[2020-04-13 20:05:26,502] multiqc [DEBUG ] No MultiQC config found: /Users/strigg/anaconda3/lib/python3.6/site-packages/multiqc_config.yaml [2020-04-13 20:05:26,502] multiqc [DEBUG ] No MultiQC config found: /Users/strigg/.multiqc_config.yaml [2020-04-13 20:05:26,503] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2020-04-13 20:05:26,503] multiqc [DEBUG ] Command used: /Users/strigg/anaconda3/bin/multiqc -d -o /Volumes/web/metacarcinus/FROGER_meth_compare/20200413 /Volumes/web/metacarcinus/FROGER_meth_compare/20200311/WGBS_MBD /Volumes/web/metacarcinus/FROGER_meth_compare/20200311/RRBS /Volumes/web/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg /Volumes/web/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg /Volumes/web/seashell/bu-mox/scrubbed/032320-Pact-C1/Pact_C1/ [2020-04-13 20:05:27,776] multiqc [DEBUG ] Latest MultiQC version is v1.8 [2020-04-13 20:05:27,776] multiqc [INFO ] This is MultiQC v1.8 [2020-04-13 20:05:27,776] multiqc [DEBUG ] Command : /Users/strigg/anaconda3/bin/multiqc -d -o /Volumes/web/metacarcinus/FROGER_meth_compare/20200413 /Volumes/web/metacarcinus/FROGER_meth_compare/20200311/WGBS_MBD /Volumes/web/metacarcinus/FROGER_meth_compare/20200311/RRBS /Volumes/web/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg /Volumes/web/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg /Volumes/web/seashell/bu-mox/scrubbed/032320-Pact-C1/Pact_C1/ [2020-04-13 20:05:27,776] multiqc [DEBUG ] Working dir : /Volumes/web/metacarcinus/FROGER_meth_compare/20200413 [2020-04-13 20:05:27,776] multiqc [INFO ] Template : default [2020-04-13 20:05:27,776] multiqc [DEBUG ] Running Python 3.6.8 |Anaconda, Inc.| (default, Dec 29 2018, 19:04:46) [GCC 4.2.1 Compatible Clang 4.0.1 (tags/RELEASE_401/final)] [2020-04-13 20:05:27,776] multiqc [INFO ] Prepending directory to sample names [2020-04-13 20:05:27,776] multiqc [INFO ] Searching : /Volumes/web/metacarcinus/FROGER_meth_compare/20200311/WGBS_MBD [2020-04-13 20:05:27,777] multiqc [INFO ] Searching : /Volumes/web/metacarcinus/FROGER_meth_compare/20200311/RRBS [2020-04-13 20:05:27,777] multiqc [INFO ] Searching : /Volumes/web/seashell/bu-mox/scrubbed/031520-TG-bs/Mcap_tg [2020-04-13 20:05:27,777] multiqc [INFO ] Searching : /Volumes/web/seashell/bu-mox/scrubbed/031520-TG-bs/Pact_tg [2020-04-13 20:05:27,777] multiqc [INFO ] Searching : /Volumes/web/seashell/bu-mox/scrubbed/032320-Pact-C1/Pact_C1 [2020-04-13 20:05:27,777] 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 [2020-04-13 20:05:27,779] multiqc [DEBUG ] Using temporary directory for creating report: /var/folders/_v/3qsffc0s69l8d4v9795nknd40000gt/T/tmp3jy6vjjz [2020-04-13 20:05:27,930] multiqc [DEBUG ] Ignoring directory as matched fn_ignore_dirs: /Volumes/web/metacarcinus/FROGER_meth_compare/20200311/WGBS_MBD/FASTQC/multiqc_data [2020-04-13 20:05:28,160] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth9_R1_001_val_1.fq.gz [2020-04-13 20:05:28,352] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Meth3_R1_001.fastq.gz_trimming_report.txt [2020-04-13 20:05:28,411] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 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[2020-04-13 20:05:35,240] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth2_R2_001_val_2_fastqc.html [2020-04-13 20:05:35,241] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth17_R2_001_val_2_fastqc.html [2020-04-13 20:05:35,241] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth10_R1_001_val_1_fastqc.html [2020-04-13 20:05:35,245] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth16_R1_001_val_1_fastqc.html [2020-04-13 20:05:35,246] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth15_R2_001_val_2.fq.gz [2020-04-13 20:05:35,247] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth5_R2_001_val_2.fq.gz [2020-04-13 20:05:35,248] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth14_R1_001_val_1.fq.gz [2020-04-13 20:05:35,248] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth13_R2_001_val_2.fq.gz [2020-04-13 20:05:35,341] multiqc [DEBUG ] File ignored by hicexplorer 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multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth16_R1_001_val_1_bismark_bt2_pe.bam [2020-04-13 20:05:43,698] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth14_R1_001_val_1_bismark_bt2_pe.bam [2020-04-13 20:05:43,699] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth11_R1_001_val_1_bismark_bt2_pe.bam [2020-04-13 20:05:43,699] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth18_R1_001_val_1_bismark_bt2_pe.bam [2020-04-13 20:05:43,699] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth10_R1_001_val_1_bismark_bt2_pe.bam [2020-04-13 20:05:43,700] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth12_R1_001_val_1_bismark_bt2_pe.bam [2020-04-13 20:05:43,700] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth13_R1_001_val_1_bismark_bt2_pe.bam [2020-04-13 20:05:43,701] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth17_R1_001_val_1_bismark_bt2_pe.bam [2020-04-13 20:05:43,702] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.bam [2020-04-13 20:05:43,704] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam.bai [2020-04-13 20:05:44,123] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Meth17_R1_001_val_1_bismark_bt2_pe._5x.tab [2020-04-13 20:05:44,182] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Meth17_R1_001_val_1_bismark_bt2_pe._5x.tab [2020-04-13 20:05:44,182] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: Meth17_R1_001_val_1_bismark_bt2_pe._5x.tab [2020-04-13 20:05:44,182] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: Meth17_R1_001_val_1_bismark_bt2_pe._5x.tab [2020-04-13 20:05:44,182] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: Meth17_R1_001_val_1_bismark_bt2_pe._5x.tab [2020-04-13 20:05:44,183] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: Meth17_R1_001_val_1_bismark_bt2_pe._5x.tab [2020-04-13 20:05:44,183] multiqc [DEBUG ] File ignored by snpeff because it exceeded search pattern filesize limit: Meth17_R1_001_val_1_bismark_bt2_pe._5x.tab [2020-04-13 20:05:44,183] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: Meth17_R1_001_val_1_bismark_bt2_pe._5x.tab [2020-04-13 20:06:01,993] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam.bai [2020-04-13 20:06:02,003] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam.bai [2020-04-13 20:06:02,004] multiqc [DEBUG ] Ignoring 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20:06:02,256] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: Meth17_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:06:02,256] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: Meth17_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:06:02,256] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: Meth17_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:06:02,256] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: Meth17_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:06:04,999] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Meth16_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:06:05,059] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Meth16_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:06:05,059] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: