[2020-10-05 22:17:23,317] multiqc [DEBUG ] No MultiQC config found: /gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/multiqc_config.yaml [2020-10-05 22:17:23,318] multiqc [DEBUG ] No MultiQC config found: /usr/lusers/strigg/.multiqc_config.yaml [2020-10-05 22:17:23,318] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2020-10-05 22:17:23,318] multiqc [DEBUG ] Command used: /gscratch/srlab/strigg/bin/anaconda3/bin/multiqc /gscratch/scrubbed/strigg/analyses/20200930/ [2020-10-05 22:17:28,600] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2020-10-05 22:17:28,600] multiqc [INFO ] This is MultiQC v1.8 [2020-10-05 22:17:28,601] multiqc [DEBUG ] Command : /gscratch/srlab/strigg/bin/anaconda3/bin/multiqc /gscratch/scrubbed/strigg/analyses/20200930/ [2020-10-05 22:17:28,601] multiqc [DEBUG ] Working dir : /gscratch/scrubbed/strigg/analyses/20200930 [2020-10-05 22:17:28,601] multiqc [INFO ] Template : default [2020-10-05 22:17:28,602] multiqc [DEBUG ] Running Python 3.7.6 | packaged by conda-forge | (default, Mar 5 2020, 15:27:18) [GCC 7.3.0] [2020-10-05 22:17:28,602] multiqc [INFO ] Searching : /gscratch/scrubbed/strigg/analyses/20200930 [2020-10-05 22:17:28,602] 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 [2020-10-05 22:17:28,603] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmp9wy0djfa [2020-10-05 22:17:29,359] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Tank3-15-16_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam.bai [2020-10-05 22:17:29,415] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Tank3-15-16_R2_001.fastq.gz_trimming_report.txt [2020-10-05 22:17:29,419] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Tank3-15-16_R2_001.fastq.gz_trimming_report.txt [2020-10-05 22:17:29,485] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Tank2-025-026_R2_001.fastq.gz_trimming_report.txt [2020-10-05 22:17:29,487] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Tank2-025-026_R2_001.fastq.gz_trimming_report.txt [2020-10-05 22:17:29,507] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Tank3-15-16_R2_001_val_2.fq.gz [2020-10-05 22:17:29,508] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Tank2-025-026_R1_001_val_1.fq.gz [2020-10-05 22:17:29,538] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Tank3-15-16_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam [2020-10-05 22:17:29,539] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Tank3-15-16_R1_001_val_1_fastqc.html [2020-10-05 22:17:29,539] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Tank2-025-026_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam.bai [2020-10-05 22:17:29,540] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Tank2-025-026_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam [2020-10-05 22:17:29,559] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Tank2-025-026_R1_001.fastq.gz_trimming_report.txt [2020-10-05 22:17:29,562] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Tank2-025-026_R1_001.fastq.gz_trimming_report.txt [2020-10-05 22:17:29,581] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Tank3-15-16_R1_001_val_1.fq.gz [2020-10-05 22:17:29,582] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Tank2-025-026_R1_001_val_1_bismark_bt2_pe.bam [2020-10-05 22:17:29,582] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Tank2-025-026_R1_001_val_1_bismark_bt2_pe.deduplicated.bam [2020-10-05 22:17:29,583] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Tank3-15-16_R1_001_val_1_bismark_bt2_pe.bam [2020-10-05 22:17:29,590] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: slurm-351966.out [2020-10-05 22:17:29,593] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: slurm-351966.out [2020-10-05 22:17:29,616] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Tank3-15-16_R1_001_val_1_bismark_bt2_pe.deduplicated.bam [2020-10-05 22:17:29,617] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Tank3-15-16_R2_001_val_2_fastqc.html [2020-10-05 22:17:29,633] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Tank3-15-16_R1_001.fastq.gz_trimming_report.txt [2020-10-05 22:17:29,635] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Tank3-15-16_R1_001.fastq.gz_trimming_report.txt [2020-10-05 22:17:29,646] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Tank2-025-026_R1_001_val_1_fastqc.html [2020-10-05 