[2018-12-12 14:15:55,515] multiqc [DEBUG ] No MultiQC config found: /home/sam/.local/lib/python2.7/site-packages/multiqc-1.6.dev0-py2.7.egg/multiqc_config.yaml [2018-12-12 14:15:55,515] multiqc [DEBUG ] No MultiQC config found: /home/sam/.multiqc_config.yaml [2018-12-12 14:15:55,515] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2018-12-12 14:15:55,515] multiqc [DEBUG ] Command used: /usr/local/bin/multiqc . [2018-12-12 14:15:56,557] multiqc [DEBUG ] Latest MultiQC version is v1.6 [2018-12-12 14:15:56,557] multiqc [INFO ] This is MultiQC v1.6.dev0 [2018-12-12 14:15:56,558] multiqc [DEBUG ] Command : /usr/local/bin/multiqc . [2018-12-12 14:15:56,558] multiqc [DEBUG ] Working dir : /home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_fastqc [2018-12-12 14:15:56,558] multiqc [INFO ] Template : default [2018-12-12 14:15:56,558] multiqc [INFO ] Searching '.' [2018-12-12 14:15:56,559] 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 [2018-12-12 14:15:56,559] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpXWjFTU [2018-12-12 14:15:56,626] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Library_Geoduck_MG_3_S1_L002_R2_001_fastqc.html [2018-12-12 14:15:56,627] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Library_Geoduck_MG_1_S3_L002_R2_001_fastqc.html [2018-12-12 14:15:56,627] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Library_Geoduck_MG_5_S6_L002_R1_001_fastqc.html [2018-12-12 14:15:56,627] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Library_Geoduck_MG_2_S4_L002_R1_001_fastqc.html [2018-12-12 14:15:56,627] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Library_Geoduck_MG_6_S5_L002_R1_001_fastqc.html [2018-12-12 14:15:56,628] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Library_Geoduck_MG_5_S6_L002_R2_001_fastqc.html [2018-12-12 14:15:56,628] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Library_Geoduck_MG_7_S2_L002_R1_001_fastqc.html [2018-12-12 14:15:56,628] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Library_Geoduck_MG_7_S2_L002_R2_001_fastqc.html [2018-12-12 14:15:56,628] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Library_Geoduck_MG_2_S4_L002_R2_001_fastqc.html [2018-12-12 14:15:56,631] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Library_Geoduck_MG_1_S3_L002_R1_001_fastqc.html [2018-12-12 14:15:56,633] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Library_Geoduck_MG_3_S1_L002_R1_001_fastqc.html [2018-12-12 14:15:56,633] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Library_Geoduck_MG_6_S5_L002_R2_001_fastqc.html [2018-12-12 14:15:56,634] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: fastqc_report.html [2018-12-12 14:15:56,665] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: fastqc_report.html [2018-12-12 14:15:56,692] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: fastqc_report.html [2018-12-12 14:15:56,719] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: fastqc_report.html [2018-12-12 14:15:56,746] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: fastqc_report.html [2018-12-12 14:15:56,773] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: fastqc_report.html [2018-12-12 14:15:56,800] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: fastqc_report.html [2018-12-12 14:15:56,827] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: fastqc_report.html [2018-12-12 14:15:56,854] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: fastqc_report.html [2018-12-12 14:15:56,881] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: fastqc_report.html [2018-12-12 14:15:56,908] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: fastqc_report.html [2018-12-12 14:15:56,935] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: fastqc_report.html [2018-12-12 