[2018-12-16 06:55:52,474] multiqc [DEBUG ] No MultiQC config found: /home/sam/.local/lib/python2.7/site-packages/multiqc-1.6.dev0-py2.7.egg/multiqc_config.yaml [2018-12-16 06:55:52,474] multiqc [DEBUG ] No MultiQC config found: /home/sam/.multiqc_config.yaml [2018-12-16 06:55:52,474] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2018-12-16 06:55:52,474] multiqc [DEBUG ] Command used: /usr/local/bin/multiqc . [2018-12-16 06:55:53,666] multiqc [DEBUG ] Latest MultiQC version is v1.6 [2018-12-16 06:55:53,666] multiqc [INFO ] This is MultiQC v1.6.dev0 [2018-12-16 06:55:53,666] multiqc [DEBUG ] Command : /usr/local/bin/multiqc . [2018-12-16 06:55:53,666] multiqc [DEBUG ] Working dir : /home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_03/20181211_metagenomics_trimmed_fastqc [2018-12-16 06:55:53,666] multiqc [INFO ] Template : default [2018-12-16 06:55:53,666] multiqc [INFO ] Searching '.' [2018-12-16 06:55:53,667] 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 [2018-12-16 06:55:53,680] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpjOo9OR [2018-12-16 06:55:53,787] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2_val_2_fastqc.html [2018-12-16 06:55:53,788] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2_val_2_fastqc.html [2018-12-16 06:55:53,790] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2_val_2_fastqc.html [2018-12-16 06:55:53,790] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1_val_1_fastqc.html [2018-12-16 06:55:53,790] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1_val_1_fastqc.html [2018-12-16 06:55:53,790] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Library_Geoduck_MG_7_S2_L002_R2_001_val_2_val_2_val_2_fastqc.html [2018-12-16 06:55:53,791] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1_val_1_fastqc.html [2018-12-16 06:55:53,791] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1_val_1_fastqc.html [2018-12-16 06:55:53,791] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1_val_1_fastqc.html [2018-12-16 06:55:53,791] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2_val_2_fastqc.html [2018-12-16 06:55:53,792] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2_val_2_fastqc.html [2018-12-16 06:55:53,794] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1_val_1_fastqc.html [2018-12-16 06:55:54,836] multiqc [DEBUG ] No samples found: custom_content [2018-12-16 06:55:54,851] multiqc [DEBUG ] No samples found: conpair [2018-12-16 06:55:54,856] multiqc [DEBUG ] No samples found: peddy [2018-12-16 06:55:54,861] multiqc [DEBUG ] No samples found: methylQA [2018-12-16 06:55:54,868] multiqc [DEBUG ] No samples found: qualimap [2018-12-16 06:55:54,872] multiqc [DEBUG ] No samples found: preseq [2018-12-16 06:55:54,877] multiqc [DEBUG ] No samples found: quast [2018-12-16 06:55:54,882] multiqc [DEBUG ] No samples found: qorts [2018-12-16 06:55:54,887] multiqc [DEBUG ] No samples found: rna_seqc [2018-12-16 06:55:54,891] multiqc [DEBUG ] No samples found: rsem [2018-12-16 06:55:54,899] multiqc [DEBUG ] No samples found: rseqc [2018-12-16 06:55:54,904] multiqc [DEBUG ] No samples found: busco [2018-12-16 06:55:54,909] multiqc [DEBUG ] No samples found: goleft_indexcov [2018-12-16 06:55:54,913] multiqc [DEBUG ] No samples found: disambiguate [2018-12-16 06:55:54,918] multiqc [DEBUG ] No samples found: supernova [2018-12-16 06:55:54,924] multiqc [DEBUG ] No samples found: deeptools [2018-12-16 06:55:54,929] multiqc [DEBUG ] No samples found: sargasso [2018-12-16 06:55:54,933] multiqc [DEBUG ] No samples found: verifybamid [2018-12-16 06:55:54,939] multiqc [DEBUG ] No samples found: homer [2018-12-16 06:55:54,944] multiqc [DEBUG ] No samples found: macs2 [2018-12-16 06:55:54,948] multiqc [DEBUG ] No samples found: theta2 [2018-12-16 06:55:54,953] multiqc [DEBUG ] No samples found: snpeff [2018-12-16 06:55:54,959] multiqc [DEBUG ] No