22:17:29,675] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: slurm-339925.out [2020-10-05 22:17:29,677] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: slurm-339925.out [2020-10-05 22:17:29,777] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Tank2-025-026_R2_001_val_2_fastqc.html [2020-10-05 22:17:29,778] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Tank2-025-026_R2_001_val_2.fq.gz [2020-10-05 22:17:34,460] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 2.2.5 [2020-10-05 22:17:34,484] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 2.2.5 [2020-10-05 22:17:34,538] multiqc [DEBUG ] No samples found: custom_content [2020-10-05 22:17:34,659] multiqc [DEBUG ] No samples found: conpair [2020-10-05 22:17:34,758] multiqc [DEBUG ] No samples found: peddy [2020-10-05 22:17:34,869] multiqc [DEBUG ] No samples found: methylQA [2020-10-05 22:17:34,970] multiqc [DEBUG ] No samples found: phantompeakqualtools [2020-10-05 22:17:35,095] multiqc [DEBUG ] No samples found: qualimap [2020-10-05 22:17:35,141] multiqc [DEBUG ] No samples found: preseq [2020-10-05 22:17:35,203] multiqc [DEBUG ] No samples found: quast [2020-10-05 22:17:35,310] multiqc [DEBUG ] No samples found: qorts [2020-10-05 22:17:35,369] multiqc [DEBUG ] No samples found: rna_seqc [2020-10-05 22:17:35,440] multiqc [DEBUG ] No samples found: rsem [2020-10-05 22:17:35,646] multiqc [DEBUG ] No samples found: rseqc [2020-10-05 22:17:35,687] multiqc [DEBUG ] No samples found: busco [2020-10-05 22:17:35,719] multiqc [DEBUG ] No samples found: goleft_indexcov [2020-10-05 22:17:35,752] multiqc [DEBUG ] No samples found: disambiguate [2020-10-05 22:17:35,819] multiqc [DEBUG ] No samples found: supernova [2020-10-05 22:17:35,992] multiqc [DEBUG ] No samples found: deeptools [2020-10-05 22:17:36,066] multiqc [DEBUG ] No samples found: sargasso [2020-10-05 22:17:36,110] multiqc [DEBUG ] No samples found: verifybamid [2020-10-05 22:17:36,166] multiqc [DEBUG ] No samples found: mirtrace [2020-10-05 22:17:36,267] multiqc [DEBUG ] No samples found: happy [2020-10-05 22:17:36,390] multiqc [DEBUG ] No samples found: homer [2020-10-05 22:17:36,425] multiqc [DEBUG ] No samples found: macs2 [2020-10-05 22:17:36,445] multiqc [DEBUG ] No samples found: theta2 [2020-10-05 22:17:36,533] multiqc [DEBUG ] No samples found: snpeff [2020-10-05 22:17:36,641] multiqc [DEBUG ] No samples found: gatk [2020-10-05 22:17:36,652] multiqc [DEBUG ] No samples found: htseq [2020-10-05 22:17:36,735] multiqc [DEBUG ] No samples found: bcftools [2020-10-05 22:17:36,785] multiqc [DEBUG ] No samples found: featureCounts [2020-10-05 22:17:36,865] multiqc [DEBUG ] No samples found: fgbio [2020-10-05 22:17:36,900] multiqc [DEBUG ] No samples found: dedup [2020-10-05 22:17:36,940] multiqc [DEBUG ] No samples found: damageprofiler [2020-10-05 22:17:37,207] multiqc [DEBUG ] No samples found: biobambam2 [2020-10-05 22:17:37,265] multiqc [DEBUG ] No samples found: mtnucratio [2020-10-05 22:17:37,271] multiqc [DEBUG ] No samples found: picard [2020-10-05 22:17:37,314] multiqc [DEBUG ] No samples found: prokka [2020-10-05 22:17:37,377] multiqc [DEBUG ] No samples found: samblaster [2020-10-05 22:17:37,528] multiqc [DEBUG ] No samples found: samtools [2020-10-05 22:17:37,564] multiqc [DEBUG ] No samples found: sexdeterrmine [2020-10-05 22:17:37,605] multiqc [DEBUG ] No samples found: bamtools [2020-10-05 22:17:37,615] multiqc [DEBUG ] No samples found: jellyfish [2020-10-05 22:17:37,709] multiqc [DEBUG ] No samples found: vcftools [2020-10-05 22:17:37,735] multiqc [DEBUG ] No samples found: longranger [2020-10-05 22:17:37,823] multiqc [DEBUG ] No samples found: stacks [2020-10-05 22:17:38,162] multiqc [DEBUG ] No samples found: bbmap [2020-10-05 22:17:38,274] multiqc.modules.bismark.bismark [INFO ] Found 2 bismark alignment reports [2020-10-05 22:17:38,280] multiqc.modules.bismark.bismark [INFO ] Found 2 bismark dedup reports [2020-10-05 22:17:38,281] multiqc.modules.bismark.bismark [INFO ] Found 2 bismark methextract reports [2020-10-05 22:17:38,337] multiqc [DEBUG ] No samples found: biscuit [2020-10-05 22:17:38,372] multiqc [DEBUG ] No samples found: hicexplorer [2020-10-05 22:17:38,430] multiqc [DEBUG ] No samples found: hicup [2020-10-05 22:17:38,512] multiqc [DEBUG ] No samples found: hicpro [2020-10-05 22:17:38,522] multiqc [DEBUG ] No samples found: salmon [2020-10-05 22:17:38,580] multiqc [DEBUG ] No samples found: kallisto [2020-10-05 22:17:38,634] multiqc [DEBUG ] No samples found: slamdunk [2020-10-05 22:17:38,682] multiqc [DEBUG ] No samples found: star [2020-10-05 22:17:38,705] multiqc [DEBUG ] No samples found: hisat2 [2020-10-05 22:17:38,763] multiqc [DEBUG ] No samples found: tophat [2020-10-05 22:17:38,825] multiqc [DEBUG ] No samples found: bowtie2 [2020-10-05 22:17:38,845] multiqc [DEBUG ] No samples found: bowtie1 [2020-10-05 22:17:38,856] multiqc [DEBUG ] No samples found: kat [2020-10-05 22:17:38,874] multiqc [DEBUG ] No samples found: leehom [2020-10-05 22:17:38,947] multiqc [DEBUG ] No samples found: adapterRemoval [2020-10-05 22:17:38,957] multiqc [DEBUG ] No samples found: clipandmerge [2020-10-05 22:17:39,029] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: Tank2-025-026_R1_001 [2020-10-05 22:17:39,032] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: Tank2-025-026_R2_001 [2020-10-05 22:17:39,035] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: Tank3-15-16_R1_001 [2020-10-05 22:17:39,038] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: Tank3-15-16_R2_001 [2020-10-05 22:17:39,095] multiqc.modules.cutadapt.cutadapt [INFO ] Found 4 reports [2020-10-05 22:17:39,128] multiqc [DEBUG ] No samples found: flexbar [2020-10-05 22:17:39,172] multiqc [DEBUG ] No samples found: trimmomatic [2020-10-05 22:17:39,191] multiqc [DEBUG ] No samples found: skewer [2020-10-05 22:17:39,237] multiqc [DEBUG ] No samples found: sortmerna [2020-10-05 22:17:39,276] multiqc [DEBUG ] No samples found: biobloomtools [2020-10-05 22:17:39,305] multiqc [DEBUG ] No samples found: fastq_screen [2020-10-05 22:17:39,341] multiqc [DEBUG ] No samples found: afterqc [2020-10-05 22:17:39,383] multiqc [DEBUG ] No samples found: fastp [2020-10-05 22:17:39,642] multiqc.modules.fastqc.fastqc [INFO ] Found 4 reports [2020-10-05 22:17:39,820] multiqc [DEBUG ] No samples found: minionqc [2020-10-05 22:17:39,857] multiqc [DEBUG ] No samples found: mosdepth [2020-10-05 22:17:39,886] multiqc [DEBUG ] No samples found: clusterflow [2020-10-05 22:17:39,921] multiqc [DEBUG ] No samples found: bcl2fastq [2020-10-05 22:17:39,979] multiqc [DEBUG ] No samples found: interop [2020-10-05 22:17:40,010] multiqc [DEBUG ] No samples found: flash [2020-10-05 22:17:40,064] multiqc [DEBUG ] No samples found: seqyclean [2020-10-05 22:17:40,092] multiqc [INFO ] Compressing plot data [2020-10-05 22:17:40,282] multiqc [INFO ] Report : multiqc_report.html [2020-10-05 22:17:40,283] multiqc [INFO ] Data : multiqc_data [2020-10-05 22:17:40,285] multiqc [DEBUG ] Moving data file from '/tmp/tmp9wy0djfa/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/gscratch/scrubbed/strigg/analyses/20200930/multiqc_data' [2020-10-05 22:17:40,286] multiqc [DEBUG ] Moving data file from '/tmp/tmp9wy0djfa/multiqc_data/multiqc_bismark_alignment.txt' to '/gscratch/scrubbed/strigg/analyses/20200930/multiqc_data' [2020-10-05 22:17:40,287] multiqc [DEBUG ] Moving data file from '/tmp/tmp9wy0djfa/multiqc_data/multiqc_bismark_dedup.txt' to '/gscratch/scrubbed/strigg/analyses/20200930/multiqc_data' [2020-10-05 22:17:40,287] multiqc [DEBUG ] Moving data file from '/tmp/tmp9wy0djfa/multiqc_data/multiqc_bismark_methextract.txt' to '/gscratch/scrubbed/strigg/analyses/20200930/multiqc_data' [2020-10-05 22:17:40,288] multiqc [DEBUG ] Moving data file from '/tmp/tmp9wy0djfa/multiqc_data/multiqc_cutadapt.txt' to '/gscratch/scrubbed/strigg/analyses/20200930/multiqc_data' [2020-10-05 22:17:40,289] multiqc [DEBUG ] Moving data file from '/tmp/tmp9wy0djfa/multiqc_data/multiqc_fastqc.txt' to '/gscratch/scrubbed/strigg/analyses/20200930/multiqc_data' [2020-10-05 22:17:40,290] multiqc [DEBUG ] Moving data file from '/tmp/tmp9wy0djfa/multiqc_data/multiqc_general_stats.txt' to '/gscratch/scrubbed/strigg/analyses/20200930/multiqc_data' [2020-10-05 22:17:40,291] multiqc [DEBUG ] Moving data file from '/tmp/tmp9wy0djfa/multiqc_data/multiqc_sources.txt' to '/gscratch/scrubbed/strigg/analyses/20200930/multiqc_data' [2020-10-05 22:17:40,291] multiqc [DEBUG ] Moving data file from '/tmp/tmp9wy0djfa/multiqc_data/multiqc_data.json' to '/gscratch/scrubbed/strigg/analyses/20200930/multiqc_data' [2020-10-05 22:17:41,290] multiqc [INFO ] MultiQC complete