[2021-06-14 13:10:56,442] multiqc [DEBUG ] No MultiQC config found: /gscratch/srlab/programs/anaconda3/lib/python3.7/site-packages/multiqc_config.yaml [2021-06-14 13:10:56,446] multiqc [DEBUG ] No MultiQC config found: /usr/lusers/sr320/.multiqc_config.yaml [2021-06-14 13:10:56,446] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-06-14 13:10:56,447] multiqc [DEBUG ] Command used: /gscratch/srlab/programs/anaconda3/bin/multiqc . [2021-06-14 13:11:01,757] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2021-06-14 13:11:01,757] multiqc [INFO ] This is MultiQC v1.8 [2021-06-14 13:11:01,758] multiqc [DEBUG ] Command : /gscratch/srlab/programs/anaconda3/bin/multiqc . [2021-06-14 13:11:01,758] multiqc [DEBUG ] Working dir : /gscratch/scrubbed/sr320/061421-oly [2021-06-14 13:11:01,758] multiqc [INFO ] Template : default [2021-06-14 13:11:01,758] multiqc [DEBUG ] Running Python 3.7.3 (default, Mar 27 2019, 22:11:17) [GCC 7.3.0] [2021-06-14 13:11:01,758] multiqc [INFO ] Searching : /gscratch/scrubbed/sr320/061421-oly [2021-06-14 13:11:01,759] 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 13:11:01,759] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpy3kn4wkn [2021-06-14 13:11:02,324] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 7_CAGATC_L001_R1_001_trimmed_bismark_bt2.bam [2021-06-14 13:11:02,345] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 6_GCCAAT_10x.bedgraph [2021-06-14 13:11:02,348] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 6_GCCAAT_10x.bedgraph [2021-06-14 13:11:02,485] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 3_TTAGGC_L001_R1_001_trimmed_bismark_bt2.bam [2021-06-14 13:11:02,511] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 8_ACTTGA_5x.tab [2021-06-14 13:11:02,512] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 8_ACTTGA_5x.tab [2021-06-14 13:11:02,513] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: 8_ACTTGA_5x.tab [2021-06-14 13:11:02,513] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: 8_ACTTGA_5x.tab [2021-06-14 13:11:02,513] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: 8_ACTTGA_5x.tab [2021-06-14 13:11:02,513] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: 8_ACTTGA_5x.tab [2021-06-14 13:11:02,534] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: 8_ACTTGA_5x.tab [2021-06-14 13:11:03,698] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 6_GCCAAT_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam [2021-06-14 13:11:03,699] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 6_GCCAAT_L001_R1_001_trimmed_bismark_bt2_SE_report.html [2021-06-14 13:11:03,704] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 7_CAGATC_10x.bedgraph [2021-06-14 13:11:03,705] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 7_CAGATC_10x.bedgraph [2021-06-14 13:11:03,793] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 8_ACTTGA_5x.bedgraph [2021-06-14 13:11:03,794] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 8_ACTTGA_5x.bedgraph [2021-06-14 13:11:03,794] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: 8_ACTTGA_5x.bedgraph [2021-06-14 13:11:03,794] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: 8_ACTTGA_5x.bedgraph [2021-06-14 13:11:03,794] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: 8_ACTTGA_5x.bedgraph [2021-06-14 13:11:03,794] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: 8_ACTTGA_5x.bedgraph [2021-06-14 13:11:03,811] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: 8_ACTTGA_5x.bedgraph [2021-06-14 13:11:04,892] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 1_ATCACG_5x.bedgraph [2021-06-14 13:11:04,893] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 1_ATCACG_5x.bedgraph [2021-06-14 13:11:04,893] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: 1_ATCACG_5x.bedgraph [2021-06-14 13:11:04,894] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: 1_ATCACG_5x.bedgraph [2021-06-14 13:11:04,894] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: 1_ATCACG_5x.bedgraph [2021-06-14 13:11:04,894] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: 1_ATCACG_5x.bedgraph [2021-06-14 13:11:05,386] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 7_CAGATC_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam [2021-06-14 13:11:05,403] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 5_ACAGTG_5x.bedgraph [2021-06-14 13:11:05,404] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 5_ACAGTG_5x.bedgraph [2021-06-14 13:11:05,404] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: 5_ACAGTG_5x.bedgraph [2021-06-14 13:11:05,404] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: 5_ACAGTG_5x.bedgraph [2021-06-14 