[2018-04-04 08:52:19,131] multiqc [DEBUG ] No MultiQC config found: /usr/local/lib/python2.7/dist-packages/multiqc-1.6.dev0-py2.7.egg/multiqc_config.yaml [2018-04-04 08:52:19,131] multiqc [DEBUG ] No MultiQC config found: /home/sam/.multiqc_config.yaml [2018-04-04 08:52:19,132] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2018-04-04 08:52:19,132] multiqc [DEBUG ] Command used: /usr/local/bin/multiqc . [2018-04-04 08:52:19,952] multiqc [DEBUG ] Latest MultiQC version is v1.5 [2018-04-04 08:52:19,953] multiqc [INFO ] This is MultiQC v1.6.dev0 [2018-04-04 08:52:19,953] multiqc [DEBUG ] Command : /usr/local/bin/multiqc . [2018-04-04 08:52:19,953] multiqc [DEBUG ] Working dir : /mnt/owl/Athaliana/20180328_fastqc_trimmed_hiseq_geoduck [2018-04-04 08:52:19,953] multiqc [INFO ] Template : default [2018-04-04 08:52:19,953] multiqc [INFO ] Searching '.' [2018-04-04 08:52:19,953] 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, homer, macs2, theta2, snpeff, gatk, htseq, bcftools, featureCounts, dedup, picard, prokka, samblaster, samtools, bamtools, jellyfish, vcftools, bbmap, bismark, hicexplorer, hicup, salmon, kallisto, slamdunk, star, hisat2, tophat, bowtie2, bowtie1, leehom, adapterRemoval, clipandmerge, cutadapt, flexbar, trimmomatic, skewer, sortmerna, biobloomtools, fastq_screen, afterqc, fastqc, clusterflow, bcl2fastq, interop [2018-04-04 08:52:19,954] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpNULZ9E [2018-04-04 08:52:19,982] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-5to7kb-5_S19_L005_R1_001_val_1_fastqc.html [2018-04-04 08:52:19,983] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-2to4kb-4_S14_L004_R1_001_val_1_fastqc.html [2018-04-04 08:52:19,984] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-2to4kb-8_S30_L008_R2_001_val_2_fastqc.html [2018-04-04 08:52:19,984] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-8_S29_L008_R2_001_val_2_fastqc.html [2018-04-04 08:52:19,985] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-8to10kb-6_S24_L006_R2_001_val_2_fastqc.html [2018-04-04 08:52:19,985] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-8to10kb-4_S16_L004_R1_001_val_1_fastqc.html [2018-04-04 08:52:19,987] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-6_S21_L006_R1_001_val_1_fastqc.html [2018-04-04 08:52:19,988] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-2to4kb-1_S2_L001_R2_001_val_2_fastqc.html [2018-04-04 08:52:19,988] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-3_S9_L003_R2_001_val_2_fastqc.html [2018-04-04 08:52:19,988] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-8to10kb-1_S4_L001_R2_001_val_2_fastqc.html [2018-04-04 08:52:19,988] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-8to10kb-7_S28_L007_R2_001_val_2_fastqc.html [2018-04-04 08:52:19,989] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-2to4kb-7_S26_L007_R2_001_val_2_fastqc.html [2018-04-04 08:52:19,990] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-5to7kb-7_S27_L007_R2_001_val_2_fastqc.html [2018-04-04 08:52:19,990] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-8to10kb-2_S8_L002_R1_001_val_1_fastqc.html [2018-04-04 08:52:19,990] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-8to10kb-6_S24_L006_R1_001_val_1_fastqc.html [2018-04-04 08:52:19,991] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-8to10kb-8_S32_L008_R1_001_val_1_fastqc.html [2018-04-04 08:52:19,992] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-2_S5_L002_R1_001_val_1_fastqc.html [2018-04-04 08:52:19,993] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-8to10kb-5_S20_L005_R1_001_val_1_fastqc.html [2018-04-04 08:52:19,993] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-5to7kb-6_S23_L006_R1_001_val_1_fastqc.html [2018-04-04 08:52:19,993] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-8to10kb-4_S16_L004_R2_001_val_2_fastqc.html [2018-04-04 08:52:19,993] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-5to7kb-4_S15_L004_R1_001_val_1_fastqc.html [2018-04-04 08:52:19,995] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-5to7kb-3_S11_L003_R2_001_val_2_fastqc.html [2018-04-04 08:52:19,995] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-5to7kb-8_S31_L008_R2_001_val_2_fastqc.html [2018-04-04 08:52:19,996] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-5to7kb-7_S27_L007_R1_001_val_1_fastqc.html [2018-04-04 08:52:19,996] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-2to4kb-2_S6_L002_R2_001_val_2_fastqc.html [2018-04-04 08:52:19,997] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-5_S17_L005_R1_001_val_1_fastqc.html [2018-04-04 08:52:19,997] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-5to7kb-4_S15_L004_R2_001_val_2_fastqc.html [2018-04-04 08:52:19,997] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-8_S29_L008_R1_001_val_1_fastqc.html [2018-04-04 08:52:19,998] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-2to4kb-6_S22_L006_R1_001_val_1_fastqc.html [2018-04-04 08:52:19,999] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-5to7kb-1_S3_L001_R1_001_val_1_fastqc.html [2018-04-04 08:52:19,999] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-2to4kb-8_S30_L008_R1_001_val_1_fastqc.html [2018-04-04 08:52:20,000] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-2to4kb-5_S18_L005_R1_001_val_1_fastqc.html [2018-04-04 08:52:20,000] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-5to7kb-5_S19_L005_R2_001_val_2_fastqc.html [2018-04-04 08:52:20,001] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-2to4kb-3_S10_L003_R1_001_val_1_fastqc.html [2018-04-04 08:52:20,001] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-2to4kb-3_S10_L003_R2_001_val_2_fastqc.html [2018-04-04 08:52:20,001] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-5to7kb-6_S23_L006_R2_001_val_2_fastqc.html [2018-04-04 08:52:20,002] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-4_S13_L004_R1_001_val_1_fastqc.html [2018-04-04 08:52:20,002] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-8to10kb-7_S28_L007_R1_001_val_1_fastqc.html [2018-04-04 08:52:20,003] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-8to10kb-5_S20_L005_R2_001_val_2_fastqc.html [2018-04-04 08:52:20,004] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-2to4kb-2_S6_L002_R1_001_val_1_fastqc.html [2018-04-04 08:52:20,004] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-7_S25_L007_R1_001_val_1_fastqc.html [2018-04-04 08:52:20,005] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-8to10kb-1_S4_L001_R1_001_val_1_fastqc.html [2018-04-04 08:52:20,005] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-1_S1_L001_R1_001_val_1_fastqc.html [2018-04-04 08:52:20,005] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-5to7kb-8_S31_L008_R1_001_val_1_fastqc.html [2018-04-04 08:52:20,008] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-2to4kb-4_S14_L004_R2_001_val_2_fastqc.html [2018-04-04 08:52:20,009] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-5_S17_L005_R2_001_val_2_fastqc.html [2018-04-04 08:52:20,009] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-6_S21_L006_R2_001_val_2_fastqc.html [2018-04-04 08:52:20,010] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-8to10kb-3_S12_L003_R2_001_val_2_fastqc.html [2018-04-04 08:52:20,011] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-2to4kb-5_S18_L005_R2_001_val_2_fastqc.html [2018-04-04 08:52:20,013] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-2to4kb-7_S26_L007_R1_001_val_1_fastqc.html [2018-04-04 08:52:20,014] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-2to4kb-6_S22_L006_R2_001_val_2_fastqc.html [2018-04-04 08:52:20,016] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-2_S5_L002_R2_001_val_2_fastqc.html [2018-04-04 08:52:20,016] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-5to7kb-1_S3_L001_R2_001_val_2_fastqc.html [2018-04-04 08:52:20,016] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-8to10kb-3_S12_L003_R1_001_val_1_fastqc.html [2018-04-04 08:52:20,016] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-5to7kb-2_S7_L002_R2_001_val_2_fastqc.html [2018-04-04 08:52:20,020] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-2to4kb-1_S2_L001_R1_001_val_1_fastqc.html [2018-04-04 08:52:20,021] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-8to10kb-2_S8_L002_R2_001_val_2_fastqc.html [2018-04-04 08:52:20,022] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-4_S13_L004_R2_001_val_2_fastqc.html [2018-04-04 08:52:20,022] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-3_S9_L003_R1_001_val_1_fastqc.html [2018-04-04 08:52:20,022] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-5to7kb-2_S7_L002_R1_001_val_1_fastqc.html [2018-04-04 08:52:20,023] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-8to10kb-8_S32_L008_R2_001_val_2_fastqc.html [2018-04-04 08:52:20,023] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-7_S25_L007_R2_001_val_2_fastqc.html [2018-04-04 08:52:20,024] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-5to7kb-3_S11_L003_R1_001_val_1_fastqc.html [2018-04-04 08:52:20,025] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-1_S1_L001_R2_001_val_2_fastqc.html [2018-04-04 08:52:20,214] multiqc [DEBUG ] No samples found: custom_content [2018-04-04 08:52:20,218] multiqc [DEBUG ] No samples found: conpair [2018-04-04 08:52:20,223] multiqc [DEBUG ] No samples found: peddy [2018-04-04 08:52:20,228] multiqc [DEBUG ] No samples found: methylQA [2018-04-04 08:52:20,232] multiqc [DEBUG ] No samples found: qualimap [2018-04-04 08:52:20,237] multiqc [DEBUG ] No samples found: preseq [2018-04-04 08:52:20,241] multiqc [DEBUG ] No samples found: quast [2018-04-04 08:52:20,245] multiqc [DEBUG ] No samples found: qorts [2018-04-04 08:52:20,249] multiqc [DEBUG ] No samples found: rna_seqc [2018-04-04 08:52:20,253] multiqc [DEBUG ] No samples found: rsem [2018-04-04 08:52:20,258] multiqc [DEBUG ] No samples found: rseqc [2018-04-04 08:52:20,262] multiqc [DEBUG ] No samples found: busco [2018-04-04 08:52:20,266] multiqc [DEBUG ] No samples found: goleft_indexcov [2018-04-04 08:52:20,271] multiqc [DEBUG ] No samples found: disambiguate [2018-04-04 08:52:20,275] multiqc [DEBUG ] No samples found: supernova [2018-04-04 08:52:20,281] multiqc [DEBUG ] No samples found: deeptools [2018-04-04 08:52:20,285] multiqc [DEBUG ] No samples found: sargasso [2018-04-04 08:52:20,289] multiqc [DEBUG ] No samples found: verifybamid [2018-04-04 08:52:20,294] multiqc [DEBUG ] No samples found: homer [2018-04-04 08:52:20,298] multiqc [DEBUG ] No samples found: macs2 [2018-04-04 08:52:20,302] multiqc [DEBUG ] No samples found: theta2 [2018-04-04 08:52:20,306] multiqc [DEBUG ] No samples found: snpeff [2018-04-04 08:52:20,310] multiqc [DEBUG ] No samples found: gatk [2018-04-04 08:52:20,314] multiqc [DEBUG ] No samples found: htseq [2018-04-04 