[2018-09-10 11:37:58,263] multiqc [DEBUG ] No MultiQC config found: /home/shared/anaconda3/lib/python3.6/site-packages/multiqc-1.5.dev0-py3.6.egg/multiqc_config.yaml [2018-09-10 11:37:58,263] multiqc [DEBUG ] No MultiQC config found: /home/sam/.multiqc_config.yaml [2018-09-10 11:37:58,263] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2018-09-10 11:37:58,263] multiqc [DEBUG ] Command used: /home/shared/anaconda3/bin/multiqc . [2018-09-10 11:37:59,103] multiqc [WARNING] MultiQC Version v1.6 now available! [2018-09-10 11:37:59,103] multiqc [INFO ] This is MultiQC v1.5.dev0 [2018-09-10 11:37:59,103] multiqc [DEBUG ] Command : /home/shared/anaconda3/bin/multiqc . [2018-09-10 11:37:59,103] multiqc [DEBUG ] Working dir : /home/sam/data/Cvirginica/concatenated/20180910_Cvirginica_oil_fastqc [2018-09-10 11:37:59,104] multiqc [INFO ] Template : default [2018-09-10 11:37:59,104] multiqc [INFO ] Searching '.' [2018-09-10 11:37:59,104] multiqc [DEBUG ] Analysing modules: afterqc, 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, picard, prokka, samblaster, samtools, bamtools, jellyfish, vcftools, bbmap, bismark, hicexplorer, hicup, salmon, kallisto, slamdunk, star, hisat2, tophat, bowtie2, bowtie1, leehom, adapterRemoval, cutadapt, flexbar, trimmomatic, skewer, sortmerna, biobloomtools, fastq_screen, fastqc, clusterflow, bcl2fastq, interop [2018-09-10 11:37:59,105] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpyp4hp6yc [2018-09-10 11:37:59,143] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 2112_lane1_TTAGGC_fastqc.html [2018-09-10 11:37:59,144] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 2112_lane1_TGACCA_fastqc.html [2018-09-10 11:37:59,144] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 2112_lane1_GCCAAT_fastqc.html [2018-09-10 11:37:59,144] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 2112_lane1_ACAGTG_fastqc.html [2018-09-10 11:37:59,151] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 2112_lane1_CAGATC_fastqc.html [2018-09-10 11:37:59,152] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 2112_lane1_ATCACG_fastqc.html [2018-09-10 11:37:59,182] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: fastqc_report.html [2018-09-10 11:37:59,220] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: fastqc_report.html [2018-09-10 11:37:59,258] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: fastqc_report.html [2018-09-10 11:37:59,298] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: fastqc_report.html [2018-09-10 11:37:59,336] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: fastqc_report.html [2018-09-10 11:37:59,373] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: fastqc_report.html [2018-09-10 11:38:00,230] multiqc [DEBUG ] No samples found: afterqc [2018-09-10 11:38:00,280] multiqc [DEBUG ] No samples found: custom_content [2018-09-10 11:38:00,299] multiqc [DEBUG ] No samples found: conpair [2018-09-10 11:38:00,318] multiqc [DEBUG ] No samples found: peddy [2018-09-10 11:38:00,331] multiqc [DEBUG ] No samples found: methylQA [2018-09-10 11:38:00,351] multiqc [DEBUG ] No samples found: qualimap [2018-09-10 11:38:00,372] multiqc [DEBUG ] No samples found: preseq [2018-09-10 11:38:00,378] multiqc [DEBUG ] No samples found: quast [2018-09-10 11:38:00,384] multiqc [DEBUG ] No samples found: qorts [2018-09-10 11:38:00,389] multiqc [DEBUG ] No samples found: rna_seqc [2018-09-10 11:38:00,395] multiqc [DEBUG ] No samples found: rsem [2018-09-10 11:38:00,405] multiqc [DEBUG ] No samples found: rseqc [2018-09-10 11:38:00,425] multiqc [DEBUG ] No samples found: busco [2018-09-10 11:38:00,443] multiqc [DEBUG ] No samples found: goleft_indexcov [2018-09-10 11:38:00,472] multiqc [DEBUG ] No samples found: disambiguate [2018-09-10 11:38:00,489] multiqc [DEBUG ] No samples found: supernova [2018-09-10 11:38:00,516] multiqc [DEBUG ] No samples found: deeptools [2018-09-10 11:38:00,532] multiqc [DEBUG ] No samples found: sargasso [2018-09-10 11:38:00,546] multiqc [DEBUG ] No samples found: verifybamid [2018-09-10 11:38:00,580] multiqc [DEBUG ] No samples found: homer [2018-09-10 11:38:00,598] multiqc [DEBUG ] No samples found: macs2 [2018-09-10 11:38:00,603] multiqc [DEBUG ] No samples found: theta2 [2018-09-10 11:38:00,627] multiqc [DEBUG ] No samples found: snpeff [2018-09-10 11:38:00,650] multiqc [DEBUG ] No samples found: gatk [2018-09-10 11:38:00,667] multiqc [DEBUG ] No