[2018-12-14 01:21:57,554] multiqc [DEBUG ] No MultiQC config found: /home/sam/.local/lib/python2.7/site-packages/multiqc-1.6.dev0-py2.7.egg/multiqc_config.yaml [2018-12-14 01:21:57,554] multiqc [DEBUG ] No MultiQC config found: /home/sam/.multiqc_config.yaml [2018-12-14 01:21:57,554] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2018-12-14 01:21:57,554] multiqc [DEBUG ] Command used: /usr/local/bin/multiqc . [2018-12-14 01:21:58,646] multiqc [DEBUG ] Latest MultiQC version is v1.6 [2018-12-14 01:21:58,646] multiqc [INFO ] This is MultiQC v1.6.dev0 [2018-12-14 01:21:58,646] multiqc [DEBUG ] Command : /usr/local/bin/multiqc . [2018-12-14 01:21:58,646] multiqc [DEBUG ] Working dir : /home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_02/20181211_metagenomics_trimmed_fastqc [2018-12-14 01:21:58,646] multiqc [INFO ] Template : default [2018-12-14 01:21:58,646] multiqc [INFO ] Searching '.' [2018-12-14 01:21:58,647] 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 [2018-12-14 01:21:58,660] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpSTMNbB [2018-12-14 01:21:58,764] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2_fastqc.html [2018-12-14 01:21:58,765] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2_fastqc.html [2018-12-14 01:21:58,766] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1_fastqc.html [2018-12-14 01:21:58,766] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Library_Geoduck_MG_7_S2_L002_R2_001_val_2_val_2_fastqc.html [2018-12-14 01:21:58,766] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2_fastqc.html [2018-12-14 01:21:58,768] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1_fastqc.html [2018-12-14 01:21:58,768] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1_fastqc.html [2018-12-14 01:21:58,769] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2_fastqc.html [2018-12-14 01:21:58,769] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2_fastqc.html [2018-12-14 01:21:58,770] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1_fastqc.html [2018-12-14 01:21:58,771] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1_fastqc.html [2018-12-14 01:21:58,771] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1_fastqc.html [2018-12-14 01:21:59,879] multiqc [DEBUG ] No samples found: custom_content [2018-12-14 01:21:59,894] multiqc [DEBUG ] No samples found: conpair [2018-12-14 01:21:59,899] multiqc [DEBUG ] No samples found: peddy [2018-12-14 01:21:59,904] multiqc [DEBUG ] No samples found: methylQA [2018-12-14 01:21:59,911] multiqc [DEBUG ] No samples found: qualimap [2018-12-14 01:21:59,916] multiqc [DEBUG ] No samples found: preseq [2018-12-14 01:21:59,921] multiqc [DEBUG ] No samples found: quast [2018-12-14 01:21:59,926] multiqc [DEBUG ] No samples found: qorts [2018-12-14 01:21:59,931] multiqc [DEBUG ] No samples found: rna_seqc [2018-12-14 01:21:59,936] multiqc [DEBUG ] No samples found: rsem [2018-12-14 01:21:59,944] multiqc [DEBUG ] No samples found: rseqc [2018-12-14 01:21:59,949] multiqc [DEBUG ] No samples found: busco [2018-12-14 01:21:59,954] multiqc [DEBUG ] No samples found: goleft_indexcov [2018-12-14 01:21:59,958] multiqc [DEBUG ] No samples found: disambiguate [2018-12-14 01:21:59,963] multiqc [DEBUG ] No samples found: supernova [2018-12-14 01:21:59,969] multiqc [DEBUG ] No samples found: deeptools [2018-12-14 01:21:59,974] multiqc [DEBUG ] No samples found: sargasso [2018-12-14 01:21:59,979] multiqc [DEBUG ] No samples found: verifybamid [2018-12-14 01:21:59,984] multiqc [DEBUG ] No samples found: homer [2018-12-14 01:21:59,989] multiqc [DEBUG ] No samples found: macs2 [2018-12-14 01:21:59,994] multiqc [DEBUG ] No samples found: theta2 [2018-12-14 01:21:59,998] multiqc [DEBUG ] No samples found: snpeff [2018-12-14 01:22:00,004] multiqc [DEBUG ] No samples found: gatk [2018-12-14 