08:52:20,319] multiqc [DEBUG ] No samples found: bcftools [2018-04-04 08:52:20,323] multiqc [DEBUG ] No samples found: featureCounts [2018-04-04 08:52:20,327] multiqc [DEBUG ] No samples found: dedup [2018-04-04 08:52:20,333] multiqc [DEBUG ] No samples found: picard [2018-04-04 08:52:20,337] multiqc [DEBUG ] No samples found: prokka [2018-04-04 08:52:20,341] multiqc [DEBUG ] No samples found: samblaster [2018-04-04 08:52:20,345] multiqc [DEBUG ] No samples found: samtools [2018-04-04 08:52:20,350] multiqc [DEBUG ] No samples found: bamtools [2018-04-04 08:52:20,354] multiqc [DEBUG ] No samples found: jellyfish [2018-04-04 08:52:20,358] multiqc [DEBUG ] No samples found: vcftools [2018-04-04 08:52:20,364] multiqc [DEBUG ] No samples found: bbmap [2018-04-04 08:52:20,368] multiqc [DEBUG ] No samples found: bismark [2018-04-04 08:52:20,372] multiqc [DEBUG ] No samples found: hicexplorer [2018-04-04 08:52:20,376] multiqc [DEBUG ] No samples found: hicup [2018-04-04 08:52:20,380] multiqc [DEBUG ] No samples found: salmon [2018-04-04 08:52:20,385] multiqc [DEBUG ] No samples found: kallisto [2018-04-04 08:52:20,391] multiqc [DEBUG ] No samples found: slamdunk [2018-04-04 08:52:20,395] multiqc [DEBUG ] No samples found: star [2018-04-04 08:52:20,399] multiqc [DEBUG ] No samples found: hisat2 [2018-04-04 08:52:20,404] multiqc [DEBUG ] No samples found: tophat [2018-04-04 08:52:20,408] multiqc [DEBUG ] No samples found: bowtie2 [2018-04-04 08:52:20,412] multiqc [DEBUG ] No samples found: bowtie1 [2018-04-04 08:52:20,416] multiqc [DEBUG ] No samples found: leehom [2018-04-04 08:52:20,420] multiqc [DEBUG ] No samples found: adapterRemoval [2018-04-04 08:52:20,424] multiqc [DEBUG ] No samples found: clipandmerge [2018-04-04 08:52:20,428] multiqc [DEBUG ] No samples found: cutadapt [2018-04-04 08:52:20,432] multiqc [DEBUG ] No samples found: flexbar [2018-04-04 08:52:20,436] multiqc [DEBUG ] No samples found: trimmomatic [2018-04-04 08:52:20,441] multiqc [DEBUG ] No samples found: skewer [2018-04-04 08:52:20,445] multiqc [DEBUG ] No samples found: sortmerna [2018-04-04 08:52:20,449] multiqc [DEBUG ] No samples found: biobloomtools [2018-04-04 08:52:20,453] multiqc [DEBUG ] No samples found: fastq_screen [2018-04-04 08:52:20,457] multiqc [DEBUG ] No samples found: afterqc [2018-04-04 08:52:28,825] multiqc.modules.fastqc.fastqc [INFO ] Found 64 reports [2018-04-04 08:52:36,171] multiqc [DEBUG ] No samples found: clusterflow [2018-04-04 08:52:36,175] multiqc [DEBUG ] No samples found: bcl2fastq [2018-04-04 08:52:36,180] multiqc [DEBUG ] No samples found: interop [2018-04-04 08:52:36,285] multiqc [INFO ] Compressing plot data [2018-04-04 08:52:45,830] multiqc [INFO ] Report : multiqc_report.html [2018-04-04 08:52:45,830] multiqc [INFO ] Data : multiqc_data [2018-04-04 08:52:45,856] multiqc [DEBUG ] Moving data file from '/tmp/tmpNULZ9E/multiqc_data/multiqc_general_stats.txt' to '/mnt/owl/Athaliana/20180328_fastqc_trimmed_hiseq_geoduck/multiqc_data' [2018-04-04 08:52:45,941] multiqc [DEBUG ] Moving data file from '/tmp/tmpNULZ9E/multiqc_data/multiqc_fastqc.txt' to '/mnt/owl/Athaliana/20180328_fastqc_trimmed_hiseq_geoduck/multiqc_data' [2018-04-04 08:52:45,949] multiqc [DEBUG ] Moving data file from '/tmp/tmpNULZ9E/multiqc_data/multiqc_sources.txt' to '/mnt/owl/Athaliana/20180328_fastqc_trimmed_hiseq_geoduck/multiqc_data' [2018-04-04 08:52:45,955] multiqc [DEBUG ] Moving data file from '/tmp/tmpNULZ9E/multiqc_data/multiqc_data.json' to '/mnt/owl/Athaliana/20180328_fastqc_trimmed_hiseq_geoduck/multiqc_data' [2018-04-04 08:52:46,219] multiqc [INFO ] MultiQC complete