[2021-06-13 12:32:11,041] multiqc [DEBUG ] No MultiQC config found: /gscratch/srlab/programs/anaconda3/lib/python3.7/site-packages/multiqc_config.yaml [2021-06-13 12:32:11,042] multiqc [DEBUG ] No MultiQC config found: /usr/lusers/sr320/.multiqc_config.yaml [2021-06-13 12:32:11,042] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-06-13 12:32:11,042] multiqc [DEBUG ] Command used: /gscratch/srlab/programs/anaconda3/bin/multiqc . [2021-06-13 12:32:16,328] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2021-06-13 12:32:16,328] multiqc [INFO ] This is MultiQC v1.8 [2021-06-13 12:32:16,329] multiqc [DEBUG ] Command : /gscratch/srlab/programs/anaconda3/bin/multiqc . [2021-06-13 12:32:16,329] multiqc [DEBUG ] Working dir : /gscratch/scrubbed/sr320/061321-oly [2021-06-13 12:32:16,329] multiqc [INFO ] Template : default [2021-06-13 12:32:16,330] multiqc [DEBUG ] Running Python 3.7.3 (default, Mar 27 2019, 22:11:17) [GCC 7.3.0] [2021-06-13 12:32:16,330] multiqc [INFO ] Searching : /gscratch/scrubbed/sr320/061321-oly [2021-06-13 12:32:16,331] 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 [2021-06-13 12:32:16,331] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpuytuj_nv [2021-06-13 12:32:16,721] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: combined_bismark_bt2_SE_report.html [2021-06-13 12:32:16,722] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: combined_bismark_bt2.bam [2021-06-13 12:32:16,722] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: combined_bismark_bt2.deduplicated.bam [2021-06-13 12:32:16,722] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: bismark_summary_report.html [2021-06-13 12:32:16,733] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: jobs.sh [2021-06-13 12:32:19,375] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 2.2.4 [2021-06-13 12:32:19,377] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 2.2.4 [2021-06-13 12:32:19,378] multiqc [DEBUG ] No samples found: custom_content [2021-06-13 12:32:19,385] multiqc [DEBUG ] No samples found: conpair [2021-06-13 12:32:19,464] multiqc [DEBUG ] No samples found: peddy [2021-06-13 12:32:19,471] multiqc [DEBUG ] No samples found: methylQA [2021-06-13 12:32:19,502] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-06-13 12:32:19,523] multiqc [DEBUG ] No samples found: qualimap [2021-06-13 12:32:19,547] multiqc [DEBUG ] No samples found: preseq [2021-06-13 12:32:19,572] multiqc [DEBUG ] No samples found: quast [2021-06-13 12:32:19,591] multiqc [DEBUG ] No samples found: qorts [2021-06-13 12:32:19,599] multiqc [DEBUG ] No samples found: rna_seqc [2021-06-13 12:32:19,618] multiqc [DEBUG ] No samples found: rsem [2021-06-13 12:32:19,629] multiqc [DEBUG ] No samples found: rseqc [2021-06-13 12:32:19,637] multiqc [DEBUG ] No samples found: busco [2021-06-13 12:32:19,669] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-06-13 12:32:19,686] multiqc [DEBUG ] No samples found: disambiguate [2021-06-13 12:32:19,693] multiqc [DEBUG ] No samples found: supernova [2021-06-13 12:32:19,729] multiqc [DEBUG ] No samples found: deeptools [2021-06-13 12:32:19,754] multiqc [DEBUG ] No samples found: sargasso [2021-06-13 12:32:19,761] multiqc [DEBUG ] No samples found: verifybamid [2021-06-13 12:32:19,788] multiqc [DEBUG ] No samples found: mirtrace [2021-06-13 12:32:19,795] multiqc [DEBUG ] No samples found: happy [2021-06-13 12:32:19,820] multiqc [DEBUG ] No samples found: homer [2021-06-13 12:32:19,827] multiqc [DEBUG ] No samples found: macs2 [2021-06-13 12:32:19,834] multiqc [DEBUG ] No samples found: theta2 [2021-06-13 12:32:19,842] multiqc [DEBUG ] No samples found: snpeff [2021-06-13 12:32:19,876] multiqc [DEBUG ] No samples found: gatk [2021-06-13 12:32:19,883] multiqc [DEBUG ] No samples found: htseq [2021-06-13 12:32:19,907] multiqc [DEBUG ] No samples found: bcftools [2021-06-13 12:32:19,914] multiqc [DEBUG ] No samples found: featureCounts [2021-06-13 12:32:19,931] multiqc [DEBUG ] No samples found: fgbio [2021-06-13 12:32:19,937] multiqc [DEBUG ] No samples found: dedup [2021-06-13 12:32:19,950] multiqc [DEBUG ] No samples found: damageprofiler [2021-06-13 12:32:20,013] multiqc [DEBUG ] No samples found: biobambam2 [2021-06-13 12:32:20,020] multiqc [DEBUG ] No samples found: mtnucratio [2021-06-13 12:32:20,026] multiqc [DEBUG ] No samples found: picard [2021-06-13 12:32:20,032] multiqc [DEBUG ] No samples found: prokka [2021-06-13 12:32:20,039] multiqc [DEBUG ] No samples found: samblaster [2021-06-13 12:32:20,071] multiqc [DEBUG ] No samples found: samtools [2021-06-13 