[2021-06-11 11:31:00,704] multiqc [DEBUG ] No MultiQC config found: /gscratch/srlab/programs/anaconda3/lib/python3.7/site-packages/multiqc_config.yaml [2021-06-11 11:31:00,707] multiqc [DEBUG ] No MultiQC config found: /usr/lusers/sr320/.multiqc_config.yaml [2021-06-11 11:31:00,707] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-06-11 11:31:00,707] multiqc [DEBUG ] Command used: /gscratch/srlab/programs/anaconda3/bin/multiqc . [2021-06-11 11:31:05,998] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2021-06-11 11:31:05,998] multiqc [INFO ] This is MultiQC v1.8 [2021-06-11 11:31:05,998] multiqc [DEBUG ] Command : /gscratch/srlab/programs/anaconda3/bin/multiqc . [2021-06-11 11:31:05,998] multiqc [DEBUG ] Working dir : /gscratch/scrubbed/sr320/061021-oly [2021-06-11 11:31:05,998] multiqc [INFO ] Template : default [2021-06-11 11:31:05,999] multiqc [DEBUG ] Running Python 3.7.3 (default, Mar 27 2019, 22:11:17) [GCC 7.3.0] [2021-06-11 11:31:05,999] multiqc [INFO ] Searching : /gscratch/scrubbed/sr320/061021-oly [2021-06-11 11:31:06,000] 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 [2021-06-11 11:31:06,000] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpusv2mqvq [2021-06-11 11:31:06,503] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: combined_bismark_bt2_SE_report.html [2021-06-11 11:31:06,503] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: combined_bismark_bt2.bam [2021-06-11 11:31:06,505] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: combined_bismark_bt2.deduplicated.bam [2021-06-11 11:31:06,601] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: combined_10x.tab [2021-06-11 11:31:06,602] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: combined_10x.tab [2021-06-11 11:31:06,602] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: combined_10x.tab [2021-06-11 11:31:06,602] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: combined_10x.tab [2021-06-11 11:31:06,602] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: combined_10x.tab [2021-06-11 11:31:06,602] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: combined_10x.tab [2021-06-11 11:31:06,602] multiqc [DEBUG ] File ignored by snpeff because it exceeded search pattern filesize limit: combined_10x.tab [2021-06-11 11:31:06,602] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: combined_10x.tab [2021-06-11 11:31:11,179] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: combined_bismark_bt2.deduplicated.sorted.bam [2021-06-11 11:31:11,179] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: bismark_summary_report.html [2021-06-11 11:31:11,185] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: job.sh [2021-06-11 11:31:11,192] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: combined_bismark_bt2.deduplicated.sorted.bam.bai [2021-06-11 11:31:11,193] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: combined_fastqc.html [2021-06-11 11:31:11,273] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: combined_10x.bedgraph [2021-06-11 11:31:11,274] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: combined_10x.bedgraph [2021-06-11 11:31:11,274] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: combined_10x.bedgraph [2021-06-11 11:31:11,274] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: combined_10x.bedgraph [2021-06-11 11:31:11,274] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: combined_10x.bedgraph [2021-06-11 11:31:11,274] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: combined_10x.bedgraph [2021-06-11 11:31:11,274] multiqc [DEBUG ] File ignored by snpeff because it exceeded search pattern filesize limit: combined_10x.bedgraph [2021-06-11 11:31:11,275] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: combined_10x.bedgraph [2021-06-11 