01:22:00,009] multiqc [DEBUG ] No samples found: htseq [2018-12-14 01:22:00,014] multiqc [DEBUG ] No samples found: bcftools [2018-12-14 01:22:00,018] multiqc [DEBUG ] No samples found: featureCounts [2018-12-14 01:22:00,023] multiqc [DEBUG ] No samples found: dedup [2018-12-14 01:22:00,030] multiqc [DEBUG ] No samples found: picard [2018-12-14 01:22:00,035] multiqc [DEBUG ] No samples found: prokka [2018-12-14 01:22:00,040] multiqc [DEBUG ] No samples found: samblaster [2018-12-14 01:22:00,045] multiqc [DEBUG ] No samples found: samtools [2018-12-14 01:22:00,050] multiqc [DEBUG ] No samples found: bamtools [2018-12-14 01:22:00,055] multiqc [DEBUG ] No samples found: jellyfish [2018-12-14 01:22:00,061] multiqc [DEBUG ] No samples found: vcftools [2018-12-14 01:22:00,068] multiqc [DEBUG ] No samples found: bbmap [2018-12-14 01:22:00,073] multiqc [DEBUG ] No samples found: bismark [2018-12-14 01:22:00,078] multiqc [DEBUG ] No samples found: hicexplorer [2018-12-14 01:22:00,083] multiqc [DEBUG ] No samples found: hicup [2018-12-14 01:22:00,087] multiqc [DEBUG ] No samples found: salmon [2018-12-14 01:22:00,092] multiqc [DEBUG ] No samples found: kallisto [2018-12-14 01:22:00,097] multiqc [DEBUG ] No samples found: slamdunk [2018-12-14 01:22:00,102] multiqc [DEBUG ] No samples found: star [2018-12-14 01:22:00,106] multiqc [DEBUG ] No samples found: hisat2 [2018-12-14 01:22:00,111] multiqc [DEBUG ] No samples found: tophat [2018-12-14 01:22:00,116] multiqc [DEBUG ] No samples found: bowtie2 [2018-12-14 01:22:00,120] multiqc [DEBUG ] No samples found: bowtie1 [2018-12-14 01:22:00,125] multiqc [DEBUG ] No samples found: leehom [2018-12-14 01:22:00,130] multiqc [DEBUG ] No samples found: adapterRemoval [2018-12-14 01:22:00,135] multiqc [DEBUG ] No samples found: clipandmerge [2018-12-14 01:22:00,139] multiqc [DEBUG ] No samples found: cutadapt [2018-12-14 01:22:00,144] multiqc [DEBUG ] No samples found: flexbar [2018-12-14 01:22:00,148] multiqc [DEBUG ] No samples found: trimmomatic [2018-12-14 01:22:00,153] multiqc [DEBUG ] No samples found: skewer [2018-12-14 01:22:00,157] multiqc [DEBUG ] No samples found: sortmerna [2018-12-14 01:22:00,162] multiqc [DEBUG ] No samples found: biobloomtools [2018-12-14 01:22:00,167] multiqc [DEBUG ] No samples found: fastq_screen [2018-12-14 01:22:00,171] multiqc [DEBUG ] No samples found: afterqc [2018-12-14 01:22:01,310] multiqc.modules.fastqc.fastqc [INFO ] Found 12 reports [2018-12-14 01:22:02,963] multiqc [DEBUG ] No samples found: clusterflow [2018-12-14 01:22:02,969] multiqc [DEBUG ] No samples found: bcl2fastq [2018-12-14 01:22:02,974] multiqc [DEBUG ] No samples found: interop [2018-12-14 01:22:02,998] multiqc [INFO ] Compressing plot data [2018-12-14 01:22:04,020] multiqc [INFO ] Report : multiqc_report.html [2018-12-14 01:22:04,021] multiqc [INFO ] Data : multiqc_data [2018-12-14 01:22:04,021] multiqc [DEBUG ] Moving data file from '/tmp/tmpSTMNbB/multiqc_data/multiqc_sources.txt' to '/home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_02/20181211_metagenomics_trimmed_fastqc/multiqc_data' [2018-12-14 01:22:04,021] multiqc [DEBUG ] Moving data file from '/tmp/tmpSTMNbB/multiqc_data/multiqc_data.json' to '/home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_02/20181211_metagenomics_trimmed_fastqc/multiqc_data' [2018-12-14 01:22:04,021] multiqc [DEBUG ] Moving data file from '/tmp/tmpSTMNbB/multiqc_data/multiqc_general_stats.txt' to '/home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_02/20181211_metagenomics_trimmed_fastqc/multiqc_data' [2018-12-14 01:22:04,021] multiqc [DEBUG ] Moving data file from '/tmp/tmpSTMNbB/multiqc_data/multiqc_fastqc.txt' to '/home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_02/20181211_metagenomics_trimmed_fastqc/multiqc_data' [2018-12-14 01:22:04,247] multiqc [INFO ] MultiQC complete