14:15:57,967] multiqc [DEBUG ] No samples found: custom_content [2018-12-12 14:15:57,978] multiqc [DEBUG ] No samples found: conpair [2018-12-12 14:15:57,983] multiqc [DEBUG ] No samples found: peddy [2018-12-12 14:15:57,989] multiqc [DEBUG ] No samples found: methylQA [2018-12-12 14:15:57,995] multiqc [DEBUG ] No samples found: qualimap [2018-12-12 14:15:58,000] multiqc [DEBUG ] No samples found: preseq [2018-12-12 14:15:58,005] multiqc [DEBUG ] No samples found: quast [2018-12-12 14:15:58,009] multiqc [DEBUG ] No samples found: qorts [2018-12-12 14:15:58,014] multiqc [DEBUG ] No samples found: rna_seqc [2018-12-12 14:15:58,019] multiqc [DEBUG ] No samples found: rsem [2018-12-12 14:15:58,026] multiqc [DEBUG ] No samples found: rseqc [2018-12-12 14:15:58,031] multiqc [DEBUG ] No samples found: busco [2018-12-12 14:15:58,036] multiqc [DEBUG ] No samples found: goleft_indexcov [2018-12-12 14:15:58,041] multiqc [DEBUG ] No samples found: disambiguate [2018-12-12 14:15:58,046] multiqc [DEBUG ] No samples found: supernova [2018-12-12 14:15:58,052] multiqc [DEBUG ] No samples found: deeptools [2018-12-12 14:15:58,057] multiqc [DEBUG ] No samples found: sargasso [2018-12-12 14:15:58,062] multiqc [DEBUG ] No samples found: verifybamid [2018-12-12 14:15:58,067] multiqc [DEBUG ] No samples found: homer [2018-12-12 14:15:58,072] multiqc [DEBUG ] No samples found: macs2 [2018-12-12 14:15:58,077] multiqc [DEBUG ] No samples found: theta2 [2018-12-12 14:15:58,081] multiqc [DEBUG ] No samples found: snpeff [2018-12-12 14:15:58,087] multiqc [DEBUG ] No samples found: gatk [2018-12-12 14:15:58,091] multiqc [DEBUG ] No samples found: htseq [2018-12-12 14:15:58,096] multiqc [DEBUG ] No samples found: bcftools [2018-12-12 14:15:58,100] multiqc [DEBUG ] No samples found: featureCounts [2018-12-12 14:15:58,105] multiqc [DEBUG ] No samples found: dedup [2018-12-12 14:15:58,113] multiqc [DEBUG ] No samples found: picard [2018-12-12 14:15:58,117] multiqc [DEBUG ] No samples found: prokka [2018-12-12 14:15:58,122] multiqc [DEBUG ] No samples found: samblaster [2018-12-12 14:15:58,128] multiqc [DEBUG ] No samples found: samtools [2018-12-12 14:15:58,132] multiqc [DEBUG ] No samples found: bamtools [2018-12-12 14:15:58,137] multiqc [DEBUG ] No samples found: jellyfish [2018-12-12 14:15:58,143] multiqc [DEBUG ] No samples found: vcftools [2018-12-12 14:15:58,151] multiqc [DEBUG ] No samples found: bbmap [2018-12-12 14:15:58,155] multiqc [DEBUG ] No samples found: bismark [2018-12-12 14:15:58,160] multiqc [DEBUG ] No samples found: hicexplorer [2018-12-12 14:15:58,165] multiqc [DEBUG ] No samples found: hicup [2018-12-12 14:15:58,169] multiqc [DEBUG ] No samples found: salmon [2018-12-12 14:15:58,174] multiqc [DEBUG ] No samples found: kallisto [2018-12-12 14:15:58,178] multiqc [DEBUG ] No samples found: slamdunk [2018-12-12 14:15:58,183] multiqc [DEBUG ] No samples found: star [2018-12-12 14:15:58,187] multiqc [DEBUG ] No samples found: hisat2 [2018-12-12 14:15:58,192] multiqc [DEBUG ] No samples found: tophat [2018-12-12 14:15:58,196] multiqc [DEBUG ] No samples found: bowtie2 [2018-12-12 14:15:58,201] multiqc [DEBUG ] No samples found: bowtie1 [2018-12-12 14:15:58,205] multiqc [DEBUG ] No samples found: leehom [2018-12-12 14:15:58,210] multiqc [DEBUG ] No samples found: adapterRemoval [2018-12-12 14:15:58,214] multiqc [DEBUG ] No samples found: clipandmerge [2018-12-12 14:15:58,219] multiqc [DEBUG ] No samples found: cutadapt [2018-12-12 14:15:58,223] multiqc [DEBUG ] No samples found: flexbar [2018-12-12 14:15:58,227] multiqc [DEBUG ] No samples found: trimmomatic [2018-12-12 14:15:58,232] multiqc [DEBUG ] No samples found: skewer [2018-12-12 14:15:58,236] multiqc [DEBUG ] No samples found: sortmerna [2018-12-12 14:15:58,241] multiqc [DEBUG ] No samples found: biobloomtools [2018-12-12 14:15:58,245] multiqc [DEBUG ] No samples found: fastq_screen [2018-12-12 14:15:58,250] multiqc [DEBUG ] No samples found: afterqc [2018-12-12 14:15:59,283] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Library_Geoduck_MG_6_S5_L002_R1_001_fastqc.zip' as already parsed 'Library_Geoduck_MG_6_S5_L002_R1_001' [2018-12-12 14:15:59,283] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Library_Geoduck_MG_7_S2_L002_R1_001_fastqc.zip' as already parsed 'Library_Geoduck_MG_7_S2_L002_R1_001' [2018-12-12 14:15:59,283] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Library_Geoduck_MG_7_S2_L002_R2_001_fastqc.zip' as already parsed 'Library_Geoduck_MG_7_S2_L002_R2_001' [2018-12-12 14:15:59,283] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Library_Geoduck_MG_3_S1_L002_R2_001_fastqc.zip' as already parsed 'Library_Geoduck_MG_3_S1_L002_R2_001' [2018-12-12 14:15:59,283] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Library_Geoduck_MG_3_S1_L002_R1_001_fastqc.zip' as already parsed 'Library_Geoduck_MG_3_S1_L002_R1_001' [2018-12-12 14:15:59,284] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Library_Geoduck_MG_1_S3_L002_R2_001_fastqc.zip' as already parsed 'Library_Geoduck_MG_1_S3_L002_R2_001' [2018-12-12 14:15:59,284] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Library_Geoduck_MG_1_S3_L002_R1_001_fastqc.zip' as already parsed 'Library_Geoduck_MG_1_S3_L002_R1_001' [2018-12-12 14:15:59,284] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Library_Geoduck_MG_6_S5_L002_R2_001_fastqc.zip' as already parsed 'Library_Geoduck_MG_6_S5_L002_R2_001' [2018-12-12 14:15:59,284] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Library_Geoduck_MG_2_S4_L002_R1_001_fastqc.zip' as already parsed 'Library_Geoduck_MG_2_S4_L002_R1_001' [2018-12-12 14:15:59,284] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Library_Geoduck_MG_5_S6_L002_R1_001_fastqc.zip' as already parsed 'Library_Geoduck_MG_5_S6_L002_R1_001' [2018-12-12 14:15:59,285] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Library_Geoduck_MG_2_S4_L002_R2_001_fastqc.zip' as already parsed 'Library_Geoduck_MG_2_S4_L002_R2_001' [2018-12-12 14:15:59,285] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Library_Geoduck_MG_5_S6_L002_R2_001_fastqc.zip' as already parsed 'Library_Geoduck_MG_5_S6_L002_R2_001' [2018-12-12 14:15:59,285] multiqc.modules.fastqc.fastqc [INFO ] Found 12 reports [2018-12-12 14:15:59,801] multiqc [DEBUG ] No samples found: clusterflow [2018-12-12 14:15:59,806] multiqc [DEBUG ] No samples found: bcl2fastq [2018-12-12 14:15:59,811] multiqc [DEBUG ] No samples found: interop [2018-12-12 14:15:59,834] multiqc [INFO ] Compressing plot data [2018-12-12 14:16:00,946] multiqc [INFO ] Report : multiqc_report.html [2018-12-12 14:16:00,947] multiqc [INFO ] Data : multiqc_data [2018-12-12 14:16:00,947] multiqc [DEBUG ] Moving data file from '/tmp/tmpXWjFTU/multiqc_data/multiqc_sources.txt' to '/home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_fastqc/multiqc_data' [2018-12-12 14:16:00,947] multiqc [DEBUG ] Moving data file from '/tmp/tmpXWjFTU/multiqc_data/multiqc_data.json' to '/home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_fastqc/multiqc_data' [2018-12-12 14:16:00,947] multiqc [DEBUG ] Moving data file from '/tmp/tmpXWjFTU/multiqc_data/multiqc_general_stats.txt' to '/home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_fastqc/multiqc_data' [2018-12-12 14:16:00,947] multiqc [DEBUG ] Moving data file from '/tmp/tmpXWjFTU/multiqc_data/multiqc_fastqc.txt' to '/home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_fastqc/multiqc_data' [2018-12-12 14:16:01,179] multiqc [INFO ] MultiQC complete