13:11:05,404] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: 5_ACAGTG_5x.bedgraph [2021-06-14 13:11:05,404] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: 5_ACAGTG_5x.bedgraph [2021-06-14 13:11:05,417] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: 5_ACAGTG_5x.bedgraph [2021-06-14 13:11:06,245] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 4_TGACCA_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam [2021-06-14 13:11:06,245] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 7_CAGATC_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam [2021-06-14 13:11:06,262] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 5_ACAGTG_5x.tab [2021-06-14 13:11:06,263] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 5_ACAGTG_5x.tab [2021-06-14 13:11:06,263] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: 5_ACAGTG_5x.tab [2021-06-14 13:11:06,263] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: 5_ACAGTG_5x.tab [2021-06-14 13:11:06,263] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: 5_ACAGTG_5x.tab [2021-06-14 13:11:06,263] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: 5_ACAGTG_5x.tab [2021-06-14 13:11:06,277] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: 5_ACAGTG_5x.tab [2021-06-14 13:11:07,134] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 2_CGATGT_L001_R1_001_trimmed_bismark_bt2_SE_report.html [2021-06-14 13:11:07,134] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 5_ACAGTG_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam [2021-06-14 13:11:07,134] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 4_TGACCA_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam [2021-06-14 13:11:07,134] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 5_ACAGTG_L001_R1_001_trimmed_bismark_bt2_SE_report.html [2021-06-14 13:11:07,134] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 5_ACAGTG_L001_R1_001_trimmed_bismark_bt2.bam [2021-06-14 13:11:07,138] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 2_CGATGT_10x.bedgraph [2021-06-14 13:11:07,139] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 2_CGATGT_10x.bedgraph [2021-06-14 13:11:07,237] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 7_CAGATC_5x.tab [2021-06-14 13:11:07,238] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 7_CAGATC_5x.tab [2021-06-14 13:11:07,238] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: 7_CAGATC_5x.tab [2021-06-14 13:11:07,238] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: 7_CAGATC_5x.tab [2021-06-14 13:11:07,238] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: 7_CAGATC_5x.tab [2021-06-14 13:11:07,238] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: 7_CAGATC_5x.tab [2021-06-14 13:11:07,839] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 6_GCCAAT_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam [2021-06-14 13:11:07,853] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 4_TGACCA_5x.tab [2021-06-14 13:11:07,854] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 4_TGACCA_5x.tab [2021-06-14 13:11:07,854] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: 4_TGACCA_5x.tab [2021-06-14 13:11:07,855] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: 4_TGACCA_5x.tab [2021-06-14 13:11:07,855] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: 4_TGACCA_5x.tab [2021-06-14 13:11:07,855] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: 4_TGACCA_5x.tab [2021-06-14 13:11:07,865] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: 4_TGACCA_5x.tab [2021-06-14 13:11:08,540] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 6_GCCAAT_5x.bedgraph [2021-06-14 13:11:08,541] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 6_GCCAAT_5x.bedgraph [2021-06-14 13:11:08,541] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: 6_GCCAAT_5x.bedgraph [2021-06-14 13:11:08,541] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: 6_GCCAAT_5x.bedgraph [2021-06-14 13:11:08,541] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: 6_GCCAAT_5x.bedgraph [2021-06-14 13:11:08,541] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: 6_GCCAAT_5x.bedgraph [2021-06-14 13:11:08,553] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: 6_GCCAAT_5x.bedgraph [2021-06-14 13:11:09,328] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 6_GCCAAT_L001_R1_001_trimmed_bismark_bt2.bam [2021-06-14 13:11:09,329] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: bismark_summary_report.html [2021-06-14 13:11:09,333] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 5_ACAGTG_10x.tab [2021-06-14 13:11:09,334] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 5_ACAGTG_10x.tab [2021-06-14 13:11:09,438] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 4_TGACCA_L001_R1_001_trimmed_bismark_bt2_SE_report.html [2021-06-14 13:11:09,449] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 1_ATCACG_5x.tab [2021-06-14 13:11:09,450] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 1_ATCACG_5x.tab [2021-06-14 13:11:09,450] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: 1_ATCACG_5x.tab [2021-06-14 13:11:09,450] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: 1_ATCACG_5x.tab [2021-06-14 13:11:09,450] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: 1_ATCACG_5x.tab [2021-06-14 13:11:09,450] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: 1_ATCACG_5x.tab [2021-06-14 13:11:09,959] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 7_CAGATC_L001_R1_001_trimmed_bismark_bt2_SE_report.html [2021-06-14 13:11:09,960] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 8_ACTTGA_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam [2021-06-14 13:11:09,963] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 1_ATCACG_10x.bedgraph [2021-06-14 13:11:09,964] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 1_ATCACG_10x.bedgraph [2021-06-14 13:11:10,030] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 4_TGACCA_10x.bedgraph [2021-06-14 13:11:10,031] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 4_TGACCA_10x.bedgraph [2021-06-14 13:11:10,107] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 1_ATCACG_L001_R1_001_trimmed_bismark_bt2.bam [2021-06-14 13:11:10,108] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 5_ACAGTG_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam [2021-06-14 13:11:10,122] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 3_TTAGGC_5x.tab [2021-06-14 13:11:10,123] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 3_TTAGGC_5x.tab [2021-06-14 13:11:10,124] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: 3_TTAGGC_5x.tab [2021-06-14 13:11:10,124] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: 3_TTAGGC_5x.tab [2021-06-14 13:11:10,124] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: 3_TTAGGC_5x.tab [2021-06-14 13:11:10,124] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: 3_TTAGGC_5x.tab [2021-06-14 13:11:10,135] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: 3_TTAGGC_5x.tab [2021-06-14 13:11:10,868] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 4_TGACCA_10x.tab [2021-06-14 13:11:10,869] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 4_TGACCA_10x.tab [2021-06-14 13:11:10,963] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 2_CGATGT_5x.tab [2021-06-14 13:11:10,964] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 2_CGATGT_5x.tab [2021-06-14 13:11:10,964] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: 2_CGATGT_5x.tab [2021-06-14 13:11:10,964] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: 2_CGATGT_5x.tab [2021-06-14 13:11:10,964] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: 2_CGATGT_5x.tab [2021-06-14 13:11:10,964] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: 2_CGATGT_5x.tab [2021-06-14 13:11:10,975] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: 2_CGATGT_5x.tab [2021-06-14 13:11:11,687] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 4_TGACCA_5x.bedgraph [2021-06-14 13:11:11,688] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 4_TGACCA_5x.bedgraph [2021-06-14 13:11:11,688] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: 4_TGACCA_5x.bedgraph [2021-06-14 13:11:11,688] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: 4_TGACCA_5x.bedgraph [2021-06-14 13:11:11,688] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: 4_TGACCA_5x.bedgraph [2021-06-14 13:11:11,688] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: 4_TGACCA_5x.bedgraph [2021-06-14 13:11:12,348] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 2_CGATGT_10x.tab [2021-06-14 13:11:12,349] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 2_CGATGT_10x.tab [2021-06-14 13:11:12,439] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 1_ATCACG_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam [2021-06-14 13:11:12,439] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 2_CGATGT_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam.bai [2021-06-14 13:11:12,453] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 2_CGATGT_5x.bedgraph [2021-06-14 13:11:12,454] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 2_CGATGT_5x.bedgraph [2021-06-14 13:11:12,454] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: 2_CGATGT_5x.bedgraph [2021-06-14 13:11:12,454] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: 