[2021-06-14 14:54:10,756] multiqc [DEBUG ] No MultiQC config found: /gscratch/srlab/programs/anaconda3/lib/python3.7/site-packages/multiqc_config.yaml [2021-06-14 14:54:10,756] multiqc [DEBUG ] No MultiQC config found: /usr/lusers/sr320/.multiqc_config.yaml [2021-06-14 14:54:10,756] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-06-14 14:54:10,756] multiqc [DEBUG ] Command used: /gscratch/srlab/programs/anaconda3/bin/multiqc . [2021-06-14 14:54:16,098] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2021-06-14 14:54:16,098] multiqc [INFO ] This is MultiQC v1.8 [2021-06-14 14:54:16,100] multiqc [DEBUG ] Command : /gscratch/srlab/programs/anaconda3/bin/multiqc . [2021-06-14 14:54:16,100] multiqc [DEBUG ] Working dir : /gscratch/scrubbed/sr320/061421-olyC [2021-06-14 14:54:16,100] multiqc [INFO ] Template : default [2021-06-14 14:54:16,100] multiqc [DEBUG ] Running Python 3.7.3 (default, Mar 27 2019, 22:11:17) [GCC 7.3.0] [2021-06-14 14:54:16,100] multiqc [INFO ] Searching : /gscratch/scrubbed/sr320/061421-olyC [2021-06-14 14:54:16,101] 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 [2021-06-14 14:54:16,101] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmp59v_zflf [2021-06-14 14:54:16,767] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: combined_bismark_bt2_SE_report.html [2021-06-14 14:54:16,767] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: combined_bismark_bt2.bam [2021-06-14 14:54:16,767] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: combined_bismark_bt2.deduplicated.bam [2021-06-14 14:54:16,924] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: combined_10x.tab [2021-06-14 14:54:16,925] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: combined_10x.tab [2021-06-14 14:54:16,925] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: combined_10x.tab [2021-06-14 14:54:16,925] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: combined_10x.tab [2021-06-14 14:54:16,925] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: combined_10x.tab [2021-06-14 14:54:16,925] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: combined_10x.tab [2021-06-14 14:54:16,925] multiqc [DEBUG ] File ignored by snpeff because it exceeded search pattern filesize limit: combined_10x.tab [2021-06-14 14:54:16,925] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: combined_10x.tab [2021-06-14 14:54:22,175] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: combined_bismark_bt2.deduplicated.sorted.bam [2021-06-14 14:54:22,176] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: bismark_summary_report.html [2021-06-14 14:54:22,183] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: job.sh [2021-06-14 14:54:22,190] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: combined_bismark_bt2.deduplicated.sorted.bam.bai [2021-06-14 14:54:22,277] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: combined_10x.bedgraph [2021-06-14 14:54:22,278] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: combined_10x.bedgraph [2021-06-14 14:54:22,278] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: combined_10x.bedgraph [2021-06-14 14:54:22,278] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: combined_10x.bedgraph [2021-06-14 14:54:22,278] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: combined_10x.bedgraph [2021-06-14 14:54:22,278] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: combined_10x.bedgraph [2021-06-14 14:54:22,278] multiqc [DEBUG ] File ignored by snpeff because it exceeded search pattern filesize limit: combined_10x.bedgraph [2021-06-14 14:54:22,278] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: combined_10x.bedgraph [2021-06-14 