[2022-02-07 09:37:58,253] multiqc [DEBUG ] No MultiQC config found: /gscratch/srlab/programs/anaconda3/lib/python3.7/site-packages/multiqc_config.yaml [2022-02-07 09:37:58,254] multiqc [DEBUG ] No MultiQC config found: /usr/lusers/sr320/.multiqc_config.yaml [2022-02-07 09:37:58,254] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-02-07 09:37:58,254] multiqc [DEBUG ] Command used: /gscratch/srlab/programs/anaconda3/bin/multiqc . [2022-02-07 09:38:03,536] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2022-02-07 09:38:03,536] multiqc [INFO ] This is MultiQC v1.8 [2022-02-07 09:38:03,537] multiqc [DEBUG ] Command : /gscratch/srlab/programs/anaconda3/bin/multiqc . [2022-02-07 09:38:03,537] multiqc [DEBUG ] Working dir : /gscratch/scrubbed/sr320/020122-CMoil [2022-02-07 09:38:03,537] multiqc [INFO ] Template : default [2022-02-07 09:38:03,537] multiqc [DEBUG ] Running Python 3.7.3 (default, Mar 27 2019, 22:11:17) [GCC 7.3.0] [2022-02-07 09:38:03,537] multiqc [INFO ] Searching : /gscratch/scrubbed/sr320/020122-CMoil [2022-02-07 09:38:03,538] 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 [2022-02-07 09:38:03,538] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmp6gwvi203 [2022-02-07 09:38:04,186] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.sorted.bam.bai [2022-02-07 09:38:04,186] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.bam [2022-02-07 09:38:04,186] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.sorted.bam.bai [2022-02-07 09:38:04,187] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.sorted.bam [2022-02-07 09:38:04,294] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: slurm-2553187.out [2022-02-07 09:38:04,296] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: slurm-2553187.out [2022-02-07 09:38:04,532] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: slurm-2553197.out [2022-02-07 09:38:04,534] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: slurm-2553197.out [2022-02-07 09:38:04,612] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bam [2022-02-07 09:38:04,613] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2_SE_report.html [2022-02-07 09:38:04,624] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2_SE_report.html [2022-02-07 09:38:04,628] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: slurm-2553185.out [2022-02-07 09:38:04,630] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: slurm-2553185.out [2022-02-07 09:38:04,638] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.bam [2022-02-07 09:38:04,659] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: bismark_summary_report.html [2022-02-07 09:38:04,664] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: slurm-2557227.out [2022-02-07 09:38:04,665] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: slurm-2557227.out [2022-02-07 09:38:04,724] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: slurm-2553722.out [2022-02-07 09:38:04,726] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: slurm-2553722.out [2022-02-07 09:38:04,746] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.bam [2022-02-07 09:38:04,746] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.sorted.bam [2022-02-07 09:38:04,762] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: slurm-2553183.out [2022-02-07 09:38:04,810] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: slurm-2553207.out [2022-02-07 09:38:04,812] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: slurm-2553207.out [2022-02-07 09:38:04,910] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.sorted.bam [2022-02-07 09:38:04,910] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.bam [2022-02-07 09:38:04,911] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.bam [2022-02-07 09:38:04,915] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: job07.sh [2022-02-07 09:38:04,939] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2_SE_report.html [2022-02-07 09:38:04,940] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.sorted.bam [2022-02-07 09:38:04,975] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: slurm-2555183.out [2022-02-07 