samples found: htseq [2018-09-10 11:38:00,691] multiqc [DEBUG ] No samples found: bcftools [2018-09-10 11:38:00,713] multiqc [DEBUG ] No samples found: featureCounts [2018-09-10 11:38:00,751] multiqc [DEBUG ] No samples found: picard [2018-09-10 11:38:00,758] multiqc [DEBUG ] No samples found: prokka [2018-09-10 11:38:00,774] multiqc [DEBUG ] No samples found: samblaster [2018-09-10 11:38:00,783] multiqc [DEBUG ] No samples found: samtools [2018-09-10 11:38:00,812] multiqc [DEBUG ] No samples found: bamtools [2018-09-10 11:38:00,819] multiqc [DEBUG ] No samples found: jellyfish [2018-09-10 11:38:00,841] multiqc [DEBUG ] No samples found: vcftools [2018-09-10 11:38:00,872] multiqc [DEBUG ] No samples found: bbmap [2018-09-10 11:38:00,892] multiqc [DEBUG ] No samples found: bismark [2018-09-10 11:38:00,913] multiqc [DEBUG ] No samples found: hicexplorer [2018-09-10 11:38:00,929] multiqc [DEBUG ] No samples found: hicup [2018-09-10 11:38:00,935] multiqc [DEBUG ] No samples found: salmon [2018-09-10 11:38:00,940] multiqc [DEBUG ] No samples found: kallisto [2018-09-10 11:38:00,960] multiqc [DEBUG ] No samples found: slamdunk [2018-09-10 11:38:00,966] multiqc [DEBUG ] No samples found: star [2018-09-10 11:38:00,983] multiqc [DEBUG ] No samples found: hisat2 [2018-09-10 11:38:01,006] multiqc [DEBUG ] No samples found: tophat [2018-09-10 11:38:01,031] multiqc [DEBUG ] No samples found: bowtie2 [2018-09-10 11:38:01,049] multiqc [DEBUG ] No samples found: bowtie1 [2018-09-10 11:38:01,064] multiqc [DEBUG ] No samples found: leehom [2018-09-10 11:38:01,086] multiqc [DEBUG ] No samples found: adapterRemoval [2018-09-10 11:38:01,107] multiqc [DEBUG ] No samples found: cutadapt [2018-09-10 11:38:01,130] multiqc [DEBUG ] No samples found: flexbar [2018-09-10 11:38:01,136] multiqc [DEBUG ] No samples found: trimmomatic [2018-09-10 11:38:01,141] multiqc [DEBUG ] No samples found: skewer [2018-09-10 11:38:01,147] multiqc [DEBUG ] No samples found: sortmerna [2018-09-10 11:38:01,160] multiqc [DEBUG ] No samples found: biobloomtools [2018-09-10 11:38:01,177] multiqc [DEBUG ] No samples found: fastq_screen [2018-09-10 11:38:01,449] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping '2112_lane1_ATCACG_fastqc.zip' as already parsed '2112_lane1_ATCACG' [2018-09-10 11:38:01,450] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping '2112_lane1_CAGATC_fastqc.zip' as already parsed '2112_lane1_CAGATC' [2018-09-10 11:38:01,450] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping '2112_lane1_ACAGTG_fastqc.zip' as already parsed '2112_lane1_ACAGTG' [2018-09-10 11:38:01,450] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping '2112_lane1_TTAGGC_fastqc.zip' as already parsed '2112_lane1_TTAGGC' [2018-09-10 11:38:01,451] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping '2112_lane1_GCCAAT_fastqc.zip' as already parsed '2112_lane1_GCCAAT' [2018-09-10 11:38:01,451] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping '2112_lane1_TGACCA_fastqc.zip' as already parsed '2112_lane1_TGACCA' [2018-09-10 11:38:01,451] multiqc.modules.fastqc.fastqc [INFO ] Found 6 reports [2018-09-10 11:38:01,673] multiqc [DEBUG ] No samples found: clusterflow [2018-09-10 11:38:01,687] multiqc [DEBUG ] No samples found: bcl2fastq [2018-09-10 11:38:01,709] multiqc [DEBUG ] No samples found: interop [2018-09-10 11:38:01,722] multiqc [INFO ] Compressing plot data [2018-09-10 11:38:01,923] multiqc [INFO ] Report : multiqc_report.html [2018-09-10 11:38:01,923] multiqc [INFO ] Data : multiqc_data [2018-09-10 11:38:01,923] multiqc [DEBUG ] Moving data file from '/tmp/tmpyp4hp6yc/multiqc_data/multiqc_general_stats.txt' to '/home/sam/data/Cvirginica/concatenated/20180910_Cvirginica_oil_fastqc/multiqc_data' [2018-09-10 11:38:01,923] multiqc [DEBUG ] Moving data file from '/tmp/tmpyp4hp6yc/multiqc_data/multiqc_fastqc.txt' to '/home/sam/data/Cvirginica/concatenated/20180910_Cvirginica_oil_fastqc/multiqc_data' [2018-09-10 11:38:01,923] multiqc [DEBUG ] Moving data file from '/tmp/tmpyp4hp6yc/multiqc_data/multiqc_data.json' to '/home/sam/data/Cvirginica/concatenated/20180910_Cvirginica_oil_fastqc/multiqc_data' [2018-09-10 11:38:01,924] multiqc [DEBUG ] Moving data file from '/tmp/tmpyp4hp6yc/multiqc_data/multiqc_sources.txt' to '/home/sam/data/Cvirginica/concatenated/20180910_Cvirginica_oil_fastqc/multiqc_data' [2018-09-10 11:38:02,171] multiqc [INFO ] MultiQC complete