[2018-12-13 08:08:18,872] multiqc [DEBUG ] No MultiQC config found: /home/sam/.local/lib/python2.7/site-packages/multiqc-1.6.dev0-py2.7.egg/multiqc_config.yaml [2018-12-13 08:08:18,872] multiqc [DEBUG ] No MultiQC config found: /home/sam/.multiqc_config.yaml [2018-12-13 08:08:18,872] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2018-12-13 08:08:18,873] multiqc [DEBUG ] Command used: /usr/local/bin/multiqc . [2018-12-13 08:08:19,850] multiqc [DEBUG ] Latest MultiQC version is v1.6 [2018-12-13 08:08:19,850] multiqc [INFO ] This is MultiQC v1.6.dev0 [2018-12-13 08:08:19,850] multiqc [DEBUG ] Command : /usr/local/bin/multiqc . [2018-12-13 08:08:19,851] multiqc [DEBUG ] Working dir : /home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_01/20181211_metagenomics_trimmed_fastqc [2018-12-13 08:08:19,851] multiqc [INFO ] Template : default [2018-12-13 08:08:19,851] multiqc [INFO ] Searching '.' [2018-12-13 08:08:19,851] 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 [2018-12-13 08:08:19,869] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpnyZ97q [2018-12-13 08:08:19,913] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Library_Geoduck_MG_6_S5_L002_R2_001_val_2_fastqc.html [2018-12-13 08:08:19,950] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Library_Geoduck_MG_5_S6_L002_R1_001_val_1_fastqc.html [2018-12-13 08:08:19,952] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Library_Geoduck_MG_2_S4_L002_R1_001_val_1_fastqc.html [2018-12-13 08:08:19,953] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Library_Geoduck_MG_3_S1_L002_R1_001_val_1_fastqc.html [2018-12-13 08:08:19,954] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Library_Geoduck_MG_2_S4_L002_R2_001_val_2_fastqc.html [2018-12-13 08:08:19,955] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Library_Geoduck_MG_5_S6_L002_R2_001_val_2_fastqc.html [2018-12-13 08:08:19,955] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Library_Geoduck_MG_6_S5_L002_R1_001_val_1_fastqc.html [2018-12-13 08:08:19,955] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Library_Geoduck_MG_7_S2_L002_R1_001_val_1_fastqc.html [2018-12-13 08:08:19,957] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Library_Geoduck_MG_1_S3_L002_R1_001_val_1_fastqc.html [2018-12-13 08:08:19,957] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Library_Geoduck_MG_3_S1_L002_R2_001_val_2_fastqc.html [2018-12-13 08:08:19,957] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Library_Geoduck_MG_1_S3_L002_R2_001_val_2_fastqc.html [2018-12-13 08:08:19,957] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Library_Geoduck_MG_7_S2_L002_R2_001_val_2_fastqc.html [2018-12-13 08:08:20,982] multiqc [DEBUG ] No samples found: custom_content [2018-12-13 08:08:20,993] multiqc [DEBUG ] No samples found: conpair [2018-12-13 08:08:20,998] multiqc [DEBUG ] No samples found: peddy [2018-12-13 08:08:21,003] multiqc [DEBUG ] No samples found: methylQA [2018-12-13 08:08:21,010] multiqc [DEBUG ] No samples found: qualimap [2018-12-13 08:08:21,015] multiqc [DEBUG ] No samples found: preseq [2018-12-13 08:08:21,020] multiqc [DEBUG ] No samples found: quast [2018-12-13 08:08:21,025] multiqc [DEBUG ] No samples found: qorts [2018-12-13 08:08:21,030] multiqc [DEBUG ] No samples found: rna_seqc [2018-12-13 08:08:21,034] multiqc [DEBUG ] No samples found: rsem [2018-12-13 08:08:21,042] multiqc [DEBUG ] No samples found: rseqc [2018-12-13 08:08:21,059] multiqc [DEBUG ] No samples found: busco [2018-12-13 08:08:21,064] multiqc [DEBUG ] No samples found: goleft_indexcov [2018-12-13 08:08:21,069] multiqc [DEBUG ] No samples found: disambiguate [2018-12-13 08:08:21,074] multiqc [DEBUG ] No samples found: supernova [2018-12-13 08:08:21,081] multiqc [DEBUG ] No samples found: deeptools [2018-12-13 08:08:21,086] multiqc [DEBUG ] No samples found: sargasso [2018-12-13 08:08:21,091] multiqc [DEBUG ] No samples found: verifybamid [2018-12-13 08:08:21,097] multiqc [DEBUG ] No samples found: homer [2018-12-13 08:08:21,102] multiqc [DEBUG ] No samples found: macs2 [2018-12-13 08:08:21,106] multiqc [DEBUG ] No samples found: theta2 [2018-12-13 08:08:21,112] multiqc [DEBUG ] No samples found: snpeff [2018-12-13 08:08:21,118] multiqc [DEBUG ] No samples found: gatk [2018-12-13 08:08:21,123] multiqc [DEBUG ] No samples found: htseq [2018-12-13 08:08:21,128] multiqc [DEBUG ] No samples found: bcftools [2018-12-13 08:08:21,133] multiqc [DEBUG ] No samples found: featureCounts [2018-12-13 08:08:21,138] multiqc [DEBUG ] No samples found: dedup [2018-12-13 08:08:21,147] multiqc [DEBUG ] No samples found: picard [2018-12-13 08:08:21,151] multiqc [DEBUG ] No samples found: prokka [2018-12-13 08:08:21,156] multiqc [DEBUG ] No samples found: samblaster [2018-12-13 08:08:21,163] multiqc [DEBUG ] No samples found: samtools [2018-12-13 08:08:21,169] multiqc [DEBUG ] No samples found: bamtools [2018-12-13 08:08:21,174] multiqc [DEBUG ] No samples found: jellyfish [2018-12-13 08:08:21,180] multiqc [DEBUG ] No samples found: vcftools [2018-12-13 08:08:21,189] multiqc [DEBUG ] No samples found: bbmap [2018-12-13 08:08:21,194] multiqc [DEBUG ] No samples found: bismark [2018-12-13 08:08:21,199] multiqc [DEBUG ] No samples found: hicexplorer [2018-12-13 08:08:21,203] multiqc [DEBUG ] No samples found: hicup [2018-12-13 08:08:21,208] multiqc [DEBUG ] No samples found: salmon [2018-12-13 08:08:21,213] multiqc [DEBUG ] No samples found: kallisto [2018-12-13 08:08:21,218] multiqc [DEBUG ] No samples found: slamdunk [2018-12-13 08:08:21,223] multiqc [DEBUG ] No samples found: star [2018-12-13 08:08:21,228] multiqc [DEBUG ] No samples found: hisat2 [2018-12-13 08:08:21,232] multiqc [DEBUG ] No samples found: tophat [2018-12-13 08:08:21,238] multiqc [DEBUG ] No samples found: bowtie2 [2018-12-13 08:08:21,243] multiqc [DEBUG ] No samples found: bowtie1 [2018-12-13 08:08:21,248] multiqc [DEBUG ] No samples found: leehom [2018-12-13 08:08:21,253] multiqc [DEBUG ] No samples found: adapterRemoval [2018-12-13 08:08:21,258] multiqc [DEBUG ] No samples found: clipandmerge [2018-12-13 08:08:21,263] multiqc [DEBUG ] No samples found: cutadapt [2018-12-13 08:08:21,267] multiqc [DEBUG ] No samples found: flexbar [2018-12-13 08:08:21,272] multiqc [DEBUG ] No samples found: trimmomatic [2018-12-13 08:08:21,277] multiqc [DEBUG ] No samples found: skewer [2018-12-13 08:08:21,282] multiqc [DEBUG ] No samples found: sortmerna [2018-12-13 08:08:21,287] multiqc [DEBUG ] No samples found: biobloomtools [2018-12-13 08:08:21,292] multiqc [DEBUG ] No samples found: fastq_screen [2018-12-13 08:08:21,297] multiqc [DEBUG ] No samples found: afterqc [2018-12-13 08:08:22,459] multiqc.modules.fastqc.fastqc [INFO ] Found 12 reports [2018-12-13 08:08:22,963] multiqc [DEBUG ] No samples found: clusterflow [2018-12-13 08:08:22,968] multiqc [DEBUG ] No samples found: bcl2fastq [2018-12-13 08:08:22,974] multiqc [DEBUG ] No samples found: interop [2018-12-13 08:08:22,998] multiqc [INFO ] Compressing plot data [2018-12-13 08:08:24,028] multiqc [INFO ] Report : multiqc_report.html [2018-12-13 08:08:24,029] multiqc [INFO ] Data : multiqc_data [2018-12-13 08:08:24,029] multiqc [DEBUG ] Moving data file from '/tmp/tmpnyZ97q/multiqc_data/multiqc_sources.txt' to '/home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_01/20181211_metagenomics_trimmed_fastqc/multiqc_data' [2018-12-13 08:08:24,029] multiqc [DEBUG ] Moving data file from '/tmp/tmpnyZ97q/multiqc_data/multiqc_data.json' to '/home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_01/20181211_metagenomics_trimmed_fastqc/multiqc_data' [2018-12-13 08:08:24,029] multiqc [DEBUG ] Moving data file from '/tmp/tmpnyZ97q/multiqc_data/multiqc_general_stats.txt' to '/home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_01/20181211_metagenomics_trimmed_fastqc/multiqc_data' [2018-12-13 08:08:24,029] multiqc [DEBUG ] Moving data file from '/tmp/tmpnyZ97q/multiqc_data/multiqc_fastqc.txt' to '/home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_01/20181211_metagenomics_trimmed_fastqc/multiqc_data' [2018-12-13 08:08:24,261] multiqc [INFO ] MultiQC complete