11:31:19,480] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 2.2.4 [2021-06-11 11:31:19,495] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 2.2.4 [2021-06-11 11:31:19,523] multiqc [DEBUG ] No samples found: custom_content [2021-06-11 11:31:19,584] multiqc [DEBUG ] No samples found: conpair [2021-06-11 11:31:19,658] multiqc [DEBUG ] No samples found: peddy [2021-06-11 11:31:19,747] multiqc [DEBUG ] No samples found: methylQA [2021-06-11 11:31:19,796] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-06-11 11:31:19,858] multiqc [DEBUG ] No samples found: qualimap [2021-06-11 11:31:19,888] multiqc [DEBUG ] No samples found: preseq [2021-06-11 11:31:19,926] multiqc [DEBUG ] No samples found: quast [2021-06-11 11:31:19,951] multiqc [DEBUG ] No samples found: qorts [2021-06-11 11:31:19,988] multiqc [DEBUG ] No samples found: rna_seqc [2021-06-11 11:31:20,028] multiqc [DEBUG ] No samples found: rsem [2021-06-11 11:31:20,135] multiqc [DEBUG ] No samples found: rseqc [2021-06-11 11:31:20,165] multiqc [DEBUG ] No samples found: busco [2021-06-11 11:31:20,202] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-06-11 11:31:20,227] multiqc [DEBUG ] No samples found: disambiguate [2021-06-11 11:31:20,244] multiqc [DEBUG ] No samples found: supernova [2021-06-11 11:31:20,361] multiqc [DEBUG ] No samples found: deeptools [2021-06-11 11:31:20,405] multiqc [DEBUG ] No samples found: sargasso [2021-06-11 11:31:20,484] multiqc [DEBUG ] No samples found: verifybamid [2021-06-11 11:31:20,508] multiqc [DEBUG ] No samples found: mirtrace [2021-06-11 11:31:20,562] multiqc [DEBUG ] No samples found: happy [2021-06-11 11:31:20,607] multiqc [DEBUG ] No samples found: homer [2021-06-11 11:31:20,618] multiqc [DEBUG ] No samples found: macs2 [2021-06-11 11:31:20,627] multiqc [DEBUG ] No samples found: theta2 [2021-06-11 11:31:20,653] multiqc [DEBUG ] No samples found: snpeff [2021-06-11 11:31:20,701] multiqc [DEBUG ] No samples found: gatk [2021-06-11 11:31:20,723] multiqc [DEBUG ] No samples found: htseq [2021-06-11 11:31:20,751] multiqc [DEBUG ] No samples found: bcftools [2021-06-11 11:31:20,758] multiqc [DEBUG ] No samples found: featureCounts [2021-06-11 11:31:20,767] multiqc [DEBUG ] No samples found: fgbio [2021-06-11 11:31:20,774] multiqc [DEBUG ] No samples found: dedup [2021-06-11 11:31:20,791] multiqc [DEBUG ] No samples found: damageprofiler [2021-06-11 11:31:20,981] multiqc [DEBUG ] No samples found: biobambam2 [2021-06-11 11:31:21,010] multiqc [DEBUG ] No samples found: mtnucratio [2021-06-11 11:31:21,016] multiqc [DEBUG ] No samples found: picard [2021-06-11 11:31:21,040] multiqc [DEBUG ] No samples found: prokka [2021-06-11 11:31:21,049] multiqc [DEBUG ] No samples found: samblaster [2021-06-11 11:31:21,084] multiqc [DEBUG ] No samples found: samtools [2021-06-11 11:31:21,108] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-06-11 11:31:21,141] multiqc [DEBUG ] No samples found: bamtools [2021-06-11 11:31:21,149] multiqc [DEBUG ] No samples found: jellyfish [2021-06-11 11:31:21,180] multiqc [DEBUG ] No samples found: vcftools [2021-06-11 11:31:21,211] multiqc [DEBUG ] No samples found: longranger [2021-06-11 11:31:21,242] multiqc [DEBUG ] No samples found: stacks [2021-06-11 11:31:21,322] multiqc [DEBUG ] No samples found: bbmap [2021-06-11 11:31:21,379] multiqc.modules.bismark.bismark [INFO ] Found 1 bismark alignment reports [2021-06-11 11:31:21,383] multiqc.modules.bismark.bismark [INFO ] Found 1 bismark dedup reports [2021-06-11 11:31:21,384] multiqc.modules.bismark.bismark [INFO ] Found 1 bismark methextract reports [2021-06-11 11:31:21,429] multiqc [DEBUG ] No samples found: biscuit [2021-06-11 11:31:21,449] multiqc [DEBUG ] No samples found: hicexplorer [2021-06-11 11:31:21,474] multiqc [DEBUG ] No samples found: hicup [2021-06-11 11:31:21,500] multiqc [DEBUG ] No samples found: hicpro [2021-06-11 11:31:21,523] multiqc [DEBUG ] No samples found: salmon [2021-06-11 11:31:21,544] multiqc [DEBUG ] No samples found: kallisto [2021-06-11 11:31:21,583] multiqc [DEBUG ] No samples found: slamdunk [2021-06-11 11:31:21,604] multiqc [DEBUG ] No samples found: star [2021-06-11 11:31:21,631] multiqc [DEBUG ] No samples found: hisat2 [2021-06-11 11:31:21,645] multiqc [DEBUG ] No samples found: tophat [2021-06-11 11:31:21,668] multiqc [DEBUG ] No samples found: bowtie2 [2021-06-11 11:31:21,714] multiqc [DEBUG ] No samples found: bowtie1 [2021-06-11 11:31:21,725] multiqc [DEBUG ] No samples found: kat [2021-06-11 11:31:21,735] multiqc [DEBUG ] No samples found: leehom [2021-06-11 11:31:21,764] multiqc [DEBUG ] No samples found: adapterRemoval [2021-06-11 11:31:21,773] multiqc [DEBUG ] No samples found: clipandmerge [2021-06-11 11:31:21,788] multiqc [DEBUG ] No samples found: cutadapt [2021-06-11 11:31:21,797] multiqc [DEBUG ] No samples found: flexbar [2021-06-11 11:31:21,816] multiqc [DEBUG ] No samples found: trimmomatic [2021-06-11 11:31:21,849] multiqc [DEBUG ] No samples found: skewer [2021-06-11 11:31:21,859] multiqc [DEBUG ] No samples found: sortmerna [2021-06-11 11:31:21,901] multiqc [DEBUG ] No samples found: biobloomtools [2021-06-11 11:31:21,930] multiqc [DEBUG ] No samples found: fastq_screen [2021-06-11 11:31:21,965] multiqc [DEBUG ] No samples found: afterqc [2021-06-11 11:31:21,990] multiqc [DEBUG ] No samples found: fastp [2021-06-11 11:31:22,122] multiqc.modules.fastqc.fastqc [INFO ] Found 1 reports [2021-06-11 11:31:22,235] multiqc [DEBUG ] No samples found: minionqc [2021-06-11 11:31:22,256] multiqc [DEBUG ] No samples found: mosdepth [2021-06-11 11:31:22,281] multiqc [DEBUG ] No samples found: clusterflow [2021-06-11 11:31:22,309] multiqc [DEBUG ] No samples found: bcl2fastq [2021-06-11 11:31:22,330] multiqc [DEBUG ] No samples found: interop [2021-06-11 11:31:22,351] multiqc [DEBUG ] No samples found: flash [2021-06-11 11:31:22,376] multiqc [DEBUG ] No samples found: seqyclean [2021-06-11 11:31:22,383] multiqc [INFO ] Compressing plot data [2021-06-11 11:31:22,420] multiqc [INFO ] Report : multiqc_report.html [2021-06-11 11:31:22,420] multiqc [INFO ] Data : multiqc_data [2021-06-11 11:31:22,422] multiqc [DEBUG ] Moving data file from '/tmp/tmpusv2mqvq/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/gscratch/scrubbed/sr320/061021-oly/multiqc_data' [2021-06-11 11:31:22,423] multiqc [DEBUG ] Moving data file from '/tmp/tmpusv2mqvq/multiqc_data/multiqc_bismark_alignment.txt' to '/gscratch/scrubbed/sr320/061021-oly/multiqc_data' [2021-06-11 11:31:22,424] multiqc [DEBUG ] Moving data file from '/tmp/tmpusv2mqvq/multiqc_data/multiqc_bismark_dedup.txt' to '/gscratch/scrubbed/sr320/061021-oly/multiqc_data' [2021-06-11 11:31:22,425] multiqc [DEBUG ] Moving data file from '/tmp/tmpusv2mqvq/multiqc_data/multiqc_bismark_methextract.txt' to '/gscratch/scrubbed/sr320/061021-oly/multiqc_data' [2021-06-11 11:31:22,426] multiqc [DEBUG ] Moving data file from '/tmp/tmpusv2mqvq/multiqc_data/multiqc_fastqc.txt' to '/gscratch/scrubbed/sr320/061021-oly/multiqc_data' [2021-06-11 11:31:22,427] multiqc [DEBUG ] Moving data file from '/tmp/tmpusv2mqvq/multiqc_data/multiqc_general_stats.txt' to '/gscratch/scrubbed/sr320/061021-oly/multiqc_data' [2021-06-11 11:31:22,428] multiqc [DEBUG ] Moving data file from '/tmp/tmpusv2mqvq/multiqc_data/multiqc_sources.txt' to '/gscratch/scrubbed/sr320/061021-oly/multiqc_data' [2021-06-11 11:31:22,429] multiqc [DEBUG ] Moving data file from '/tmp/tmpusv2mqvq/multiqc_data/multiqc_data.json' to '/gscratch/scrubbed/sr320/061021-oly/multiqc_data' [2021-06-11 11:31:23,153] multiqc [INFO ] MultiQC complete