samples found: gatk [2018-12-16 06:55:54,964] multiqc [DEBUG ] No samples found: htseq [2018-12-16 06:55:54,968] multiqc [DEBUG ] No samples found: bcftools [2018-12-16 06:55:54,973] multiqc [DEBUG ] No samples found: featureCounts [2018-12-16 06:55:54,977] multiqc [DEBUG ] No samples found: dedup [2018-12-16 06:55:54,985] multiqc [DEBUG ] No samples found: picard [2018-12-16 06:55:54,990] multiqc [DEBUG ] No samples found: prokka [2018-12-16 06:55:54,994] multiqc [DEBUG ] No samples found: samblaster [2018-12-16 06:55:55,000] multiqc [DEBUG ] No samples found: samtools [2018-12-16 06:55:55,005] multiqc [DEBUG ] No samples found: bamtools [2018-12-16 06:55:55,010] multiqc [DEBUG ] No samples found: jellyfish [2018-12-16 06:55:55,015] multiqc [DEBUG ] No samples found: vcftools [2018-12-16 06:55:55,023] multiqc [DEBUG ] No samples found: bbmap [2018-12-16 06:55:55,028] multiqc [DEBUG ] No samples found: bismark [2018-12-16 06:55:55,033] multiqc [DEBUG ] No samples found: hicexplorer [2018-12-16 06:55:55,037] multiqc [DEBUG ] No samples found: hicup [2018-12-16 06:55:55,042] multiqc [DEBUG ] No samples found: salmon [2018-12-16 06:55:55,046] multiqc [DEBUG ] No samples found: kallisto [2018-12-16 06:55:55,051] multiqc [DEBUG ] No samples found: slamdunk [2018-12-16 06:55:55,056] multiqc [DEBUG ] No samples found: star [2018-12-16 06:55:55,061] multiqc [DEBUG ] No samples found: hisat2 [2018-12-16 06:55:55,065] multiqc [DEBUG ] No samples found: tophat [2018-12-16 06:55:55,070] multiqc [DEBUG ] No samples found: bowtie2 [2018-12-16 06:55:55,075] multiqc [DEBUG ] No samples found: bowtie1 [2018-12-16 06:55:55,080] multiqc [DEBUG ] No samples found: leehom [2018-12-16 06:55:55,085] multiqc [DEBUG ] No samples found: adapterRemoval [2018-12-16 06:55:55,090] multiqc [DEBUG ] No samples found: clipandmerge [2018-12-16 06:55:55,094] multiqc [DEBUG ] No samples found: cutadapt [2018-12-16 06:55:55,099] multiqc [DEBUG ] No samples found: flexbar [2018-12-16 06:55:55,103] multiqc [DEBUG ] No samples found: trimmomatic [2018-12-16 06:55:55,108] multiqc [DEBUG ] No samples found: skewer [2018-12-16 06:55:55,112] multiqc [DEBUG ] No samples found: sortmerna [2018-12-16 06:55:55,117] multiqc [DEBUG ] No samples found: biobloomtools [2018-12-16 06:55:55,122] multiqc [DEBUG ] No samples found: fastq_screen [2018-12-16 06:55:55,126] multiqc [DEBUG ] No samples found: afterqc [2018-12-16 06:55:57,093] multiqc.modules.fastqc.fastqc [INFO ] Found 12 reports [2018-12-16 06:55:58,535] multiqc [DEBUG ] No samples found: clusterflow [2018-12-16 06:55:58,540] multiqc [DEBUG ] No samples found: bcl2fastq [2018-12-16 06:55:58,546] multiqc [DEBUG ] No samples found: interop [2018-12-16 06:55:58,569] multiqc [INFO ] Compressing plot data [2018-12-16 06:55:59,842] multiqc [INFO ] Report : multiqc_report.html [2018-12-16 06:55:59,842] multiqc [INFO ] Data : multiqc_data [2018-12-16 06:55:59,842] multiqc [DEBUG ] Moving data file from '/tmp/tmpjOo9OR/multiqc_data/multiqc_sources.txt' to '/home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_03/20181211_metagenomics_trimmed_fastqc/multiqc_data' [2018-12-16 06:55:59,842] multiqc [DEBUG ] Moving data file from '/tmp/tmpjOo9OR/multiqc_data/multiqc_data.json' to '/home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_03/20181211_metagenomics_trimmed_fastqc/multiqc_data' [2018-12-16 06:55:59,842] multiqc [DEBUG ] Moving data file from '/tmp/tmpjOo9OR/multiqc_data/multiqc_general_stats.txt' to '/home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_03/20181211_metagenomics_trimmed_fastqc/multiqc_data' [2018-12-16 06:55:59,842] multiqc [DEBUG ] Moving data file from '/tmp/tmpjOo9OR/multiqc_data/multiqc_fastqc.txt' to '/home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_03/20181211_metagenomics_trimmed_fastqc/multiqc_data' [2018-12-16 06:56:00,073] multiqc [INFO ] MultiQC complete