[2018-03-28 10:18:57,070] multiqc [DEBUG ] No MultiQC config found: /usr/local/lib/python2.7/dist-packages/multiqc-1.6.dev0-py2.7.egg/multiqc_config.yaml [2018-03-28 10:18:57,070] multiqc [DEBUG ] No MultiQC config found: /home/sam/.multiqc_config.yaml [2018-03-28 10:18:57,071] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2018-03-28 10:18:57,071] multiqc [DEBUG ] Command used: /usr/local/bin/multiqc . [2018-03-28 10:18:58,043] multiqc [DEBUG ] Latest MultiQC version is v1.5 [2018-03-28 10:18:58,043] multiqc [INFO ] This is MultiQC v1.6.dev0 [2018-03-28 10:18:58,044] multiqc [DEBUG ] Command : /usr/local/bin/multiqc . [2018-03-28 10:18:58,044] multiqc [DEBUG ] Working dir : /mnt/owl/Athaliana/20180328_fastqc [2018-03-28 10:18:58,044] multiqc [INFO ] Template : default [2018-03-28 10:18:58,044] multiqc [INFO ] Searching '.' [2018-03-28 10:18:58,044] 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 [2018-03-28 10:18:58,044] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpczzat7 [2018-03-28 10:18:58,064] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-6_S21_L006_R2_001_fastqc.html [2018-03-28 10:18:58,074] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-2to4kb-6_S22_L006_R2_001_fastqc.html [2018-03-28 10:18:58,075] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-2to4kb-4_S14_L004_R1_001_fastqc.html [2018-03-28 10:18:58,075] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-8to10kb-5_S20_L005_R2_001_fastqc.html [2018-03-28 10:18:58,075] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-8to10kb-1_S4_L001_R1_001_fastqc.html [2018-03-28 10:18:58,075] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-5to7kb-4_S15_L004_R1_001_fastqc.html [2018-03-28 10:18:58,075] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-2to4kb-3_S10_L003_R1_001_fastqc.html [2018-03-28 10:18:58,076] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-8to10kb-4_S16_L004_R2_001_fastqc.html [2018-03-28 10:18:58,077] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-2to4kb-1_S2_L001_R1_001_fastqc.html [2018-03-28 10:18:58,077] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-5to7kb-6_S23_L006_R1_001_fastqc.html [2018-03-28 10:18:58,077] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-4_S13_L004_R1_001_fastqc.html [2018-03-28 10:18:58,078] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-3_S9_L003_R2_001_fastqc.html [2018-03-28 10:18:58,079] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-5to7kb-6_S23_L006_R2_001_fastqc.html [2018-03-28 10:18:58,080] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-5to7kb-5_S19_L005_R1_001_fastqc.html [2018-03-28 10:18:58,080] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-2to4kb-5_S18_L005_R2_001_fastqc.html [2018-03-28 10:18:58,080] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-4_S13_L004_R2_001_fastqc.html [2018-03-28 10:18:58,082] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-8_S29_L008_R1_001_fastqc.html [2018-03-28 10:18:58,082] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-8to10kb-1_S4_L001_R2_001_fastqc.html [2018-03-28 10:18:58,083] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-5to7kb-4_S15_L004_R2_001_fastqc.html [2018-03-28 10:18:58,083] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-8to10kb-7_S28_L007_R2_001_fastqc.html [2018-03-28 10:18:58,084] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-2to4kb-3_S10_L003_R2_001_fastqc.html [2018-03-28 10:18:58,084] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-5to7kb-7_S27_L007_R2_001_fastqc.html [2018-03-28 10:18:58,084] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-5to7kb-5_S19_L005_R2_001_fastqc.html [2018-03-28 10:18:58,087] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-2to4kb-4_S14_L004_R2_001_fastqc.html [2018-03-28 10:18:58,088] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-7_S25_L007_R1_001_fastqc.html [2018-03-28 10:18:58,089] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-8to10kb-3_S12_L003_R2_001_fastqc.html [2018-03-28 10:18:58,091] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-2to4kb-1_S2_L001_R2_001_fastqc.html [2018-03-28 10:18:58,092] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-6_S21_L006_R1_001_fastqc.html [2018-03-28 10:18:58,094] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-5to7kb-2_S7_L002_R1_001_fastqc.html [2018-03-28 10:18:58,094] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-2to4kb-6_S22_L006_R1_001_fastqc.html [2018-03-28 10:18:58,094] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-2_S5_L002_R2_001_fastqc.html [2018-03-28 10:18:58,094] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-5to7kb-3_S11_L003_R1_001_fastqc.html [2018-03-28 10:18:58,095] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-8_S29_L008_R2_001_fastqc.html [2018-03-28 10:18:58,095] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-2to4kb-5_S18_L005_R1_001_fastqc.html [2018-03-28 10:18:58,844] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-5_S17_L005_R2_001_fastqc.html [2018-03-28 10:18:58,844] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-8to10kb-6_S24_L006_R1_001_fastqc.html [2018-03-28 10:18:58,845] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-5to7kb-8_S31_L008_R1_001_fastqc.html [2018-03-28 10:18:58,845] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-3_S9_L003_R1_001_fastqc.html [2018-03-28 10:18:58,846] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-5to7kb-2_S7_L002_R2_001_fastqc.html [2018-03-28 10:18:58,847] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-5to7kb-1_S3_L001_R1_001_fastqc.html [2018-03-28 10:18:58,847] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-2to4kb-7_S26_L007_R1_001_fastqc.html [2018-03-28 10:19:00,755] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-8to10kb-8_S32_L008_R2_001_fastqc.html [2018-03-28 10:19:00,756] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-1_S1_L001_R1_001_fastqc.html [2018-03-28 10:19:00,759] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-5to7kb-1_S3_L001_R2_001_fastqc.html [2018-03-28 10:19:00,760] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-5to7kb-7_S27_L007_R1_001_fastqc.html [2018-03-28 10:19:00,762] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-5_S17_L005_R1_001_fastqc.html [2018-03-28 10:19:00,763] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-8to10kb-8_S32_L008_R1_001_fastqc.html [2018-03-28 10:19:00,768] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-1_S1_L001_R2_001_fastqc.html [2018-03-28 10:19:00,770] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-7_S25_L007_R2_001_fastqc.html [2018-03-28 10:19:00,771] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-5to7kb-3_S11_L003_R2_001_fastqc.html [2018-03-28 10:19:00,775] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-8to10kb-2_S8_L002_R2_001_fastqc.html [2018-03-28 10:19:00,775] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-8to10kb-5_S20_L005_R1_001_fastqc.html [2018-03-28 10:19:00,779] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-2_S5_L002_R1_001_fastqc.html [2018-03-28 10:19:00,781] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-2to4kb-8_S30_L008_R2_001_fastqc.html [2018-03-28 10:19:00,783] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-2to4kb-2_S6_L002_R1_001_fastqc.html [2018-03-28 10:19:00,787] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-8to10kb-4_S16_L004_R1_001_fastqc.html [2018-03-28 10:19:00,788] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-8to10kb-3_S12_L003_R1_001_fastqc.html [2018-03-28 10:19:00,791] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-8to10kb-7_S28_L007_R1_001_fastqc.html [2018-03-28 10:19:00,793] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-8to10kb-6_S24_L006_R2_001_fastqc.html [2018-03-28 10:19:00,797] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-2to4kb-2_S6_L002_R2_001_fastqc.html [2018-03-28 10:19:00,797] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-2to4kb-7_S26_L007_R2_001_fastqc.html [2018-03-28 10:19:00,800] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-5to7kb-8_S31_L008_R2_001_fastqc.html [2018-03-28 10:19:00,801] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-2to4kb-8_S30_L008_R1_001_fastqc.html [2018-03-28 10:19:00,801] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-NMP-gDNA-8to10kb-2_S8_L002_R1_001_fastqc.html [2018-03-28 10:19:00,994] multiqc [DEBUG ] No samples found: custom_content [2018-03-28 10:19:00,998] multiqc [DEBUG ] No samples found: conpair [2018-03-28 10:19:01,003] multiqc [DEBUG ] No samples found: peddy [2018-03-28 10:19:01,007] multiqc [DEBUG ] No samples found: methylQA [2018-03-28 10:19:01,011] multiqc [DEBUG ] No samples found: qualimap [2018-03-28 10:19:01,016] multiqc [DEBUG ] No samples found: preseq [2018-03-28 10:19:01,020] multiqc [DEBUG ] No samples found: quast [2018-03-28 10:19:01,024] multiqc [DEBUG ] No samples found: qorts [2018-03-28 10:19:01,028] multiqc [DEBUG ] No samples found: rna_seqc [2018-03-28 10:19:01,032] multiqc [DEBUG ] No samples found: rsem [2018-03-28 10:19:01,037] multiqc [DEBUG ] No samples found: rseqc [2018-03-28 10:19:01,042] multiqc [DEBUG ] No samples found: busco [2018-03-28 10:19:01,046] multiqc [DEBUG ] No samples found: goleft_indexcov [2018-03-28 10:19:01,050] multiqc [DEBUG ] No samples found: disambiguate [2018-03-28 10:19:01,055] multiqc [DEBUG ] No samples found: supernova [2018-03-28 10:19:01,060] multiqc [DEBUG ] No samples found: deeptools [2018-03-28 10:19:01,064] multiqc [DEBUG ] No samples found: sargasso [2018-03-28 10:19:01,068] multiqc [DEBUG ] No samples found: verifybamid [2018-03-28 10:19:01,072] multiqc [DEBUG ] No samples found: homer [2018-03-28 10:19:01,077] multiqc [DEBUG ] No samples found: macs2 [2018-03-28 10:19:01,081] multiqc [DEBUG ] No samples found: theta2 [2018-03-28 10:19:01,085] multiqc [DEBUG ] No samples found: snpeff [2018-03-28 10:19:01,091] multiqc [DEBUG ] No samples found: gatk [2018-03-28 10:19:01,095] multiqc [DEBUG ] No samples found: htseq [2018-03-28 10:19:01,099] multiqc [DEBUG ] No samples found: bcftools [2018-03-28 10:19:01,103] multiqc [DEBUG ] No samples found: featureCounts [2018-03-28 10:19:01,107] multiqc [DEBUG ] No samples found: dedup [2018-03-28 10:19:01,113] multiqc [DEBUG ] No samples found: picard [2018-03-28 10:19:01,117] multiqc [DEBUG ] No samples found: prokka [2018-03-28 10:19:01,121] multiqc [DEBUG ] No samples found: samblaster [2018-03-28 10:19:01,125] multiqc [DEBUG ] No samples found: samtools [2018-03-28 10:19:01,129] multiqc [DEBUG ] No samples found: bamtools [2018-03-28 10:19:01,134] multiqc [DEBUG ] No samples found: jellyfish [2018-03-28 10:19:01,138] multiqc [DEBUG ] No samples found: vcftools [2018-03-28 10:19:01,144] multiqc [DEBUG ] No samples found: bbmap [2018-03-28 10:19:01,148] multiqc [DEBUG ] No samples found: bismark [2018-03-28 10:19:01,152] multiqc [DEBUG ] No samples found: hicexplorer [2018-03-28 10:19:01,156] multiqc [DEBUG ] No samples found: hicup [2018-03-28 10:19:01,160] multiqc [DEBUG ] No samples found: salmon [2018-03-28 10:19:01,164] multiqc [DEBUG ] No samples found: kallisto [2018-03-28 10:19:01,169] multiqc [DEBUG ] No samples found: slamdunk [2018-03-28 10:19:01,173] multiqc [DEBUG ] No samples found: star [2018-03-28 10:19:01,177] multiqc [DEBUG ] No samples found: hisat2 [2018-03-28 10:19:01,181] multiqc [DEBUG ] No samples found: tophat [2018-03-28 10:19:01,185] multiqc [DEBUG ] No samples found: bowtie2 [2018-03-28 10:19:01,189] multiqc [DEBUG ] No samples found: bowtie1 [2018-03-28 10:19:01,193] multiqc [DEBUG ] No samples found: leehom [2018-03-28 10:19:01,197] multiqc [DEBUG ] No samples found: adapterRemoval [2018-03-28 10:19:01,202] multiqc [DEBUG ] No samples found: clipandmerge [2018-03-28 10:19:01,206] multiqc [DEBUG ] No samples found: cutadapt [2018-03-28 10:19:01,210] multiqc [DEBUG ] No samples found: flexbar [2018-03-28 10:19:01,214] multiqc [DEBUG ] No samples found: trimmomatic [2018-03-28 10:19:01,218] multiqc [DEBUG ] No samples found: skewer [2018-03-28 10:19:01,222] multiqc [DEBUG ] No samples found: sortmerna [2018-03-28 10:19:01,226] multiqc [DEBUG ] No samples found: biobloomtools [2018-03-28 10:19:01,231] multiqc [DEBUG ] No samples found: fastq_screen [2018-03-28 10:19:01,235] multiqc [DEBUG ] No samples found: afterqc [2018-03-28 10:19:08,474] multiqc.modules.fastqc.fastqc [INFO ] Found 64 reports [2018-03-28 10:19:15,982] multiqc [DEBUG ] No samples found: clusterflow [2018-03-28 10:19:15,986] multiqc [DEBUG ] No samples found: bcl2fastq [2018-03-28 10:19:15,990] multiqc [DEBUG ] No samples found: interop [2018-03-28 10:19:16,097] multiqc [INFO ] Compressing plot data [2018-03-28 10:19:28,400] multiqc [INFO ] Report : multiqc_report.html [2018-03-28 10:19:28,400] multiqc [INFO ] Data : multiqc_data [2018-03-28 10:19:28,473] multiqc [DEBUG ] Moving data file from '/tmp/tmpczzat7/multiqc_data/multiqc_general_stats.txt' to '/mnt/owl/Athaliana/20180328_fastqc/multiqc_data' [2018-03-28 10:19:28,481] multiqc [DEBUG ] Moving data file from '/tmp/tmpczzat7/multiqc_data/multiqc_fastqc.txt' to '/mnt/owl/Athaliana/20180328_fastqc/multiqc_data' [2018-03-28 10:19:28,487] multiqc [DEBUG ] Moving data file from '/tmp/tmpczzat7/multiqc_data/multiqc_sources.txt' to '/mnt/owl/Athaliana/20180328_fastqc/multiqc_data' [2018-03-28 10:19:28,493] multiqc [DEBUG ] Moving data file from '/tmp/tmpczzat7/multiqc_data/multiqc_data.json' to '/mnt/owl/Athaliana/20180328_fastqc/multiqc_data' [2018-03-28 10:19:29,571] multiqc [INFO ] MultiQC complete