Meth16_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:06:05,059] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: Meth16_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:06:05,060] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: Meth16_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:06:05,060] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: Meth16_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:06:05,129] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: Meth16_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:06:09,286] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam [2020-04-13 20:06:09,289] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.bam [2020-04-13 20:06:09,295] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.bam [2020-04-13 20:06:09,783] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-13 20:06:09,843] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-13 20:06:09,843] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-13 20:06:09,843] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-13 20:06:09,843] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-13 20:06:09,843] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-13 20:06:09,843] multiqc [DEBUG ] File ignored by snpeff because it exceeded search pattern filesize limit: Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-13 20:06:09,843] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: Meth17_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-13 20:06:26,951] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam.bai [2020-04-13 20:06:27,183] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded 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20:06:27,318] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: Meth16_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-13 20:06:31,505] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Meth18_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:06:31,578] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Meth18_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:06:33,688] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam [2020-04-13 20:06:33,956] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-13 20:06:34,016] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-13 20:06:34,016] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-13 20:06:34,016] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-13 20:06:34,016] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-13 20:06:34,016] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: Meth17_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-13 20:06:36,504] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.bam [2020-04-13 20:06:36,838] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-13 20:06:36,897] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-13 20:06:36,897] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-13 20:06:36,898] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-13 20:06:36,898] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-13 20:06:36,898] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-13 20:06:37,081] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: Meth18_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-13 20:06:48,193] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam.bai [2020-04-13 20:06:48,195] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth11_R1_001_val_1_bismark_bt2_pe.bam [2020-04-13 20:06:48,196] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth18_R1_001_val_1_bismark_bt2_pe.bam [2020-04-13 20:06:48,205] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam.bai [2020-04-13 20:06:48,206] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth10_R1_001_val_1_bismark_bt2_pe.bam [2020-04-13 20:06:48,207] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth12_R1_001_val_1_bismark_bt2_pe.bam [2020-04-13 20:06:48,487] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Meth18_R1_001_val_1_bismark_bt2_pe._5x.tab [2020-04-13 20:06:48,515] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Meth18_R1_001_val_1_bismark_bt2_pe._5x.tab [2020-04-13 20:06:48,515] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: Meth18_R1_001_val_1_bismark_bt2_pe._5x.tab [2020-04-13 20:06:48,515] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: Meth18_R1_001_val_1_bismark_bt2_pe._5x.tab [2020-04-13 20:06:48,515] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: Meth18_R1_001_val_1_bismark_bt2_pe._5x.tab [2020-04-13 20:06:48,515] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: Meth18_R1_001_val_1_bismark_bt2_pe._5x.tab [2020-04-13 20:06:48,692] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: Meth18_R1_001_val_1_bismark_bt2_pe._5x.tab [2020-04-13 20:07:00,702] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Meth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-13 20:07:00,862] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Meth18_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-13 20:07:02,801] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam [2020-04-13 20:07:02,812] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth17_R1_001_val_1_bismark_bt2_pe.bam [2020-04-13 20:07:02,820] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam [2020-04-13 20:07:02,832] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth13_R1_001_val_1_bismark_bt2_pe.sorted.bam [2020-04-13 20:07:02,849] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth15_R1_001_val_1_bismark_bt2_pe.bam [2020-04-13 20:07:02,862] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth13_R1_001_val_1_bismark_bt2_pe.sorted.bam.bai [2020-04-13 20:07:02,868] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth14_R1_001_val_1_bismark_bt2_pe.sorted.bam [2020-04-13 20:07:02,880] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth14_R1_001_val_1_bismark_bt2_pe.bam [2020-04-13 20:07:02,895] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth13_R1_001_val_1_bismark_bt2_pe.bam [2020-04-13 20:07:02,898] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth15_R1_001_val_1_bismark_bt2_pe.sorted.bam.bai [2020-04-13 20:07:02,907] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth15_R1_001_val_1_bismark_bt2_pe.sorted.bam [2020-04-13 20:07:02,916] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth14_R1_001_val_1_bismark_bt2_pe.sorted.bam.bai [2020-04-13 20:07:02,921] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth6_R1_001_val_1_bismark_bt2_pe.bam [2020-04-13 20:07:02,929] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth1_R1_001_val_1_bismark_bt2_pe.bam [2020-04-13 20:07:02,935] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth8_R1_001_val_1_bismark_bt2_pe.bam [2020-04-13 20:07:02,940] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth2_R1_001_val_1_bismark_bt2_pe.bam [2020-04-13 20:07:02,945] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth5_R1_001_val_1_bismark_bt2_pe.bam [2020-04-13 20:07:02,947] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth3_R1_001_val_1_bismark_bt2_pe.bam [2020-04-13 20:07:02,949] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth9_R1_001_val_1_bismark_bt2_pe.bam [2020-04-13 20:07:02,958] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth7_R1_001_val_1_bismark_bt2_pe.bam [2020-04-13 20:07:02,960] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth4_R1_001_val_1_bismark_bt2_pe.bam [2020-04-13 20:07:02,965] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth1_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam.bai [2020-04-13 20:07:02,968] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth2_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam.bai [2020-04-13 20:07:02,978] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth2_R1_001_val_1_bismark_bt2_pe.deduplicated.bam [2020-04-13 20:07:02,994] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth3_R1_001_val_1_bismark_bt2_pe.deduplicated.bam [2020-04-13 20:07:02,996] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth9_R1_001_val_1_bismark_bt2_pe.deduplicated.bam [2020-04-13 20:07:03,006] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth7_R1_001_val_1_bismark_bt2_pe.deduplicated.bam [2020-04-13 20:07:03,007] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth7_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam [2020-04-13 20:07:03,008] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth7_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam.bai [2020-04-13 20:07:03,023] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth1_R1_001_val_1_bismark_bt2_pe.bam [2020-04-13 20:07:03,026] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth8_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam [2020-04-13 20:07:03,033] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth8_R1_001_val_1_bismark_bt2_pe.bam [2020-04-13 20:07:03,041] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth9_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam.bai [2020-04-13 20:07:03,043] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth1_R1_001_val_1_bismark_bt2_pe.deduplicated.bam [2020-04-13 20:07:03,054] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth2_R1_001_val_1_bismark_bt2_pe.bam [2020-04-13 20:07:03,056] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth3_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam [2020-04-13 20:07:03,075] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth3_R1_001_val_1_bismark_bt2_pe.bam [2020-04-13 20:07:03,076] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth2_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam [2020-04-13 20:07:03,077] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth9_R1_001_val_1_bismark_bt2_pe.bam [2020-04-13 20:07:03,084] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth3_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam.bai [2020-04-13 20:07:03,105] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth8_R1_001_val_1_bismark_bt2_pe.deduplicated.bam [2020-04-13 20:07:03,110] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth8_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam.bai [2020-04-13 20:07:03,115] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth1_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam [2020-04-13 20:07:03,126] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth9_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam [2020-04-13 20:07:03,133] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth7_R1_001_val_1_bismark_bt2_pe.bam [2020-04-13 20:07:03,161] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth6_R1_001_val_1_bismark_bt2_pe.bam [2020-04-13 20:07:03,171] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth5_R1_001_val_1_bismark_bt2_pe.sorted.bam [2020-04-13 20:07:03,172] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth5_R1_001_val_1_bismark_bt2_pe.sorted.bam.bai [2020-04-13 20:07:03,176] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth6_R1_001_val_1_bismark_bt2_pe.sorted.bam [2020-04-13 20:07:03,178] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth4_R1_001_val_1_bismark_bt2_pe.sorted.bam.bai [2020-04-13 20:07:03,192] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth5_R1_001_val_1_bismark_bt2_pe.bam [2020-04-13 20:07:03,207] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth4_R1_001_val_1_bismark_bt2_pe.sorted.bam [2020-04-13 20:07:03,219] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth6_R1_001_val_1_bismark_bt2_pe.sorted.bam.bai [2020-04-13 20:07:03,233] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth4_R1_001_val_1_bismark_bt2_pe.bam [2020-04-13 20:07:03,240] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth6_R1_001_val_1_bismark_bt2_pe.bam [2020-04-13 20:07:03,247] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth1_R1_001_val_1_bismark_bt2_pe.bam [2020-04-13 20:07:03,253] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth8_R1_001_val_1_bismark_bt2_pe.bam [2020-04-13 20:07:03,258] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth2_R1_001_val_1_bismark_bt2_pe.bam [2020-04-13 20:07:03,263] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth5_R1_001_val_1_bismark_bt2_pe.bam [2020-04-13 20:07:03,265] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth3_R1_001_val_1_bismark_bt2_pe.bam [2020-04-13 20:07:03,267] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth9_R1_001_val_1_bismark_bt2_pe.bam [2020-04-13 20:07:03,276] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth7_R1_001_val_1_bismark_bt2_pe.bam [2020-04-13 20:07:03,278] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth4_R1_001_val_1_bismark_bt2_pe.bam [2020-04-13 20:07:03,282] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth8_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.sorted.bam.bai [2020-04-13 20:07:03,286] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth1_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam.bai [2020-04-13 20:07:03,289] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth2_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam.bai [2020-04-13 20:07:03,292] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth1_R1_001_val_1_bismark_bt2_pe.sorted.bam.bai [2020-04-13 20:07:03,303] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth2_R1_001_val_1_bismark_bt2_pe.deduplicated.bam [2020-04-13 20:07:03,308] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth3_R1_001_val_1_bismark_bt2_pe.sorted.bam [2020-04-13 20:07:03,686] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Meth1_R1_001_val_1_bismark_bt2_pe._5x.tab [2020-04-13 20:07:03,749] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Meth1_R1_001_val_1_bismark_bt2_pe._5x.tab [2020-04-13 20:07:03,750] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: Meth1_R1_001_val_1_bismark_bt2_pe._5x.tab [2020-04-13 20:07:03,750] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: Meth1_R1_001_val_1_bismark_bt2_pe._5x.tab [2020-04-13 20:07:03,750] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: Meth1_R1_001_val_1_bismark_bt2_pe._5x.tab [2020-04-13 20:07:03,750] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: Meth1_R1_001_val_1_bismark_bt2_pe._5x.tab [2020-04-13 20:07:03,750] multiqc [DEBUG ] File ignored by snpeff because it exceeded search pattern filesize limit: Meth1_R1_001_val_1_bismark_bt2_pe._5x.tab [2020-04-13 20:07:03,750] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: Meth1_R1_001_val_1_bismark_bt2_pe._5x.tab [2020-04-13 20:07:18,329] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth7_R1_001_val_1_bismark_bt2_pe.sorted.bam.bai [2020-04-13 20:07:18,697] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Meth7_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:07:18,726] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Meth7_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:07:18,726] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: Meth7_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:07:18,726] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: Meth7_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:07:18,726] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: Meth7_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:07:18,726] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: Meth7_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:07:18,726] multiqc [DEBUG ] File ignored by snpeff because it exceeded search pattern filesize limit: Meth7_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:07:18,726] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: Meth7_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:07:37,051] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Meth3_R1_001_val_1_bismark_bt2_pe._5x.tab [2020-04-13 20:07:37,131] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Meth3_R1_001_val_1_bismark_bt2_pe._5x.tab [2020-04-13 20:07:37,131] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: Meth3_R1_001_val_1_bismark_bt2_pe._5x.tab [2020-04-13 20:07:37,131] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: Meth3_R1_001_val_1_bismark_bt2_pe._5x.tab [2020-04-13 20:07:37,131] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: Meth3_R1_001_val_1_bismark_bt2_pe._5x.tab [2020-04-13 20:07:37,131] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: Meth3_R1_001_val_1_bismark_bt2_pe._5x.tab [2020-04-13 20:07:39,713] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth3_R1_001_val_1_bismark_bt2_pe.deduplicated.bam [2020-04-13 20:07:39,715] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth9_R1_001_val_1_bismark_bt2_pe.deduplicated.bam [2020-04-13 20:07:39,718] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth1_R1_001_val_1_bismark_bt2_pe.sorted.bam [2020-04-13 20:07:39,726] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth9_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.sorted.bam [2020-04-13 20:07:39,729] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth7_R1_001_val_1_bismark_bt2_pe.deduplicated.bam [2020-04-13 20:07:39,732] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth7_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam [2020-04-13 20:07:39,734] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth7_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam.bai [2020-04-13 20:07:39,737] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth8_R1_001_val_1_bismark_bt2_pe.sorted.bam.bai [2020-04-13 20:07:39,738] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth2_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.sorted.bam [2020-04-13 20:07:40,086] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Meth9_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:07:40,144] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Meth9_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:07:40,144] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: Meth9_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:07:40,144] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: Meth9_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:07:40,144] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: Meth9_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:07:40,144] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: Meth9_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:07:40,144] multiqc [DEBUG ] File ignored by snpeff because it exceeded search pattern filesize limit: Meth9_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:07:40,144] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: Meth9_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:07:52,765] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Meth3_R1_001_val_1_bismark_bt2_pe.deduplicated._5x.tab [2020-04-13 20:07:52,793] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Meth3_R1_001_val_1_bismark_bt2_pe.deduplicated._5x.tab [2020-04-13 20:07:52,793] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: Meth3_R1_001_val_1_bismark_bt2_pe.deduplicated._5x.tab [2020-04-13 20:07:52,793] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: Meth3_R1_001_val_1_bismark_bt2_pe.deduplicated._5x.tab [2020-04-13 20:07:52,793] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: Meth3_R1_001_val_1_bismark_bt2_pe.deduplicated._5x.tab [2020-04-13 20:07:52,794] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: Meth3_R1_001_val_1_bismark_bt2_pe.deduplicated._5x.tab [2020-04-13 20:07:55,534] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Meth2_R1_001_val_1_bismark_bt2_pe._5x.tab [2020-04-13 20:07:55,594] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Meth2_R1_001_val_1_bismark_bt2_pe._5x.tab [2020-04-13 20:07:55,595] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: Meth2_R1_001_val_1_bismark_bt2_pe._5x.tab [2020-04-13 20:07:55,595] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: Meth2_R1_001_val_1_bismark_bt2_pe._5x.tab [2020-04-13 20:07:55,595] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: Meth2_R1_001_val_1_bismark_bt2_pe._5x.tab [2020-04-13 20:07:55,595] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: Meth2_R1_001_val_1_bismark_bt2_pe._5x.tab [2020-04-13 20:07:58,472] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Meth2_R1_001_val_1_bismark_bt2_pe.deduplicated._10x.tab [2020-04-13 20:07:58,554] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Meth2_R1_001_val_1_bismark_bt2_pe.deduplicated._10x.tab [2020-04-13 20:07:59,968] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth3_R1_001_val_1_bismark_bt2_pe.sorted.bam.bai [2020-04-13 20:08:00,414] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Meth7_R1_001_val_1_bismark_bt2_pe.deduplicated._10x.tab [2020-04-13 20:08:00,473] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Meth7_R1_001_val_1_bismark_bt2_pe.deduplicated._10x.tab [2020-04-13 20:08:00,473] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: Meth7_R1_001_val_1_bismark_bt2_pe.deduplicated._10x.tab [2020-04-13 20:08:00,474] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: Meth7_R1_001_val_1_bismark_bt2_pe.deduplicated._10x.tab [2020-04-13 20:08:00,474] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: Meth7_R1_001_val_1_bismark_bt2_pe.deduplicated._10x.tab [2020-04-13 20:08:00,474] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: Meth7_R1_001_val_1_bismark_bt2_pe.deduplicated._10x.tab [2020-04-13 20:08:00,474] multiqc [DEBUG ] File ignored by snpeff because it exceeded search pattern filesize limit: Meth7_R1_001_val_1_bismark_bt2_pe.deduplicated._10x.tab [2020-04-13 20:08:00,474] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: Meth7_R1_001_val_1_bismark_bt2_pe.deduplicated._10x.tab [2020-04-13 20:08:18,546] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth1_R1_001_val_1_bismark_bt2_pe.bam [2020-04-13 20:08:18,547] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth8_R1_001_val_1_bismark_bt2_pe.sorted.bam [2020-04-13 20:08:18,552] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth8_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam [2020-04-13 20:08:18,745] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Meth1_R1_001_val_1_bismark_bt2_pe.deduplicated._5x.tab [2020-04-13 20:08:18,842] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Meth1_R1_001_val_1_bismark_bt2_pe.deduplicated._5x.tab [2020-04-13 20:08:20,535] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth8_R1_001_val_1_bismark_bt2_pe.bam [2020-04-13 20:08:20,769] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Meth1_R1_001_val_1_bismark_bt2_pe.deduplicated._10x.bedgraph [2020-04-13 20:08:20,829] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Meth1_R1_001_val_1_bismark_bt2_pe.deduplicated._10x.bedgraph [2020-04-13 20:08:21,850] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth2_R1_001_val_1_bismark_bt2_pe.sorted.bam.bai [2020-04-13 20:08:22,045] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-13 20:08:22,121] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-13 20:08:22,121] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-13 20:08:22,121] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-13 20:08:22,121] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-13 20:08:22,121] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: Meth2_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-13 20:08:24,724] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth7_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.sorted.bam [2020-04-13 20:08:24,725] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth9_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam.bai [2020-04-13 20:08:24,727] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth1_R1_001_val_1_bismark_bt2_pe.deduplicated.bam [2020-04-13 20:08:24,902] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Meth2_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:08:24,962] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Meth2_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:08:26,900] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-13 20:08:26,929] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-13 20:08:26,929] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-13 20:08:26,929] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-13 20:08:26,929] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-13 20:08:26,929] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-13 20:08:26,929] multiqc [DEBUG ] File ignored by snpeff because it exceeded search pattern filesize limit: Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-13 20:08:26,929] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: Meth7_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-13 20:08:43,840] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth2_R1_001_val_1_bismark_bt2_pe.bam [2020-04-13 20:08:43,843] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth3_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam [2020-04-13 20:08:44,042] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-13 20:08:44,126] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-13 20:08:44,127] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-13 20:08:44,127] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-13 20:08:44,127] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-13 20:08:44,127] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: Meth3_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-13 20:08:46,972] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Meth9_R1_001_val_1_bismark_bt2_pe.deduplicated._10x.bedgraph [2020-04-13 20:08:47,030] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Meth9_R1_001_val_1_bismark_bt2_pe.deduplicated._10x.bedgraph [2020-04-13 20:08:47,030] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: Meth9_R1_001_val_1_bismark_bt2_pe.deduplicated._10x.bedgraph [2020-04-13 20:08:47,030] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: Meth9_R1_001_val_1_bismark_bt2_pe.deduplicated._10x.bedgraph [2020-04-13 20:08:47,030] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: Meth9_R1_001_val_1_bismark_bt2_pe.deduplicated._10x.bedgraph [2020-04-13 20:08:47,031] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: Meth9_R1_001_val_1_bismark_bt2_pe.deduplicated._10x.bedgraph [2020-04-13 20:08:47,031] multiqc [DEBUG ] File ignored by snpeff because it exceeded search pattern filesize limit: Meth9_R1_001_val_1_bismark_bt2_pe.deduplicated._10x.bedgraph [2020-04-13 20:08:47,031] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: Meth9_R1_001_val_1_bismark_bt2_pe.deduplicated._10x.bedgraph [2020-04-13 20:08:58,855] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Meth1_R1_001_val_1_bismark_bt2_pe.deduplicated._10x.tab [2020-04-13 20:08:58,939] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Meth1_R1_001_val_1_bismark_bt2_pe.deduplicated._10x.tab [2020-04-13 20:09:00,029] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth9_R1_001_val_1_bismark_bt2_pe.sorted.bam [2020-04-13 20:09:00,033] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth1_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.sorted.bam.bai [2020-04-13 20:09:00,036] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth1_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.sorted.bam [2020-04-13 20:09:00,046] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth2_R1_001_val_1_bismark_bt2_pe.sorted.bam [2020-04-13 20:09:00,054] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth3_R1_001_val_1_bismark_bt2_pe.bam [2020-04-13 20:09:00,056] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth2_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam [2020-04-13 20:09:00,489] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Meth7_R1_001_val_1_bismark_bt2_pe.deduplicated._10x.bedgraph [2020-04-13 20:09:00,548] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Meth7_R1_001_val_1_bismark_bt2_pe.deduplicated._10x.bedgraph [2020-04-13 20:09:00,548] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: Meth7_R1_001_val_1_bismark_bt2_pe.deduplicated._10x.bedgraph [2020-04-13 20:09:00,548] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: Meth7_R1_001_val_1_bismark_bt2_pe.deduplicated._10x.bedgraph [2020-04-13 20:09:00,548] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: Meth7_R1_001_val_1_bismark_bt2_pe.deduplicated._10x.bedgraph [2020-04-13 20:09:00,549] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: Meth7_R1_001_val_1_bismark_bt2_pe.deduplicated._10x.bedgraph [2020-04-13 20:09:00,549] multiqc [DEBUG ] File ignored by snpeff because it exceeded search pattern filesize limit: Meth7_R1_001_val_1_bismark_bt2_pe.deduplicated._10x.bedgraph [2020-04-13 20:09:00,549] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: Meth7_R1_001_val_1_bismark_bt2_pe.deduplicated._10x.bedgraph [2020-04-13 20:09:17,466] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth9_R1_001_val_1_bismark_bt2_pe.bam [2020-04-13 20:09:17,618] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Meth2_R1_001_val_1_bismark_bt2_pe.deduplicated._10x.bedgraph [2020-04-13 20:09:17,645] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Meth2_R1_001_val_1_bismark_bt2_pe.deduplicated._10x.bedgraph [2020-04-13 20:09:18,710] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth7_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.sorted.bam.bai [2020-04-13 20:09:18,716] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth3_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam.bai [2020-04-13 20:09:18,719] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth3_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.sorted.bam [2020-04-13 20:09:19,059] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-13 20:09:19,117] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-13 20:09:19,117] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-13 20:09:19,118] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-13 20:09:19,118] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-13 20:09:19,118] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-13 20:09:19,118] multiqc [DEBUG ] File ignored by snpeff because it exceeded search pattern filesize limit: Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-13 20:09:19,118] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: Meth9_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-13 20:09:30,824] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth3_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.sorted.bam.bai [2020-04-13 20:09:31,076] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Meth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-13 20:09:31,103] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Meth2_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-13 20:09:32,317] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Meth1_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:09:32,432] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Meth1_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:09:32,432] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: Meth1_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:09:32,432] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: Meth1_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:09:32,432] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: Meth1_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:09:32,432] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: Meth1_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:09:35,242] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth9_R1_001_val_1_bismark_bt2_pe.sorted.bam.bai [2020-04-13 20:09:35,253] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth8_R1_001_val_1_bismark_bt2_pe.deduplicated.bam [2020-04-13 20:09:35,495] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Meth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-13 20:09:35,594] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Meth3_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-13 20:09:37,299] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-13 20:09:37,360] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-13 20:09:37,360] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-13 20:09:37,360] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-13 20:09:37,360] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-13 20:09:37,360] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-13 20:09:37,360] multiqc [DEBUG ] File ignored by snpeff because it exceeded search pattern filesize limit: Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-13 20:09:37,360] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: Meth1_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-13 20:09:51,662] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Meth3_R1_001_val_1_bismark_bt2_pe.deduplicated._10x.tab [2020-04-13 20:09:51,764] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Meth3_R1_001_val_1_bismark_bt2_pe.deduplicated._10x.tab [2020-04-13 20:09:52,951] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth8_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam.bai [2020-04-13 20:09:53,340] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Meth9_R1_001_val_1_bismark_bt2_pe.deduplicated._10x.tab [2020-04-13 20:09:53,445] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Meth9_R1_001_val_1_bismark_bt2_pe.deduplicated._10x.tab [2020-04-13 20:09:53,445] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: Meth9_R1_001_val_1_bismark_bt2_pe.deduplicated._10x.tab [2020-04-13 20:09:53,446] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: Meth9_R1_001_val_1_bismark_bt2_pe.deduplicated._10x.tab [2020-04-13 20:09:53,446] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: Meth9_R1_001_val_1_bismark_bt2_pe.deduplicated._10x.tab [2020-04-13 20:09:53,446] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: Meth9_R1_001_val_1_bismark_bt2_pe.deduplicated._10x.tab [2020-04-13 20:09:53,446] multiqc [DEBUG ] File ignored by snpeff because it exceeded search pattern filesize limit: Meth9_R1_001_val_1_bismark_bt2_pe.deduplicated._10x.tab [2020-04-13 20:09:53,446] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: Meth9_R1_001_val_1_bismark_bt2_pe.deduplicated._10x.tab [2020-04-13 20:10:05,772] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth2_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.sorted.bam.bai [2020-04-13 20:10:05,774] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth1_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam [2020-04-13 20:10:05,972] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Meth2_R1_001_val_1_bismark_bt2_pe.deduplicated._5x.tab [2020-04-13 20:10:06,049] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Meth2_R1_001_val_1_bismark_bt2_pe.deduplicated._5x.tab [2020-04-13 20:10:06,049] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: Meth2_R1_001_val_1_bismark_bt2_pe.deduplicated._5x.tab [2020-04-13 20:10:06,049] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: Meth2_R1_001_val_1_bismark_bt2_pe.deduplicated._5x.tab [2020-04-13 20:10:06,049] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: Meth2_R1_001_val_1_bismark_bt2_pe.deduplicated._5x.tab [2020-04-13 20:10:06,049] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: Meth2_R1_001_val_1_bismark_bt2_pe.deduplicated._5x.tab [2020-04-13 20:10:08,745] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth8_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.sorted.bam [2020-04-13 20:10:08,760] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth7_R1_001_val_1_bismark_bt2_pe.sorted.bam [2020-04-13 20:10:08,763] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth9_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam [2020-04-13 20:10:08,929] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Meth3_R1_001_val_1_bismark_bt2_pe.deduplicated._10x.bedgraph [2020-04-13 20:10:08,988] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Meth3_R1_001_val_1_bismark_bt2_pe.deduplicated._10x.bedgraph [2020-04-13 20:10:10,321] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth9_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.sorted.bam.bai [2020-04-13 20:10:10,323] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth7_R1_001_val_1_bismark_bt2_pe.bam [2020-04-13 20:10:10,522] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-13 20:10:10,619] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-13 20:10:10,620] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-13 20:10:10,620] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-13 20:10:10,620] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-13 20:10:10,620] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: Meth1_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-13 20:10:13,519] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Meth3_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:10:13,599] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Meth3_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:10:15,418] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-13 20:10:15,479] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-13 20:10:15,479] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-13 20:10:15,479] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-13 20:10:15,480] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-13 20:10:15,480] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-13 20:10:15,639] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: Meth6_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-13 20:10:25,571] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth6_R1_001_val_1_bismark_bt2_pe.bam [2020-04-13 20:10:25,801] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-13 20:10:25,861] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-13 20:10:25,861] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-13 20:10:25,861] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-13 20:10:25,861] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-13 20:10:25,862] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-13 20:10:25,941] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: Meth4_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-13 20:10:30,786] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth5_R1_001_val_1_bismark_bt2_pe.sorted.bam [2020-04-13 20:10:30,789] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth5_R1_001_val_1_bismark_bt2_pe.sorted.bam.bai [2020-04-13 20:10:30,795] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth6_R1_001_val_1_bismark_bt2_pe.sorted.bam [2020-04-13 20:10:30,798] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth4_R1_001_val_1_bismark_bt2_pe.sorted.bam.bai [2020-04-13 20:10:30,815] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth5_R1_001_val_1_bismark_bt2_pe.bam [2020-04-13 20:10:31,128] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Meth4_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:10:31,208] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Meth4_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:10:31,208] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: Meth4_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:10:31,208] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: Meth4_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:10:31,208] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: Meth4_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:10:31,208] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: Meth4_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:10:31,296] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: Meth4_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:10:36,599] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth4_R1_001_val_1_bismark_bt2_pe.sorted.bam [2020-04-13 20:10:36,951] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Meth6_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:10:37,009] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Meth6_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:10:37,009] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: Meth6_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:10:37,009] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: Meth6_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:10:37,010] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: Meth6_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:10:37,010] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: Meth6_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:10:37,010] multiqc [DEBUG ] File ignored by snpeff because it exceeded search pattern filesize limit: Meth6_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:10:37,010] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: Meth6_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-13 20:10:47,616] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth6_R1_001_val_1_bismark_bt2_pe.sorted.bam.bai [2020-04-13 20:10:47,641] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth4_R1_001_val_1_bismark_bt2_pe.bam [2020-04-13 20:10:47,983] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.0.3 [2020-04-13 20:10:47,984] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.0.3 [2020-04-13 20:10:47,985] multiqc [DEBUG ] No samples found: custom_content [2020-04-13 20:10:47,991] multiqc [DEBUG ] No samples found: conpair [2020-04-13 20:10:47,996] multiqc [DEBUG ] No samples found: peddy [2020-04-13 20:10:48,002] multiqc [DEBUG ] No samples found: methylQA [2020-04-13 20:10:48,007] multiqc [DEBUG ] No samples found: phantompeakqualtools [2020-04-13 20:10:48,014] multiqc [DEBUG ] No samples found: qualimap [2020-04-13 20:10:48,020] multiqc [DEBUG ] No samples found: preseq [2020-04-13 20:10:48,025] multiqc [DEBUG ] No samples found: quast [2020-04-13 20:10:48,031] multiqc [DEBUG ] No samples found: qorts [2020-04-13 20:10:48,036] multiqc [DEBUG ] No samples found: rna_seqc [2020-04-13 20:10:48,042] multiqc [DEBUG ] No samples found: rsem [2020-04-13 20:10:48,050] multiqc [DEBUG ] No samples found: rseqc [2020-04-13 20:10:48,055] multiqc [DEBUG ] No samples found: busco [2020-04-13 20:10:48,061] multiqc [DEBUG ] No samples found: goleft_indexcov [2020-04-13 20:10:48,066] multiqc [DEBUG ] No samples found: disambiguate [2020-04-13 20:10:48,072] multiqc [DEBUG ] No samples found: supernova [2020-04-13 20:10:48,083] multiqc [DEBUG ] No samples found: deeptools [2020-04-13 20:10:48,089] multiqc [DEBUG ] No samples found: sargasso [2020-04-13 20:10:48,095] multiqc [DEBUG ] No samples found: verifybamid [2020-04-13 20:10:48,100] multiqc [DEBUG ] No samples found: mirtrace [2020-04-13 20:10:48,106] multiqc [DEBUG ] No samples found: happy [2020-04-13 20:10:48,112] multiqc [DEBUG ] No samples found: homer [2020-04-13 20:10:48,118] multiqc [DEBUG ] No samples found: macs2 [2020-04-13 20:10:48,123] multiqc [DEBUG ] No samples found: theta2 [2020-04-13 20:10:48,129] multiqc [DEBUG ] No samples found: snpeff [2020-04-13 20:10:48,136] multiqc [DEBUG ] No samples found: gatk [2020-04-13 20:10:48,141] multiqc [DEBUG ] No samples found: htseq [2020-04-13 20:10:48,147] multiqc [DEBUG ] No samples found: bcftools [2020-04-13 20:10:48,152] multiqc [DEBUG ] No samples found: featureCounts [2020-04-13 20:10:48,158] multiqc [DEBUG ] No samples found: fgbio [2020-04-13 20:10:48,164] multiqc [DEBUG ] No samples found: dedup [2020-04-13 20:10:48,169] multiqc [DEBUG ] No samples found: damageprofiler [2020-04-13 20:10:48,180] multiqc [DEBUG ] No samples found: biobambam2 [2020-04-13 20:10:48,185] multiqc [DEBUG ] No samples found: mtnucratio [2020-04-13 20:10:48,190] multiqc [DEBUG ] No samples found: picard [2020-04-13 20:10:48,196] multiqc [DEBUG ] No samples found: prokka [2020-04-13 20:10:48,201] multiqc [DEBUG ] No samples found: samblaster [2020-04-13 20:10:48,209] multiqc [DEBUG ] No samples found: samtools [2020-04-13 20:10:48,215] multiqc [DEBUG ] No samples found: sexdeterrmine [2020-04-13 20:10:48,220] multiqc [DEBUG ] No samples found: bamtools [2020-04-13 20:10:48,226] multiqc [DEBUG ] No samples found: jellyfish [2020-04-13 20:10:48,233] multiqc [DEBUG ] No samples found: vcftools [2020-04-13 20:10:48,238] multiqc [DEBUG ] No samples found: longranger [2020-04-13 20:10:48,244] multiqc [DEBUG ] No samples found: stacks [2020-04-13 20:10:48,254] multiqc [DEBUG ] No samples found: bbmap [2020-04-13 20:10:48,852] multiqc.modules.bismark.bismark [DEBUG ] Duplicate methylation extraction sample log found! Overwriting: Volumes | web | seashell | bu-mox | scrubbed | 032320-Pact-C1 | Pact_C1 | dedup | Meth1_R1_001_val_1 [2020-04-13 20:10:49,029] multiqc.modules.bismark.bismark [INFO ] Found 27 bismark alignment reports [2020-04-13 20:10:49,035] multiqc.modules.bismark.bismark [INFO ] Found 18 bismark dedup reports [2020-04-13 20:10:49,036] multiqc.modules.bismark.bismark [INFO ] Found 27 bismark methextract reports [2020-04-13 20:10:49,111] multiqc [DEBUG ] No samples found: biscuit [2020-04-13 20:10:49,117] multiqc [DEBUG ] No samples found: hicexplorer [2020-04-13 20:10:49,123] multiqc [DEBUG ] No samples found: hicup [2020-04-13 20:10:49,129] multiqc [DEBUG ] No samples found: hicpro [2020-04-13 20:10:49,134] multiqc [DEBUG ] No samples found: salmon [2020-04-13 20:10:49,140] multiqc [DEBUG ] No samples found: kallisto [2020-04-13 20:10:49,145] multiqc [DEBUG ] No samples found: slamdunk [2020-04-13 20:10:49,151] multiqc [DEBUG ] No samples found: star [2020-04-13 20:10:49,156] multiqc [DEBUG ] No samples found: hisat2 [2020-04-13 20:10:49,162] multiqc [DEBUG ] No samples found: tophat [2020-04-13 20:10:49,168] multiqc [DEBUG ] No samples found: bowtie2 [2020-04-13 20:10:49,174] multiqc [DEBUG ] No samples found: bowtie1 [2020-04-13 20:10:49,180] multiqc [DEBUG ] No samples found: kat [2020-04-13 20:10:49,185] multiqc [DEBUG ] No samples found: leehom [2020-04-13 20:10:49,190] multiqc [DEBUG ] No samples found: adapterRemoval [2020-04-13 20:10:49,197] multiqc [DEBUG ] No samples found: clipandmerge [2020-04-13 20:10:49,347] multiqc.modules.cutadapt.cutadapt [INFO ] Found 36 reports [2020-04-13 20:10:49,376] multiqc [DEBUG ] No samples found: flexbar [2020-04-13 20:10:49,381] multiqc [DEBUG ] No samples found: trimmomatic [2020-04-13 20:10:49,387] multiqc [DEBUG ] No samples found: skewer [2020-04-13 20:10:49,392] multiqc [DEBUG ] No samples found: sortmerna [2020-04-13 20:10:49,398] multiqc [DEBUG ] No samples found: biobloomtools [2020-04-13 20:10:49,405] multiqc [DEBUG ] No samples found: fastq_screen [2020-04-13 20:10:49,410] multiqc [DEBUG ] No samples found: afterqc [2020-04-13 20:10:49,416] multiqc [DEBUG ] No samples found: fastp [2020-04-13 20:11:04,530] multiqc.modules.fastqc.fastqc [INFO ] Found 36 reports [2020-04-13 20:11:05,951] multiqc [DEBUG ] No samples found: minionqc [2020-04-13 20:11:05,957] multiqc [DEBUG ] No samples found: mosdepth [2020-04-13 20:11:05,963] multiqc [DEBUG ] No samples found: clusterflow [2020-04-13 20:11:05,968] multiqc [DEBUG ] No samples found: bcl2fastq [2020-04-13 20:11:05,974] multiqc [DEBUG ] No samples found: interop [2020-04-13 20:11:05,979] multiqc [DEBUG ] No samples found: flash [2020-04-13 20:11:05,985] multiqc [DEBUG ] No samples found: seqyclean [2020-04-13 20:11:06,182] multiqc [INFO ] Compressing plot data [2020-04-13 20:11:08,815] multiqc [INFO ] Report : multiqc_report.html [2020-04-13 20:11:08,815] multiqc [INFO ] Data : multiqc_data [2020-04-13 20:11:08,817] multiqc [DEBUG ] Moving data file from '/var/folders/_v/3qsffc0s69l8d4v9795nknd40000gt/T/tmp3jy6vjjz/multiqc_data/multiqc_bismark_alignment.txt' to '/Volumes/web/metacarcinus/FROGER_meth_compare/20200413/multiqc_data' [2020-04-13 20:11:08,825] multiqc [DEBUG ] Moving data file from '/var/folders/_v/3qsffc0s69l8d4v9795nknd40000gt/T/tmp3jy6vjjz/multiqc_data/multiqc_bismark_dedup.txt' to '/Volumes/web/metacarcinus/FROGER_meth_compare/20200413/multiqc_data' [2020-04-13 20:11:08,831] multiqc [DEBUG ] Moving data file from '/var/folders/_v/3qsffc0s69l8d4v9795nknd40000gt/T/tmp3jy6vjjz/multiqc_data/multiqc_bismark_methextract.txt' to '/Volumes/web/metacarcinus/FROGER_meth_compare/20200413/multiqc_data' [2020-04-13 20:11:08,840] multiqc [DEBUG ] Moving data file from '/var/folders/_v/3qsffc0s69l8d4v9795nknd40000gt/T/tmp3jy6vjjz/multiqc_data/multiqc_cutadapt.txt' to '/Volumes/web/metacarcinus/FROGER_meth_compare/20200413/multiqc_data' [2020-04-13 20:11:08,847] multiqc [DEBUG ] Moving data file from '/var/folders/_v/3qsffc0s69l8d4v9795nknd40000gt/T/tmp3jy6vjjz/multiqc_data/multiqc_data.json' to '/Volumes/web/metacarcinus/FROGER_meth_compare/20200413/multiqc_data' [2020-04-13 20:11:09,305] multiqc [DEBUG ] Moving data file from '/var/folders/_v/3qsffc0s69l8d4v9795nknd40000gt/T/tmp3jy6vjjz/multiqc_data/multiqc_fastqc.txt' to '/Volumes/web/metacarcinus/FROGER_meth_compare/20200413/multiqc_data' [2020-04-13 20:11:09,312] multiqc [DEBUG ] Moving data file from '/var/folders/_v/3qsffc0s69l8d4v9795nknd40000gt/T/tmp3jy6vjjz/multiqc_data/multiqc_general_stats.txt' to '/Volumes/web/metacarcinus/FROGER_meth_compare/20200413/multiqc_data' [2020-04-13 20:11:09,321] multiqc [DEBUG ] Moving data file from '/var/folders/_v/3qsffc0s69l8d4v9795nknd40000gt/T/tmp3jy6vjjz/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/Volumes/web/metacarcinus/FROGER_meth_compare/20200413/multiqc_data' [2020-04-13 20:11:09,327] multiqc [DEBUG ] Moving data file from '/var/folders/_v/3qsffc0s69l8d4v9795nknd40000gt/T/tmp3jy6vjjz/multiqc_data/multiqc_sources.txt' to '/Volumes/web/metacarcinus/FROGER_meth_compare/20200413/multiqc_data' [2020-04-13 20:11:09,558] multiqc [INFO ] MultiQC complete