[2020-03-13 18:39:07,448] multiqc [DEBUG ] No MultiQC config found: /gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/multiqc_config.yaml [2020-03-13 18:39:07,449] multiqc [DEBUG ] No MultiQC config found: /usr/lusers/strigg/.multiqc_config.yaml [2020-03-13 18:39:07,449] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2020-03-13 18:39:07,449] multiqc [DEBUG ] Command used: /gscratch/srlab/strigg/bin/anaconda3/bin/multiqc /gscratch/scrubbed/strigg/analyses/20200311/RRBS/FASTQC/. [2020-03-13 18:39:12,458] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2020-03-13 18:39:12,458] multiqc [INFO ] This is MultiQC v1.8 [2020-03-13 18:39:12,459] multiqc [DEBUG ] Command : /gscratch/srlab/strigg/bin/anaconda3/bin/multiqc /gscratch/scrubbed/strigg/analyses/20200311/RRBS/FASTQC/. [2020-03-13 18:39:12,459] multiqc [DEBUG ] Working dir : /gscratch/scrubbed/strigg/analyses/20200311 [2020-03-13 18:39:12,460] multiqc [INFO ] Template : default [2020-03-13 18:39:12,460] multiqc [DEBUG ] Running Python 3.7.3 (default, Mar 27 2019, 22:11:17) [GCC 7.3.0] [2020-03-13 18:39:12,460] multiqc [INFO ] Searching : /gscratch/scrubbed/strigg/analyses/20200311/RRBS/FASTQC [2020-03-13 18:39:12,461] multiqc [DEBUG ] Analysing modules: custom_content, conpair, peddy, methylQA, phantompeakqualtools, qualimap, preseq, quast, qorts, rna_seqc, rsem, rseqc, busco, goleft_indexcov, disambiguate, supernova, deeptools, sargasso, verifybamid, mirtrace, happy, homer, macs2, theta2, snpeff, gatk, htseq, bcftools, featureCounts, fgbio, dedup, damageprofiler, biobambam2, mtnucratio, picard, prokka, samblaster, samtools, sexdeterrmine, bamtools, jellyfish, vcftools, longranger, stacks, bbmap, bismark, biscuit, hicexplorer, hicup, hicpro, salmon, kallisto, slamdunk, star, hisat2, tophat, bowtie2, bowtie1, kat, leehom, adapterRemoval, clipandmerge, cutadapt, flexbar, trimmomatic, skewer, sortmerna, biobloomtools, fastq_screen, afterqc, fastp, fastqc, minionqc, mosdepth, clusterflow, bcl2fastq, interop, flash, seqyclean [2020-03-13 18:39:12,461] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpcnupfbiu [2020-03-13 18:39:12,571] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth4_R1_001_val_1_fastqc.html [2020-03-13 18:39:12,594] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth13_R1_001_val_1_fastqc.html [2020-03-13 18:39:12,614] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth5_R1_001_val_1_fastqc.html [2020-03-13 18:39:12,614] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth15_R2_001_val_2_fastqc.html [2020-03-13 18:39:12,614] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth14_R2_001_val_2_fastqc.html [2020-03-13 18:39:12,616] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth6_R1_001_val_1_fastqc.html [2020-03-13 18:39:12,616] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth14_R1_001_val_1_fastqc.html [2020-03-13 18:39:12,616] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth5_R2_001_val_2_fastqc.html [2020-03-13 18:39:12,617] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth6_R2_001_val_2_fastqc.html [2020-03-13 18:39:12,617] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth15_R1_001_val_1_fastqc.html [2020-03-13 18:39:12,619] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth4_R2_001_val_2_fastqc.html [2020-03-13 18:39:12,619] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth13_R2_001_val_2_fastqc.html [2020-03-13 18:39:12,982] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.1.0 [2020-03-13 