[2018-04-10 13:13:24,220] multiqc [DEBUG ] No MultiQC config found: /usr/local/lib/python2.7/dist-packages/multiqc-1.6.dev0-py2.7.egg/multiqc_config.yaml [2018-04-10 13:13:24,220] multiqc [DEBUG ] No MultiQC config found: /home/sam/.multiqc_config.yaml [2018-04-10 13:13:24,220] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2018-04-10 13:13:24,220] multiqc [DEBUG ] Command used: /usr/local/bin/multiqc . [2018-04-10 13:13:25,318] multiqc [DEBUG ] Latest MultiQC version is v1.5 [2018-04-10 13:13:25,319] multiqc [INFO ] This is MultiQC v1.6.dev0 [2018-04-10 13:13:25,319] multiqc [DEBUG ] Command : /usr/local/bin/multiqc . [2018-04-10 13:13:25,319] multiqc [DEBUG ] Working dir : /home/sam/20180410_trimgalore_trim14bp_Cvirginica_MBD/20180410_fastqc_trimgalore_trim14bp_Cvirginica_MBD [2018-04-10 13:13:25,319] multiqc [INFO ] Template : default [2018-04-10 13:13:25,319] multiqc [INFO ] Searching '.' [2018-04-10 13:13:25,319] 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 [2018-04-10 13:13:25,320] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpyG7E6H [2018-04-10 13:13:25,356] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr2096_9_s1_R1_val_1_fastqc.html [2018-04-10 13:13:25,366] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr2096_6_s1_R1_val_1_fastqc.html [2018-04-10 13:13:25,367] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr2096_6_s1_R2_val_2_fastqc.html [2018-04-10 13:13:25,368] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr2096_10_s1_R1_val_1_fastqc.html [2018-04-10 13:13:25,368] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr2096_7_s1_R2_val_2_fastqc.html [2018-04-10 13:13:25,369] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr2096_3_s1_R2_val_2_fastqc.html [2018-04-10 13:13:25,370] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr2096_9_s1_R2_val_2_fastqc.html [2018-04-10 13:13:25,370] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr2096_5_s1_R1_val_1_fastqc.html [2018-04-10 13:13:25,372] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr2096_4_s1_R2_val_2_fastqc.html [2018-04-10 13:13:25,373] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr2096_4_s1_R1_val_1_fastqc.html [2018-04-10 13:13:25,373] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr2096_10_s1_R2_val_2_fastqc.html [2018-04-10 13:13:25,373] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr2096_2_s1_R2_val_2_fastqc.html [2018-04-10 13:13:25,375] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr2096_1_s1_R1_val_1_fastqc.html [2018-04-10 13:13:25,375] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr2096_5_s1_R2_val_2_fastqc.html [2018-04-10 13:13:25,376] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr2096_3_s1_R1_val_1_fastqc.html [2018-04-10 13:13:25,376] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr2096_2_s1_R1_val_1_fastqc.html [2018-04-10 13:13:25,377] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr2096_8_s1_R1_val_1_fastqc.html [2018-04-10 13:13:25,378] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr2096_8_s1_R2_val_2_fastqc.html [2018-04-10 13:13:25,379] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr2096_1_s1_R2_val_2_fastqc.html [2018-04-10 13:13:25,379] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr2096_7_s1_R1_val_1_fastqc.html [2018-04-10 13:13:25,863] multiqc [DEBUG ] No samples found: custom_content [2018-04-10 13:13:25,868] multiqc [DEBUG ] No samples found: conpair [2018-04-10 13:13:25,872] multiqc [DEBUG ] No samples found: peddy [2018-04-10 13:13:25,876] multiqc [DEBUG ] No samples found: methylQA [2018-04-10 13:13:25,881] multiqc [DEBUG ] No samples found: qualimap [2018-04-10 13:13:25,885] multiqc [DEBUG ] No samples found: preseq [2018-04-10 13:13:25,890] multiqc [DEBUG ] No samples found: quast [2018-04-10 13:13:25,894] multiqc [DEBUG ] No samples found: qorts [2018-04-10 13:13:25,900] multiqc [DEBUG ] No samples found: rna_seqc [2018-04-10 13:13:25,904] multiqc [DEBUG ] No samples found: rsem [2018-04-10 13:13:25,909] multiqc [DEBUG ] No samples found: rseqc [2018-04-10 13:13:25,913] multiqc [DEBUG ] No samples found: busco [2018-04-10 13:13:25,918] multiqc [DEBUG ] No samples found: goleft_indexcov [2018-04-10 13:13:25,922] multiqc [DEBUG ] No samples found: disambiguate [2018-04-10 13:13:25,926] multiqc [DEBUG ] No samples found: supernova [2018-04-10 13:13:25,932] multiqc [DEBUG ] No samples