14:54:31,119] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 2.2.4 [2021-06-14 14:54:31,150] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 2.2.4 [2021-06-14 14:54:31,183] multiqc [DEBUG ] No samples found: custom_content [2021-06-14 14:54:31,220] multiqc [DEBUG ] No samples found: conpair [2021-06-14 14:54:31,274] multiqc [DEBUG ] No samples found: peddy [2021-06-14 14:54:31,322] multiqc [DEBUG ] No samples found: methylQA [2021-06-14 14:54:31,339] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-06-14 14:54:31,441] multiqc [DEBUG ] No samples found: qualimap [2021-06-14 14:54:31,482] multiqc [DEBUG ] No samples found: preseq [2021-06-14 14:54:31,517] multiqc [DEBUG ] No samples found: quast [2021-06-14 14:54:31,529] multiqc [DEBUG ] No samples found: qorts [2021-06-14 14:54:31,623] multiqc [DEBUG ] No samples found: rna_seqc [2021-06-14 14:54:31,646] multiqc [DEBUG ] No samples found: rsem [2021-06-14 14:54:31,743] multiqc [DEBUG ] No samples found: rseqc [2021-06-14 14:54:31,762] multiqc [DEBUG ] No samples found: busco [2021-06-14 14:54:31,809] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-06-14 14:54:31,824] multiqc [DEBUG ] No samples found: disambiguate [2021-06-14 14:54:31,853] multiqc [DEBUG ] No samples found: supernova [2021-06-14 14:54:31,944] multiqc [DEBUG ] No samples found: deeptools [2021-06-14 14:54:31,965] multiqc [DEBUG ] No samples found: sargasso [2021-06-14 14:54:32,008] multiqc [DEBUG ] No samples found: verifybamid [2021-06-14 14:54:32,031] multiqc [DEBUG ] No samples found: mirtrace [2021-06-14 14:54:32,064] multiqc [DEBUG ] No samples found: happy [2021-06-14 14:54:32,094] multiqc [DEBUG ] No samples found: homer [2021-06-14 14:54:32,160] multiqc [DEBUG ] No samples found: macs2 [2021-06-14 14:54:32,170] multiqc [DEBUG ] No samples found: theta2 [2021-06-14 14:54:32,193] multiqc [DEBUG ] No samples found: snpeff [2021-06-14 14:54:32,242] multiqc [DEBUG ] No samples found: gatk [2021-06-14 14:54:32,304] multiqc [DEBUG ] No samples found: htseq [2021-06-14 14:54:32,336] multiqc [DEBUG ] No samples found: bcftools [2021-06-14 14:54:32,346] multiqc [DEBUG ] No samples found: featureCounts [2021-06-14 14:54:32,360] multiqc [DEBUG ] No samples found: fgbio [2021-06-14 14:54:32,369] multiqc [DEBUG ] No samples found: dedup [2021-06-14 14:54:32,391] multiqc [DEBUG ] No samples found: damageprofiler [2021-06-14 14:54:32,508] multiqc [DEBUG ] No samples found: biobambam2 [2021-06-14 14:54:32,527] multiqc [DEBUG ] No samples found: mtnucratio [2021-06-14 14:54:32,532] multiqc [DEBUG ] No samples found: picard [2021-06-14 14:54:32,559] multiqc [DEBUG ] No samples found: prokka [2021-06-14 14:54:32,570] multiqc [DEBUG ] No samples found: samblaster [2021-06-14 14:54:32,642] multiqc [DEBUG ] No samples found: samtools [2021-06-14 14:54:32,685] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-06-14 14:54:32,725] multiqc [DEBUG ] No samples found: bamtools [2021-06-14 14:54:32,736] multiqc [DEBUG ] No samples found: jellyfish [2021-06-14 14:54:32,753] multiqc [DEBUG ] No samples found: vcftools [2021-06-14 14:54:32,764] multiqc [DEBUG ] No samples found: longranger [2021-06-14 14:54:32,787] multiqc [DEBUG ] No samples found: stacks [2021-06-14 14:54:32,849] multiqc [DEBUG ] No samples found: bbmap [2021-06-14 14:54:32,900] multiqc.modules.bismark.bismark [INFO ] Found 1 bismark alignment reports [2021-06-14 14:54:32,907] multiqc.modules.bismark.bismark [INFO ] Found 1 bismark dedup reports [2021-06-14 14:54:32,916] multiqc.modules.bismark.bismark [INFO ] Found 1 bismark methextract reports [2021-06-14 14:54:32,950] multiqc [DEBUG ] No samples found: biscuit [2021-06-14 14:54:32,976] multiqc [DEBUG ] No