2_CGATGT_5x.bedgraph [2021-06-14 13:11:12,454] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: 2_CGATGT_5x.bedgraph [2021-06-14 13:11:12,454] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: 2_CGATGT_5x.bedgraph [2021-06-14 13:11:13,151] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 7_CAGATC_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam.bai [2021-06-14 13:11:13,151] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 8_ACTTGA_L001_R1_001_trimmed_bismark_bt2_SE_report.html [2021-06-14 13:11:13,152] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 8_ACTTGA_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam [2021-06-14 13:11:13,164] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 7_CAGATC_5x.bedgraph [2021-06-14 13:11:13,165] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 7_CAGATC_5x.bedgraph [2021-06-14 13:11:13,165] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: 7_CAGATC_5x.bedgraph [2021-06-14 13:11:13,165] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: 7_CAGATC_5x.bedgraph [2021-06-14 13:11:13,165] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: 7_CAGATC_5x.bedgraph [2021-06-14 13:11:13,165] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: 7_CAGATC_5x.bedgraph [2021-06-14 13:11:13,745] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 8_ACTTGA_L001_R1_001_trimmed_bismark_bt2.bam [2021-06-14 13:11:13,746] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 3_TTAGGC_L001_R1_001_trimmed_bismark_bt2_SE_report.html [2021-06-14 13:11:13,746] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 4_TGACCA_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam.bai [2021-06-14 13:11:13,746] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 1_ATCACG_L001_R1_001_trimmed_bismark_bt2_SE_report.html [2021-06-14 13:11:13,746] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 2_CGATGT_L001_R1_001_trimmed_bismark_bt2.bam [2021-06-14 13:11:13,751] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 8_ACTTGA_10x.tab [2021-06-14 13:11:13,752] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 8_ACTTGA_10x.tab [2021-06-14 13:11:13,890] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 8_ACTTGA_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam.bai [2021-06-14 13:11:13,894] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 8_ACTTGA_10x.bedgraph [2021-06-14 13:11:13,895] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 8_ACTTGA_10x.bedgraph [2021-06-14 13:11:14,032] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 3_TTAGGC_10x.tab [2021-06-14 13:11:14,033] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 3_TTAGGC_10x.tab [2021-06-14 13:11:14,122] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 1_ATCACG_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam.bai [2021-06-14 13:11:14,126] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 3_TTAGGC_10x.bedgraph [2021-06-14 13:11:14,127] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 3_TTAGGC_10x.bedgraph [2021-06-14 13:11:14,212] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 6_GCCAAT_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam.bai [2021-06-14 13:11:14,228] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 6_GCCAAT_5x.tab [2021-06-14 13:11:14,229] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 6_GCCAAT_5x.tab [2021-06-14 13:11:14,229] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: 6_GCCAAT_5x.tab [2021-06-14 13:11:14,229] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: 6_GCCAAT_5x.tab [2021-06-14 13:11:14,229] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: 6_GCCAAT_5x.tab [2021-06-14 13:11:14,229] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: 6_GCCAAT_5x.tab [2021-06-14 13:11:14,242] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: 6_GCCAAT_5x.tab [2021-06-14 13:11:15,049] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: job.sh [2021-06-14 13:11:15,059] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 7_CAGATC_10x.tab [2021-06-14 13:11:15,060] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 7_CAGATC_10x.tab [2021-06-14 13:11:15,133] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 5_ACAGTG_10x.bedgraph [2021-06-14 13:11:15,134] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 5_ACAGTG_10x.bedgraph [2021-06-14 13:11:15,235] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 3_TTAGGC_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam [2021-06-14 13:11:15,249] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 3_TTAGGC_5x.bedgraph [2021-06-14 13:11:15,250] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 3_TTAGGC_5x.bedgraph [2021-06-14 13:11:15,250] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: 3_TTAGGC_5x.bedgraph [2021-06-14 13:11:15,250] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: 3_TTAGGC_5x.bedgraph [2021-06-14 13:11:15,250] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: 3_TTAGGC_5x.bedgraph [2021-06-14 13:11:15,250] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: 3_TTAGGC_5x.bedgraph [2021-06-14 13:11:15,261] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: 3_TTAGGC_5x.bedgraph [2021-06-14 13:11:15,965] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 2_CGATGT_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam [2021-06-14 13:11:15,966] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 3_TTAGGC_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam.bai [2021-06-14 13:11:15,970] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 6_GCCAAT_10x.tab [2021-06-14 13:11:15,971] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 6_GCCAAT_10x.tab [2021-06-14 13:11:16,073] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 1_ATCACG_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam [2021-06-14 13:11:16,077] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 1_ATCACG_10x.tab [2021-06-14 13:11:16,078] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 1_ATCACG_10x.tab [2021-06-14 13:11:16,142] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 2_CGATGT_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam [2021-06-14 13:11:16,142] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 3_TTAGGC_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam [2021-06-14 13:11:16,142] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 4_TGACCA_L001_R1_001_trimmed_bismark_bt2.bam [2021-06-14 13:11:16,143] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 5_ACAGTG_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam.bai [2021-06-14 13:11:20,582] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 2.2.4 [2021-06-14 13:11:20,589] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 2.2.4 [2021-06-14 13:11:20,617] multiqc [DEBUG ] No samples found: custom_content [2021-06-14 13:11:20,682] multiqc [DEBUG ] No samples found: conpair [2021-06-14 13:11:20,776] multiqc [DEBUG ] No samples found: peddy [2021-06-14 13:11:20,850] multiqc [DEBUG ] No samples found: methylQA [2021-06-14 13:11:20,872] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-06-14 13:11:20,974] multiqc [DEBUG ] No samples found: qualimap [2021-06-14 13:11:21,013] multiqc [DEBUG ] No samples found: preseq [2021-06-14 13:11:21,065] multiqc [DEBUG ] No samples found: quast [2021-06-14 13:11:21,103] multiqc [DEBUG ] No samples found: qorts [2021-06-14 13:11:21,160] multiqc [DEBUG ] No samples found: rna_seqc [2021-06-14 13:11:21,231] multiqc [DEBUG ] No samples found: rsem [2021-06-14 13:11:21,324] multiqc [DEBUG ] No samples found: rseqc [2021-06-14 13:11:21,356] multiqc [DEBUG ] No samples found: busco [2021-06-14 13:11:21,404] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-06-14 13:11:21,449] multiqc [DEBUG ] No samples found: disambiguate [2021-06-14 13:11:21,475] multiqc [DEBUG ] No samples found: supernova [2021-06-14 13:11:21,562] multiqc [DEBUG ] No samples found: deeptools [2021-06-14 13:11:21,604] multiqc [DEBUG ] No samples found: sargasso [2021-06-14 13:11:21,634] multiqc [DEBUG ] No samples found: verifybamid [2021-06-14 13:11:21,658] multiqc [DEBUG ] No samples found: mirtrace [2021-06-14 13:11:21,683] multiqc [DEBUG ] No samples found: happy [2021-06-14 13:11:21,743] multiqc [DEBUG ] No samples found: homer [2021-06-14 13:11:21,782] multiqc [DEBUG ] No samples found: macs2 [2021-06-14 13:11:21,792] multiqc [DEBUG ] No samples found: theta2 [2021-06-14 13:11:21,843] multiqc [DEBUG ] No samples found: snpeff [2021-06-14 13:11:21,903] multiqc [DEBUG ] No samples found: gatk [2021-06-14 13:11:21,923] multiqc [DEBUG ] No samples found: htseq [2021-06-14 13:11:21,956] multiqc [DEBUG ] No samples found: bcftools [2021-06-14 13:11:21,964] multiqc [DEBUG ] No samples found: featureCounts [2021-06-14 13:11:21,973] multiqc [DEBUG ] No samples found: fgbio [2021-06-14 13:11:21,981] multiqc [DEBUG ] No samples found: dedup [2021-06-14 13:11:22,002] multiqc [DEBUG ] No samples found: damageprofiler [2021-06-14 13:11:22,213] multiqc [DEBUG ] No samples found: biobambam2 [2021-06-14 13:11:22,232] multiqc [DEBUG ] No samples found: mtnucratio [2021-06-14 13:11:22,237] multiqc [DEBUG ] No samples found: picard [2021-06-14 13:11:22,264] multiqc [DEBUG ] No samples found: prokka [2021-06-14 13:11:22,273] multiqc [DEBUG ] No samples found: samblaster [2021-06-14 