2018-01-29 13:42:13,657] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR012_S1_L002_R2_001_val_2_fastqc.html [2018-01-29 13:42:13,658] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR014_AD014_S5_L001_R2_001_val_2_fastqc.html [2018-01-29 13:42:13,658] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR013_AD013_S2_L001_R1_001_val_1_fastqc.html [2018-01-29 13:42:13,658] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR019_S7_L001_R1_001_val_1_fastqc.html [2018-01-29 13:42:13,658] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR006_S3_L001_R2_001_val_2_fastqc.html [2018-01-29 13:42:13,660] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NR015_AD015_S6_L002_R1_001_val_1_fastqc.html [2018-01-29 13:42:13,660] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: AD002_S9_L001_R1_001_val_1_fastqc.html [2018-01-29 13:42:14,568] multiqc [DEBUG ] No samples found: afterqc [2018-01-29 13:42:14,612] multiqc [DEBUG ] No samples found: custom_content [2018-01-29 13:42:14,631] multiqc [DEBUG ] No samples found: conpair [2018-01-29 13:42:14,641] multiqc [DEBUG ] No samples found: peddy [2018-01-29 13:42:14,654] multiqc [DEBUG ] No samples found: methylQA [2018-01-29 13:42:14,665] multiqc [DEBUG ] No samples found: qualimap [2018-01-29 13:42:14,679] multiqc [DEBUG ] No samples found: preseq [2018-01-29 13:42:14,684] multiqc [DEBUG ] No samples found: quast [2018-01-29 13:42:14,691] multiqc [DEBUG ] No samples found: qorts [2018-01-29 13:42:14,696] multiqc [DEBUG ] No samples found: rna_seqc [2018-01-29 13:42:14,701] multiqc [DEBUG ] No samples found: rsem [2018-01-29 13:42:14,712] multiqc [DEBUG ] No samples found: rseqc [2018-01-29 13:42:14,724] multiqc [DEBUG ] No samples found: busco [2018-01-29 13:42:14,741] multiqc [DEBUG ] No samples found: goleft_indexcov [2018-01-29 13:42:14,762] multiqc [DEBUG ] No samples found: disambiguate [2018-01-29 13:42:14,779] multiqc [DEBUG ] No samples found: supernova [2018-01-29 13:42:14,798] multiqc [DEBUG ] No samples found: deeptools [2018-01-29 13:42:14,814] multiqc [DEBUG ] No samples found: sargasso [2018-01-29 13:42:14,819] multiqc [DEBUG ] No samples found: verifybamid [2018-01-29 13:42:14,845] multiqc [DEBUG ] No samples found: homer [2018-01-29 13:42:14,851] multiqc [DEBUG ] No samples found: macs2 [2018-01-29 13:42:14,856] multiqc [DEBUG ] No samples found: theta2 [2018-01-29 13:42:14,867] multiqc [DEBUG ] No samples found: snpeff [2018-01-29 13:42:14,890] multiqc [DEBUG ] No samples found: gatk [2018-01-29 13:42:14,898] multiqc [DEBUG ] No samples found: htseq [2018-01-29 13:42:14,922] multiqc [DEBUG ] No samples found: bcftools [2018-01-29 13:42:14,942] multiqc [DEBUG ] No samples found: featureCounts [2018-01-29 13:42:14,958] multiqc [DEBUG ] No samples found: picard [2018-01-29 13:42:14,963] multiqc [DEBUG ] No samples found: prokka [2018-01-29 13:42:14,972] multiqc [DEBUG ] No samples found: samblaster [2018-01-29 13:42:14,979] multiqc [DEBUG ] No samples found: samtools [2018-01-29 13:42:15,002] multiqc [DEBUG ] No samples found: bamtools [2018-01-29 13:42:15,007] multiqc [DEBUG ] No samples found: jellyfish [2018-01-29 13:42:15,015] multiqc [DEBUG ] No samples found: vcftools [2018-01-29 13:42:15,037] multiqc [DEBUG ] No samples found: bbmap [2018-01-29 13:42:15,048] multiqc [DEBUG ] No samples found: bismark [2018-01-29 13:42:15,059] multiqc [DEBUG ] No samples found: hicexplorer [2018-01-29 13:42:15,064] multiqc [DEBUG ] No samples found: hicup [2018-01-29 13:42:15,070] multiqc [DEBUG ] No samples found: salmon [2018-01-29 13:42:15,075] multiqc [DEBUG ] No samples found: kallisto [2018-01-29 13:42:15,092] multiqc [DEBUG ] No samples found: slamdunk [2018-01-29 13:42:15,097] multiqc [DEBUG ] No samples found: star [2018-01-29 13:42:15,115] multiqc [DEBUG ] No samples found: hisat2 [2018-01-29 13:42:15,138] multiqc [DEBUG ] No samples found: tophat [2018-01-29 13:42:15,171] multiqc [DEBUG ] No samples found: bowtie2 [2018-01-29 13:42:15,181] multiqc [DEBUG ] No samples found: bowtie1 [2018-01-29 13:42:15,204] multiqc [DEBUG ] No samples found: leehom [2018-01-29 13:42:15,226] multiqc [DEBUG ] No samples found: adapterRemoval [2018-01-29 13:42:15,239] multiqc [DEBUG ] No samples found: cutadapt [2018-01-29 13:42:15,254] multiqc [DEBUG ] No samples found: flexbar [2018-01-29 13:42:15,259] multiqc [DEBUG ] No samples found: trimmomatic [2018-01-29 13:42:15,275] multiqc [DEBUG ] No samples found: skewer [2018-01-29 13:42:15,280] multiqc [DEBUG ] No samples found: sortmerna [2018-01-29 13:42:15,317] multiqc [DEBUG ] No samples found: biobloomtools [2018-01-29 13:42:15,334] multiqc [DEBUG ] No samples found: fastq_screen [2018-01-29 13:42:22,564] multiqc.modules.fastqc.fastqc [INFO ] Found 36 reports [2018-01-29 13:42:23,031] multiqc [DEBUG ] No samples found: clusterflow [2018-01-29 13:42:23,045] multiqc [DEBUG ] No samples found: bcl2fastq [2018-01-29 13:42:23,058] multiqc [DEBUG ] No samples found: interop [2018-01-29 13:42:23,131] multiqc [INFO ] Compressing plot data [2018-01-29 13:42:24,069] multiqc [INFO ] Report : multiqc_report.html [2018-01-29 13:42:24,070] multiqc [INFO ] Data : multiqc_data [2018-01-29 13:42:24,070] multiqc [DEBUG ] Moving data file from '/tmp/tmp4x3km9rj/multiqc_data/multiqc_general_stats.txt' to '/home/sam/data/geoduck_illumina/trimmed/multiqc_data' [2018-01-29 13:42:24,070] multiqc [DEBUG ] Moving data file from '/tmp/tmp4x3km9rj/multiqc_data/multiqc_fastqc.txt' to '/home/sam/data/geoduck_illumina/trimmed/multiqc_data' [2018-01-29 13:42:24,070] multiqc [DEBUG ] Moving data file from '/tmp/tmp4x3km9rj/multiqc_data/multiqc_data.json' to '/home/sam/data/geoduck_illumina/trimmed/multiqc_data' [2018-01-29 13:42:24,070] multiqc [DEBUG ] Moving data file from '/tmp/tmp4x3km9rj/multiqc_data/multiqc_sources.txt' to '/home/sam/data/geoduck_illumina/trimmed/multiqc_data' [2018-01-29 13:42:24,303] multiqc [INFO ] MultiQC complete