12:32:20,078] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-06-13 12:32:20,085] multiqc [DEBUG ] No samples found: bamtools [2021-06-13 12:32:20,092] multiqc [DEBUG ] No samples found: jellyfish [2021-06-13 12:32:20,100] multiqc [DEBUG ] No samples found: vcftools [2021-06-13 12:32:20,129] multiqc [DEBUG ] No samples found: longranger [2021-06-13 12:32:20,133] multiqc [DEBUG ] No samples found: stacks [2021-06-13 12:32:20,148] multiqc [DEBUG ] No samples found: bbmap [2021-06-13 12:32:20,175] multiqc.modules.bismark.bismark [INFO ] Found 1 bismark alignment reports [2021-06-13 12:32:20,178] multiqc.modules.bismark.bismark [INFO ] Found 1 bismark dedup reports [2021-06-13 12:32:20,183] multiqc.modules.bismark.bismark [INFO ] Found 1 bismark methextract reports [2021-06-13 12:32:20,233] multiqc [DEBUG ] No samples found: biscuit [2021-06-13 12:32:20,257] multiqc [DEBUG ] No samples found: hicexplorer [2021-06-13 12:32:20,263] multiqc [DEBUG ] No samples found: hicup [2021-06-13 12:32:20,288] multiqc [DEBUG ] No samples found: hicpro [2021-06-13 12:32:20,294] multiqc [DEBUG ] No samples found: salmon [2021-06-13 12:32:20,301] multiqc [DEBUG ] No samples found: kallisto [2021-06-13 12:32:20,322] multiqc [DEBUG ] No samples found: slamdunk [2021-06-13 12:32:20,330] multiqc [DEBUG ] No samples found: star [2021-06-13 12:32:20,357] multiqc [DEBUG ] No samples found: hisat2 [2021-06-13 12:32:20,363] multiqc [DEBUG ] No samples found: tophat [2021-06-13 12:32:20,371] multiqc [DEBUG ] No samples found: bowtie2 [2021-06-13 12:32:20,379] multiqc [DEBUG ] No samples found: bowtie1 [2021-06-13 12:32:20,386] multiqc [DEBUG ] No samples found: kat [2021-06-13 12:32:20,406] multiqc [DEBUG ] No samples found: leehom [2021-06-13 12:32:20,429] multiqc [DEBUG ] No samples found: adapterRemoval [2021-06-13 12:32:20,434] multiqc [DEBUG ] No samples found: clipandmerge [2021-06-13 12:32:20,439] multiqc [DEBUG ] No samples found: cutadapt [2021-06-13 12:32:20,443] multiqc [DEBUG ] No samples found: flexbar [2021-06-13 12:32:20,459] multiqc [DEBUG ] No samples found: trimmomatic [2021-06-13 12:32:20,464] multiqc [DEBUG ] No samples found: skewer [2021-06-13 12:32:20,469] multiqc [DEBUG ] No samples found: sortmerna [2021-06-13 12:32:20,473] multiqc [DEBUG ] No samples found: biobloomtools [2021-06-13 12:32:20,492] multiqc [DEBUG ] No samples found: fastq_screen [2021-06-13 12:32:20,496] multiqc [DEBUG ] No samples found: afterqc [2021-06-13 12:32:20,515] multiqc [DEBUG ] No samples found: fastp [2021-06-13 12:32:20,545] multiqc [DEBUG ] No samples found: fastqc [2021-06-13 12:32:20,564] multiqc [DEBUG ] No samples found: minionqc [2021-06-13 12:32:20,580] multiqc [DEBUG ] No samples found: mosdepth [2021-06-13 12:32:20,607] multiqc [DEBUG ] No samples found: clusterflow [2021-06-13 12:32:20,613] multiqc [DEBUG ] No samples found: bcl2fastq [2021-06-13 12:32:20,652] multiqc [DEBUG ] No samples found: interop [2021-06-13 12:32:20,659] multiqc [DEBUG ] No samples found: flash [2021-06-13 12:32:20,698] multiqc [DEBUG ] No samples found: seqyclean [2021-06-13 12:32:20,704] multiqc [INFO ] Compressing plot data [2021-06-13 12:32:20,721] multiqc [INFO ] Report : multiqc_report.html [2021-06-13 12:32:20,722] multiqc [INFO ] Data : multiqc_data [2021-06-13 12:32:20,722] multiqc [DEBUG ] Moving data file from '/tmp/tmpuytuj_nv/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/gscratch/scrubbed/sr320/061321-oly/multiqc_data' [2021-06-13 12:32:20,723] multiqc [DEBUG ] Moving data file from '/tmp/tmpuytuj_nv/multiqc_data/multiqc_bismark_alignment.txt' to '/gscratch/scrubbed/sr320/061321-oly/multiqc_data' [2021-06-13 12:32:20,724] multiqc [DEBUG ] Moving data file from '/tmp/tmpuytuj_nv/multiqc_data/multiqc_bismark_dedup.txt' to '/gscratch/scrubbed/sr320/061321-oly/multiqc_data' [2021-06-13 12:32:20,725] multiqc [DEBUG ] Moving data file from '/tmp/tmpuytuj_nv/multiqc_data/multiqc_bismark_methextract.txt' to '/gscratch/scrubbed/sr320/061321-oly/multiqc_data' [2021-06-13 12:32:20,726] multiqc [DEBUG ] Moving data file from '/tmp/tmpuytuj_nv/multiqc_data/multiqc_general_stats.txt' to '/gscratch/scrubbed/sr320/061321-oly/multiqc_data' [2021-06-13 12:32:20,727] multiqc [DEBUG ] Moving data file from '/tmp/tmpuytuj_nv/multiqc_data/multiqc_sources.txt' to '/gscratch/scrubbed/sr320/061321-oly/multiqc_data' [2021-06-13 12:32:20,728] multiqc [DEBUG ] Moving data file from '/tmp/tmpuytuj_nv/multiqc_data/multiqc_data.json' to '/gscratch/scrubbed/sr320/061321-oly/multiqc_data' [2021-06-13 12:32:21,563] multiqc [INFO ] MultiQC complete