found: deeptools [2018-04-10 13:13:25,936] multiqc [DEBUG ] No samples found: sargasso [2018-04-10 13:13:25,940] multiqc [DEBUG ] No samples found: verifybamid [2018-04-10 13:13:25,945] multiqc [DEBUG ] No samples found: homer [2018-04-10 13:13:25,949] multiqc [DEBUG ] No samples found: macs2 [2018-04-10 13:13:25,953] multiqc [DEBUG ] No samples found: theta2 [2018-04-10 13:13:25,958] multiqc [DEBUG ] No samples found: snpeff [2018-04-10 13:13:25,962] multiqc [DEBUG ] No samples found: gatk [2018-04-10 13:13:25,967] multiqc [DEBUG ] No samples found: htseq [2018-04-10 13:13:25,971] multiqc [DEBUG ] No samples found: bcftools [2018-04-10 13:13:25,975] multiqc [DEBUG ] No samples found: featureCounts [2018-04-10 13:13:25,980] multiqc [DEBUG ] No samples found: dedup [2018-04-10 13:13:25,985] multiqc [DEBUG ] No samples found: picard [2018-04-10 13:13:25,989] multiqc [DEBUG ] No samples found: prokka [2018-04-10 13:13:25,993] multiqc [DEBUG ] No samples found: samblaster [2018-04-10 13:13:25,998] multiqc [DEBUG ] No samples found: samtools [2018-04-10 13:13:26,002] multiqc [DEBUG ] No samples found: bamtools [2018-04-10 13:13:26,006] multiqc [DEBUG ] No samples found: jellyfish [2018-04-10 13:13:26,011] multiqc [DEBUG ] No samples found: vcftools [2018-04-10 13:13:26,017] multiqc [DEBUG ] No samples found: bbmap [2018-04-10 13:13:26,021] multiqc [DEBUG ] No samples found: bismark [2018-04-10 13:13:26,025] multiqc [DEBUG ] No samples found: hicexplorer [2018-04-10 13:13:26,029] multiqc [DEBUG ] No samples found: hicup [2018-04-10 13:13:26,034] multiqc [DEBUG ] No samples found: salmon [2018-04-10 13:13:26,038] multiqc [DEBUG ] No samples found: kallisto [2018-04-10 13:13:26,042] multiqc [DEBUG ] No samples found: slamdunk [2018-04-10 13:13:26,047] multiqc [DEBUG ] No samples found: star [2018-04-10 13:13:26,051] multiqc [DEBUG ] No samples found: hisat2 [2018-04-10 13:13:26,055] multiqc [DEBUG ] No samples found: tophat [2018-04-10 13:13:26,059] multiqc [DEBUG ] No samples found: bowtie2 [2018-04-10 13:13:26,063] multiqc [DEBUG ] No samples found: bowtie1 [2018-04-10 13:13:26,067] multiqc [DEBUG ] No samples found: leehom [2018-04-10 13:13:26,072] multiqc [DEBUG ] No samples found: adapterRemoval [2018-04-10 13:13:26,076] multiqc [DEBUG ] No samples found: clipandmerge [2018-04-10 13:13:26,080] multiqc [DEBUG ] No samples found: cutadapt [2018-04-10 13:13:26,084] multiqc [DEBUG ] No samples found: flexbar [2018-04-10 13:13:26,088] multiqc [DEBUG ] No samples found: trimmomatic [2018-04-10 13:13:26,093] multiqc [DEBUG ] No samples found: skewer [2018-04-10 13:13:26,097] multiqc [DEBUG ] No samples found: sortmerna [2018-04-10 13:13:26,101] multiqc [DEBUG ] No samples found: biobloomtools [2018-04-10 13:13:26,105] multiqc [DEBUG ] No samples found: fastq_screen [2018-04-10 13:13:26,109] multiqc [DEBUG ] No samples found: afterqc [2018-04-10 13:13:28,037] multiqc.modules.fastqc.fastqc [INFO ] Found 20 reports [2018-04-10 13:13:30,124] multiqc [DEBUG ] No samples found: clusterflow [2018-04-10 13:13:30,128] multiqc [DEBUG ] No samples found: bcl2fastq [2018-04-10 13:13:30,132] multiqc [DEBUG ] No samples found: interop [2018-04-10 13:13:30,167] multiqc [INFO ] Compressing plot data [2018-04-10 13:13:32,058] multiqc [INFO ] Report : multiqc_report.html [2018-04-10 13:13:32,058] multiqc [INFO ] Data : multiqc_data [2018-04-10 13:13:32,058] multiqc [DEBUG ] Moving data file from '/tmp/tmpyG7E6H/multiqc_data/multiqc_general_stats.txt' to '/home/sam/20180410_trimgalore_trim14bp_Cvirginica_MBD/20180410_fastqc_trimgalore_trim14bp_Cvirginica_MBD/multiqc_data' [2018-04-10 13:13:32,059] multiqc [DEBUG ] Moving data file from '/tmp/tmpyG7E6H/multiqc_data/multiqc_fastqc.txt' to '/home/sam/20180410_trimgalore_trim14bp_Cvirginica_MBD/20180410_fastqc_trimgalore_trim14bp_Cvirginica_MBD/multiqc_data' [2018-04-10 13:13:32,059] multiqc [DEBUG ] Moving data file from '/tmp/tmpyG7E6H/multiqc_data/multiqc_sources.txt' to '/home/sam/20180410_trimgalore_trim14bp_Cvirginica_MBD/20180410_fastqc_trimgalore_trim14bp_Cvirginica_MBD/multiqc_data' [2018-04-10 13:13:32,059] multiqc [DEBUG ] Moving data file from '/tmp/tmpyG7E6H/multiqc_data/multiqc_data.json' to '/home/sam/20180410_trimgalore_trim14bp_Cvirginica_MBD/20180410_fastqc_trimgalore_trim14bp_Cvirginica_MBD/multiqc_data' [2018-04-10 13:13:32,255] multiqc [INFO ] MultiQC complete