09:38:04,976] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: slurm-2555183.out [2022-02-07 09:38:05,078] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: slurm-2553181.out [2022-02-07 09:38:05,083] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.sorted.bam.bai [2022-02-07 09:38:05,083] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bam [2022-02-07 09:38:05,083] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2_SE_report.html [2022-02-07 09:38:05,083] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.sorted.bam.bai [2022-02-07 09:38:05,084] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bam [2022-02-07 09:38:05,115] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: slurm-2552803.out [2022-02-07 09:38:05,116] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: slurm-2552803.out [2022-02-07 09:38:09,703] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 2.2.4 [2022-02-07 09:38:09,717] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 2.2.4 [2022-02-07 09:38:09,771] multiqc [DEBUG ] No samples found: custom_content [2022-02-07 09:38:09,822] multiqc [DEBUG ] No samples found: conpair [2022-02-07 09:38:09,874] multiqc [DEBUG ] No samples found: peddy [2022-02-07 09:38:09,948] multiqc [DEBUG ] No samples found: methylQA [2022-02-07 09:38:09,967] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-02-07 09:38:10,059] multiqc [DEBUG ] No samples found: qualimap [2022-02-07 09:38:10,101] multiqc [DEBUG ] No samples found: preseq [2022-02-07 09:38:10,126] multiqc [DEBUG ] No samples found: quast [2022-02-07 09:38:10,153] multiqc [DEBUG ] No samples found: qorts [2022-02-07 09:38:10,211] multiqc [DEBUG ] No samples found: rna_seqc [2022-02-07 09:38:10,242] multiqc [DEBUG ] No samples found: rsem [2022-02-07 09:38:10,362] multiqc [DEBUG ] No samples found: rseqc [2022-02-07 09:38:10,392] multiqc [DEBUG ] No samples found: busco [2022-02-07 09:38:10,418] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-02-07 09:38:10,434] multiqc [DEBUG ] No samples found: disambiguate [2022-02-07 09:38:10,466] multiqc [DEBUG ] No samples found: supernova [2022-02-07 09:38:10,554] multiqc [DEBUG ] No samples found: deeptools [2022-02-07 09:38:10,614] multiqc [DEBUG ] No samples found: sargasso [2022-02-07 09:38:10,636] multiqc [DEBUG ] No samples found: verifybamid [2022-02-07 09:38:10,662] multiqc [DEBUG ] No samples found: mirtrace [2022-02-07 09:38:10,684] multiqc [DEBUG ] No samples found: happy [2022-02-07 09:38:10,721] multiqc [DEBUG ] No samples found: homer [2022-02-07 09:38:10,744] multiqc [DEBUG ] No samples found: macs2 [2022-02-07 09:38:10,754] multiqc [DEBUG ] No samples found: theta2 [2022-02-07 09:38:10,787] multiqc [DEBUG ] No samples found: snpeff [2022-02-07 09:38:10,868] multiqc [DEBUG ] No samples found: gatk [2022-02-07 09:38:10,880] multiqc [DEBUG ] No samples found: htseq [2022-02-07 09:38:10,908] multiqc [DEBUG ] No samples found: bcftools [2022-02-07 09:38:10,919] multiqc [DEBUG ] No samples found: featureCounts [2022-02-07 09:38:10,933] multiqc [DEBUG ] No samples found: fgbio [2022-02-07 09:38:10,944] multiqc [DEBUG ] No samples found: dedup [2022-02-07 09:38:10,967] multiqc [DEBUG ] No samples found: damageprofiler [2022-02-07 09:38:11,182] multiqc [DEBUG ] No samples found: biobambam2 [2022-02-07 09:38:11,193] multiqc [DEBUG ] No samples found: mtnucratio [2022-02-07 09:38:11,199] multiqc [DEBUG ] No samples found: picard [2022-02-07 09:38:11,224] multiqc [DEBUG ] No samples found: prokka [2022-02-07 09:38:11,235] multiqc [DEBUG ] No samples found: samblaster [2022-02-07 09:38:11,303] multiqc [DEBUG ] No samples found: samtools [2022-02-07 09:38:11,316] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-02-07 09:38:11,366] multiqc [DEBUG ] No samples found: bamtools [2022-02-07 09:38:11,377] multiqc [DEBUG ] No samples found: jellyfish [2022-02-07 09:38:11,397] multiqc [DEBUG ] No samples found: vcftools [2022-02-07 09:38:11,421] multiqc [DEBUG ] No samples found: longranger [2022-02-07 09:38:11,454] multiqc [DEBUG ] No samples found: stacks [2022-02-07 09:38:11,516] multiqc [DEBUG ] No samples found: bbmap [2022-02-07 09:38:11,558] multiqc.modules.bismark.bismark [INFO ] Found 4 bismark alignment reports [2022-02-07 09:38:11,564] multiqc.modules.bismark.bismark [INFO ] Found 4 bismark dedup reports [2022-02-07 09:38:11,565] multiqc.modules.bismark.bismark [INFO ] Found 4 bismark methextract reports [2022-02-07 09:38:11,603] multiqc [DEBUG ] No samples found: biscuit [2022-02-07 09:38:11,634] multiqc [DEBUG ] No samples found: hicexplorer [2022-02-07 09:38:11,668] multiqc [DEBUG ] No samples found: hicup [2022-02-07 09:38:11,688] multiqc [DEBUG ] No samples found: hicpro [2022-02-07 09:38:11,699] multiqc [DEBUG ] No samples found: salmon [2022-02-07 09:38:11,732] multiqc [DEBUG ] No samples found: kallisto [2022-02-07 09:38:11,776] multiqc [DEBUG ] No samples found: slamdunk [2022-02-07 09:38:11,806] multiqc [DEBUG ] No samples found: star [2022-02-07 09:38:11,844] multiqc [DEBUG ] No samples found: hisat2 [2022-02-07 09:38:11,876] multiqc [DEBUG ] No samples found: tophat [2022-02-07 09:38:11,888] multiqc [DEBUG ] No samples found: bowtie2 [2022-02-07 09:38:11,926] multiqc [DEBUG ] No samples found: bowtie1 [2022-02-07 09:38:11,937] multiqc [DEBUG ] No samples found: kat [2022-02-07 09:38:11,947] multiqc [DEBUG ] No samples found: leehom [2022-02-07 09:38:11,981] multiqc [DEBUG ] No samples found: adapterRemoval [2022-02-07 09:38:11,992] multiqc [DEBUG ] No samples found: clipandmerge [2022-02-07 09:38:12,021] multiqc [DEBUG ] No samples found: cutadapt [2022-02-07 09:38:12,032] multiqc [DEBUG ] No samples found: flexbar [2022-02-07 09:38:12,068] multiqc [DEBUG ] No samples found: trimmomatic [2022-02-07 09:38:12,086] multiqc [DEBUG ] No samples found: skewer [2022-02-07 09:38:12,097] multiqc [DEBUG ] No samples found: sortmerna [2022-02-07 09:38:12,116] multiqc [DEBUG ] No samples found: biobloomtools [2022-02-07 09:38:12,150] multiqc [DEBUG ] No samples found: fastq_screen [2022-02-07 09:38:12,180] multiqc [DEBUG ] No samples found: afterqc [2022-02-07 09:38:12,202] multiqc [DEBUG ] No samples found: fastp [2022-02-07 09:38:12,231] multiqc [DEBUG ] No samples found: fastqc [2022-02-07 09:38:12,257] multiqc [DEBUG ] No samples found: minionqc [2022-02-07 09:38:12,269] multiqc [DEBUG ] No samples found: mosdepth [2022-02-07 09:38:12,302] multiqc [DEBUG ] No samples found: clusterflow [2022-02-07 09:38:12,323] multiqc [DEBUG ] No samples found: bcl2fastq [2022-02-07 09:38:12,370] multiqc [DEBUG ] No samples found: interop [2022-02-07 09:38:12,411] multiqc [DEBUG ] No samples found: flash [2022-02-07 09:38:12,434] multiqc [DEBUG ] No samples found: seqyclean [2022-02-07 09:38:12,460] multiqc [INFO ] Compressing plot data [2022-02-07 09:38:12,536] multiqc [INFO ] Report : multiqc_report.html [2022-02-07 09:38:12,536] multiqc [INFO ] Data : multiqc_data [2022-02-07 09:38:12,538] multiqc [DEBUG ] Moving data file from '/tmp/tmp6gwvi203/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/gscratch/scrubbed/sr320/020122-CMoil/multiqc_data' [2022-02-07 09:38:12,540] multiqc [DEBUG ] Moving data file from '/tmp/tmp6gwvi203/multiqc_data/multiqc_bismark_alignment.txt' to '/gscratch/scrubbed/sr320/020122-CMoil/multiqc_data' [2022-02-07 09:38:12,542] multiqc [DEBUG ] Moving data file from '/tmp/tmp6gwvi203/multiqc_data/multiqc_bismark_dedup.txt' to '/gscratch/scrubbed/sr320/020122-CMoil/multiqc_data' [2022-02-07 09:38:12,544] multiqc [DEBUG ] Moving data file from '/tmp/tmp6gwvi203/multiqc_data/multiqc_bismark_methextract.txt' to '/gscratch/scrubbed/sr320/020122-CMoil/multiqc_data' [2022-02-07 09:38:12,546] multiqc [DEBUG ] Moving data file from '/tmp/tmp6gwvi203/multiqc_data/multiqc_general_stats.txt' to '/gscratch/scrubbed/sr320/020122-CMoil/multiqc_data' [2022-02-07 09:38:12,547] multiqc [DEBUG ] Moving data file from '/tmp/tmp6gwvi203/multiqc_data/multiqc_sources.txt' to '/gscratch/scrubbed/sr320/020122-CMoil/multiqc_data' [2022-02-07 09:38:12,549] multiqc [DEBUG ] Moving data file from '/tmp/tmp6gwvi203/multiqc_data/multiqc_data.json' to '/gscratch/scrubbed/sr320/020122-CMoil/multiqc_data' [2022-02-07 09:38:13,368] multiqc [INFO ] MultiQC complete