samples found: hicexplorer [2021-06-14 14:54:33,001] multiqc [DEBUG ] No samples found: hicup [2021-06-14 14:54:33,020] multiqc [DEBUG ] No samples found: hicpro [2021-06-14 14:54:33,030] multiqc [DEBUG ] No samples found: salmon [2021-06-14 14:54:33,052] multiqc [DEBUG ] No samples found: kallisto [2021-06-14 14:54:33,099] multiqc [DEBUG ] No samples found: slamdunk [2021-06-14 14:54:33,119] multiqc [DEBUG ] No samples found: star [2021-06-14 14:54:33,146] multiqc [DEBUG ] No samples found: hisat2 [2021-06-14 14:54:33,204] multiqc [DEBUG ] No samples found: tophat [2021-06-14 14:54:33,226] multiqc [DEBUG ] No samples found: bowtie2 [2021-06-14 14:54:33,253] multiqc [DEBUG ] No samples found: bowtie1 [2021-06-14 14:54:33,265] multiqc [DEBUG ] No samples found: kat [2021-06-14 14:54:33,275] multiqc [DEBUG ] No samples found: leehom [2021-06-14 14:54:33,315] multiqc [DEBUG ] No samples found: adapterRemoval [2021-06-14 14:54:33,326] multiqc [DEBUG ] No samples found: clipandmerge [2021-06-14 14:54:33,352] multiqc [DEBUG ] No samples found: cutadapt [2021-06-14 14:54:33,362] multiqc [DEBUG ] No samples found: flexbar [2021-06-14 14:54:33,391] multiqc [DEBUG ] No samples found: trimmomatic [2021-06-14 14:54:33,410] multiqc [DEBUG ] No samples found: skewer [2021-06-14 14:54:33,420] multiqc [DEBUG ] No samples found: sortmerna [2021-06-14 14:54:33,487] multiqc [DEBUG ] No samples found: biobloomtools [2021-06-14 14:54:33,519] multiqc [DEBUG ] No samples found: fastq_screen [2021-06-14 14:54:33,563] multiqc [DEBUG ] No samples found: afterqc [2021-06-14 14:54:33,592] multiqc [DEBUG ] No samples found: fastp [2021-06-14 14:54:33,616] multiqc [DEBUG ] No samples found: fastqc [2021-06-14 14:54:33,635] multiqc [DEBUG ] No samples found: minionqc [2021-06-14 14:54:33,654] multiqc [DEBUG ] No samples found: mosdepth [2021-06-14 14:54:33,684] multiqc [DEBUG ] No samples found: clusterflow [2021-06-14 14:54:33,707] multiqc [DEBUG ] No samples found: bcl2fastq [2021-06-14 14:54:33,732] multiqc [DEBUG ] No samples found: interop [2021-06-14 14:54:33,742] multiqc [DEBUG ] No samples found: flash [2021-06-14 14:54:33,767] multiqc [DEBUG ] No samples found: seqyclean [2021-06-14 14:54:33,774] multiqc [INFO ] Compressing plot data [2021-06-14 14:54:33,793] multiqc [INFO ] Report : multiqc_report.html [2021-06-14 14:54:33,793] multiqc [INFO ] Data : multiqc_data [2021-06-14 14:54:33,794] multiqc [DEBUG ] Moving data file from '/tmp/tmp59v_zflf/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/gscratch/scrubbed/sr320/061421-olyC/multiqc_data' [2021-06-14 14:54:33,795] multiqc [DEBUG ] Moving data file from '/tmp/tmp59v_zflf/multiqc_data/multiqc_bismark_alignment.txt' to '/gscratch/scrubbed/sr320/061421-olyC/multiqc_data' [2021-06-14 14:54:33,796] multiqc [DEBUG ] Moving data file from '/tmp/tmp59v_zflf/multiqc_data/multiqc_bismark_dedup.txt' to '/gscratch/scrubbed/sr320/061421-olyC/multiqc_data' [2021-06-14 14:54:33,798] multiqc [DEBUG ] Moving data file from '/tmp/tmp59v_zflf/multiqc_data/multiqc_bismark_methextract.txt' to '/gscratch/scrubbed/sr320/061421-olyC/multiqc_data' [2021-06-14 14:54:33,799] multiqc [DEBUG ] Moving data file from '/tmp/tmp59v_zflf/multiqc_data/multiqc_general_stats.txt' to '/gscratch/scrubbed/sr320/061421-olyC/multiqc_data' [2021-06-14 14:54:33,800] multiqc [DEBUG ] Moving data file from '/tmp/tmp59v_zflf/multiqc_data/multiqc_sources.txt' to '/gscratch/scrubbed/sr320/061421-olyC/multiqc_data' [2021-06-14 14:54:33,801] multiqc [DEBUG ] Moving data file from '/tmp/tmp59v_zflf/multiqc_data/multiqc_data.json' to '/gscratch/scrubbed/sr320/061421-olyC/multiqc_data' [2021-06-14 14:54:34,644] multiqc [INFO ] MultiQC complete