18:39:12,984] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.1.0 [2020-03-13 18:39:12,986] multiqc [DEBUG ] No samples found: custom_content [2020-03-13 18:39:12,991] multiqc [DEBUG ] No samples found: conpair [2020-03-13 18:39:12,995] multiqc [DEBUG ] No samples found: peddy [2020-03-13 18:39:13,001] multiqc [DEBUG ] No samples found: methylQA [2020-03-13 18:39:13,005] multiqc [DEBUG ] No samples found: phantompeakqualtools [2020-03-13 18:39:13,013] multiqc [DEBUG ] No samples found: qualimap [2020-03-13 18:39:13,017] multiqc [DEBUG ] No samples found: preseq [2020-03-13 18:39:13,021] multiqc [DEBUG ] No samples found: quast [2020-03-13 18:39:13,026] multiqc [DEBUG ] No samples found: qorts [2020-03-13 18:39:13,030] multiqc [DEBUG ] No samples found: rna_seqc [2020-03-13 18:39:13,034] multiqc [DEBUG ] No samples found: rsem [2020-03-13 18:39:13,041] multiqc [DEBUG ] No samples found: rseqc [2020-03-13 18:39:13,045] multiqc [DEBUG ] No samples found: busco [2020-03-13 18:39:13,050] multiqc [DEBUG ] No samples found: goleft_indexcov [2020-03-13 18:39:13,054] multiqc [DEBUG ] No samples found: disambiguate [2020-03-13 18:39:13,058] multiqc [DEBUG ] No samples found: supernova [2020-03-13 18:39:13,064] multiqc [DEBUG ] No samples found: deeptools [2020-03-13 18:39:13,068] multiqc [DEBUG ] No samples found: sargasso [2020-03-13 18:39:13,071] multiqc [DEBUG ] No samples found: verifybamid [2020-03-13 18:39:13,075] multiqc [DEBUG ] No samples found: mirtrace [2020-03-13 18:39:13,078] multiqc [DEBUG ] No samples found: happy [2020-03-13 18:39:13,083] multiqc [DEBUG ] No samples found: homer [2020-03-13 18:39:13,087] multiqc [DEBUG ] No samples found: macs2 [2020-03-13 18:39:13,090] multiqc [DEBUG ] No samples found: theta2 [2020-03-13 18:39:13,093] multiqc [DEBUG ] No samples found: snpeff [2020-03-13 18:39:13,097] multiqc [DEBUG ] No samples found: gatk [2020-03-13 18:39:13,101] multiqc [DEBUG ] No samples found: htseq [2020-03-13 18:39:13,105] multiqc [DEBUG ] No samples found: bcftools [2020-03-13 18:39:13,108] multiqc [DEBUG ] No samples found: featureCounts [2020-03-13 18:39:13,112] multiqc [DEBUG ] No samples found: fgbio [2020-03-13 18:39:13,115] multiqc [DEBUG ] No samples found: dedup [2020-03-13 18:39:13,119] multiqc [DEBUG ] No samples found: damageprofiler [2020-03-13 18:39:13,126] multiqc [DEBUG ] No samples found: biobambam2 [2020-03-13 18:39:13,129] multiqc [DEBUG ] No samples found: mtnucratio [2020-03-13 18:39:13,132] multiqc [DEBUG ] No samples found: picard [2020-03-13 18:39:13,135] multiqc [DEBUG ] No samples found: prokka [2020-03-13 18:39:13,139] multiqc [DEBUG ] No samples found: samblaster [2020-03-13 18:39:13,143] multiqc [DEBUG ] No samples found: samtools [2020-03-13 18:39:13,146] multiqc [DEBUG ] No samples found: sexdeterrmine [2020-03-13 18:39:13,150] multiqc [DEBUG ] No samples found: bamtools [2020-03-13 18:39:13,153] multiqc [DEBUG ] No samples found: jellyfish [2020-03-13 18:39:13,157] multiqc [DEBUG ] No samples found: vcftools [2020-03-13 18:39:13,161] multiqc [DEBUG ] No samples found: longranger [2020-03-13 18:39:13,164] multiqc [DEBUG ] No samples found: stacks [2020-03-13 18:39:13,171] multiqc [DEBUG ] No samples found: bbmap [2020-03-13 18:39:13,174] multiqc [DEBUG ] No samples found: bismark [2020-03-13 18:39:13,178] multiqc [DEBUG ] No samples found: biscuit [2020-03-13 18:39:13,181] multiqc [DEBUG ] No samples found: hicexplorer [2020-03-13 18:39:13,184] multiqc [DEBUG ] No samples found: hicup [2020-03-13 18:39:13,188] multiqc [DEBUG ] No samples found: hicpro [2020-03-13 18:39:13,191] multiqc [DEBUG ] No samples found: salmon [2020-03-13 18:39:13,194] multiqc [DEBUG ] No samples found: kallisto [2020-03-13 18:39:13,198] multiqc [DEBUG ] No samples found: slamdunk [2020-03-13 18:39:13,201] multiqc [DEBUG ] No samples found: star [2020-03-13 18:39:13,205] multiqc [DEBUG ] No samples found: hisat2 [2020-03-13 18:39:13,208] multiqc [DEBUG ] No samples found: tophat [2020-03-13 18:39:13,212] multiqc [DEBUG ] No samples found: bowtie2 [2020-03-13 18:39:13,215] multiqc [DEBUG ] No samples found: bowtie1 [2020-03-13 18:39:13,218] multiqc [DEBUG ] No samples found: kat [2020-03-13 18:39:13,221] multiqc [DEBUG ] No samples found: leehom [2020-03-13 18:39:13,225] multiqc [DEBUG ] No samples found: adapterRemoval [2020-03-13 18:39:13,228] multiqc [DEBUG ] No samples found: clipandmerge [2020-03-13 18:39:13,231] multiqc [DEBUG ] No samples found: cutadapt [2020-03-13 18:39:13,235] multiqc [DEBUG ] No samples found: flexbar [2020-03-13 18:39:13,239] multiqc [DEBUG ] No samples found: trimmomatic [2020-03-13 18:39:13,242] multiqc [DEBUG ] No samples found: skewer [2020-03-13 18:39:13,245] multiqc [DEBUG ] No samples found: sortmerna [2020-03-13 18:39:13,248] multiqc [DEBUG ] No samples found: biobloomtools [2020-03-13 18:39:13,252] multiqc [DEBUG ] No samples found: fastq_screen [2020-03-13 18:39:13,255] multiqc [DEBUG ] No samples found: afterqc [2020-03-13 18:39:13,259] multiqc [DEBUG ] No samples found: fastp [2020-03-13 18:39:16,199] multiqc.modules.fastqc.fastqc [INFO ] Found 12 reports [2020-03-13 18:39:16,603] multiqc [DEBUG ] No samples found: minionqc [2020-03-13 18:39:16,606] multiqc [DEBUG ] No samples found: mosdepth [2020-03-13 18:39:16,610] multiqc [DEBUG ] No samples found: clusterflow [2020-03-13 18:39:16,613] multiqc [DEBUG ] No samples found: bcl2fastq [2020-03-13 18:39:16,616] multiqc [DEBUG ] No samples found: interop [2020-03-13 18:39:16,620] multiqc [DEBUG ] No samples found: flash [2020-03-13 18:39:16,623] multiqc [DEBUG ] No samples found: seqyclean [2020-03-13 18:39:16,641] multiqc [INFO ] Compressing plot data [2020-03-13 18:39:16,835] multiqc [WARNING] Previous MultiQC output found! Adjusting filenames.. [2020-03-13 18:39:16,835] multiqc [WARNING] Use -f or --force to overwrite existing reports instead [2020-03-13 18:39:16,835] multiqc [INFO ] Report : multiqc_report_1.html [2020-03-13 18:39:16,835] multiqc [INFO ] Data : multiqc_data_1 [2020-03-13 18:39:16,836] multiqc [DEBUG ] Moving data file from '/tmp/tmpcnupfbiu/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/gscratch/scrubbed/strigg/analyses/20200311/multiqc_data_1' [2020-03-13 18:39:16,837] multiqc [DEBUG ] Moving data file from '/tmp/tmpcnupfbiu/multiqc_data/multiqc_fastqc.txt' to '/gscratch/scrubbed/strigg/analyses/20200311/multiqc_data_1' [2020-03-13 18:39:16,838] multiqc [DEBUG ] Moving data file from '/tmp/tmpcnupfbiu/multiqc_data/multiqc_general_stats.txt' to '/gscratch/scrubbed/strigg/analyses/20200311/multiqc_data_1' [2020-03-13 18:39:16,839] multiqc [DEBUG ] Moving data file from '/tmp/tmpcnupfbiu/multiqc_data/multiqc_sources.txt' to '/gscratch/scrubbed/strigg/analyses/20200311/multiqc_data_1' [2020-03-13 18:39:16,839] multiqc [DEBUG ] Moving data file from '/tmp/tmpcnupfbiu/multiqc_data/multiqc_data.json' to '/gscratch/scrubbed/strigg/analyses/20200311/multiqc_data_1' [2020-03-13 18:39:16,942] multiqc [INFO ] MultiQC complete