13:11:22,339] multiqc [DEBUG ] No samples found: samtools [2021-06-14 13:11:22,374] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-06-14 13:11:22,466] multiqc [DEBUG ] No samples found: bamtools [2021-06-14 13:11:22,476] multiqc [DEBUG ] No samples found: jellyfish [2021-06-14 13:11:22,506] multiqc [DEBUG ] No samples found: vcftools [2021-06-14 13:11:22,540] multiqc [DEBUG ] No samples found: longranger [2021-06-14 13:11:22,560] multiqc [DEBUG ] No samples found: stacks [2021-06-14 13:11:22,646] multiqc [DEBUG ] No samples found: bbmap [2021-06-14 13:11:22,705] multiqc.modules.bismark.bismark [INFO ] Found 8 bismark alignment reports [2021-06-14 13:11:22,709] multiqc.modules.bismark.bismark [INFO ] Found 8 bismark dedup reports [2021-06-14 13:11:22,710] multiqc.modules.bismark.bismark [INFO ] Found 8 bismark methextract reports [2021-06-14 13:11:22,754] multiqc [DEBUG ] No samples found: biscuit [2021-06-14 13:11:22,774] multiqc [DEBUG ] No samples found: hicexplorer [2021-06-14 13:11:22,792] multiqc [DEBUG ] No samples found: hicup [2021-06-14 13:11:22,828] multiqc [DEBUG ] No samples found: hicpro [2021-06-14 13:11:22,838] multiqc [DEBUG ] No samples found: salmon [2021-06-14 13:11:22,867] multiqc [DEBUG ] No samples found: kallisto [2021-06-14 13:11:22,901] multiqc [DEBUG ] No samples found: slamdunk [2021-06-14 13:11:22,934] multiqc [DEBUG ] No samples found: star [2021-06-14 13:11:22,963] multiqc [DEBUG ] No samples found: hisat2 [2021-06-14 13:11:22,994] multiqc [DEBUG ] No samples found: tophat [2021-06-14 13:11:23,019] multiqc [DEBUG ] No samples found: bowtie2 [2021-06-14 13:11:23,045] multiqc [DEBUG ] No samples found: bowtie1 [2021-06-14 13:11:23,055] multiqc [DEBUG ] No samples found: kat [2021-06-14 13:11:23,063] multiqc [DEBUG ] No samples found: leehom [2021-06-14 13:11:23,110] multiqc [DEBUG ] No samples found: adapterRemoval [2021-06-14 13:11:23,118] multiqc [DEBUG ] No samples found: clipandmerge [2021-06-14 13:11:23,149] multiqc [DEBUG ] No samples found: cutadapt [2021-06-14 13:11:23,157] multiqc [DEBUG ] No samples found: flexbar [2021-06-14 13:11:23,195] multiqc [DEBUG ] No samples found: trimmomatic [2021-06-14 13:11:23,231] multiqc [DEBUG ] No samples found: skewer [2021-06-14 13:11:23,242] multiqc [DEBUG ] No samples found: sortmerna [2021-06-14 13:11:23,263] multiqc [DEBUG ] No samples found: biobloomtools [2021-06-14 13:11:23,303] multiqc [DEBUG ] No samples found: fastq_screen [2021-06-14 13:11:23,379] multiqc [DEBUG ] No samples found: afterqc [2021-06-14 13:11:23,447] multiqc [DEBUG ] No samples found: fastp [2021-06-14 13:11:23,471] multiqc [DEBUG ] No samples found: fastqc [2021-06-14 13:11:23,517] multiqc [DEBUG ] No samples found: minionqc [2021-06-14 13:11:23,570] multiqc [DEBUG ] No samples found: mosdepth [2021-06-14 13:11:23,600] multiqc [DEBUG ] No samples found: clusterflow [2021-06-14 13:11:23,632] multiqc [DEBUG ] No samples found: bcl2fastq [2021-06-14 13:11:23,677] multiqc [DEBUG ] No samples found: interop [2021-06-14 13:11:23,703] multiqc [DEBUG ] No samples found: flash [2021-06-14 13:11:23,740] multiqc [DEBUG ] No samples found: seqyclean [2021-06-14 13:11:23,769] multiqc [INFO ] Compressing plot data [2021-06-14 13:11:23,811] multiqc [INFO ] Report : multiqc_report.html [2021-06-14 13:11:23,812] multiqc [INFO ] Data : multiqc_data [2021-06-14 13:11:23,812] multiqc [DEBUG ] Moving data file from '/tmp/tmpy3kn4wkn/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/gscratch/scrubbed/sr320/061421-oly/multiqc_data' [2021-06-14 13:11:23,813] multiqc [DEBUG ] Moving data file from '/tmp/tmpy3kn4wkn/multiqc_data/multiqc_bismark_alignment.txt' to '/gscratch/scrubbed/sr320/061421-oly/multiqc_data' [2021-06-14 13:11:23,814] multiqc [DEBUG ] Moving data file from '/tmp/tmpy3kn4wkn/multiqc_data/multiqc_bismark_dedup.txt' to '/gscratch/scrubbed/sr320/061421-oly/multiqc_data' [2021-06-14 13:11:23,815] multiqc [DEBUG ] Moving data file from '/tmp/tmpy3kn4wkn/multiqc_data/multiqc_bismark_methextract.txt' to '/gscratch/scrubbed/sr320/061421-oly/multiqc_data' [2021-06-14 13:11:23,816] multiqc [DEBUG ] Moving data file from '/tmp/tmpy3kn4wkn/multiqc_data/multiqc_general_stats.txt' to '/gscratch/scrubbed/sr320/061421-oly/multiqc_data' [2021-06-14 13:11:23,817] multiqc [DEBUG ] Moving data file from '/tmp/tmpy3kn4wkn/multiqc_data/multiqc_sources.txt' to '/gscratch/scrubbed/sr320/061421-oly/multiqc_data' [2021-06-14 13:11:23,818] multiqc [DEBUG ] Moving data file from '/tmp/tmpy3kn4wkn/multiqc_data/multiqc_data.json' to '/gscratch/scrubbed/sr320/061421-oly/multiqc_data' [2021-06-14 13:11:24,697] multiqc [INFO ] MultiQC complete