[2020-04-24 08:53:01,917] multiqc [DEBUG ] No MultiQC config found: /Users/strigg/anaconda3/lib/python3.6/site-packages/multiqc_config.yaml [2020-04-24 08:53:01,917] multiqc [DEBUG ] No MultiQC config found: /Users/strigg/.multiqc_config.yaml [2020-04-24 08:53:01,917] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2020-04-24 08:53:01,917] multiqc [DEBUG ] Command used: /Users/strigg/anaconda3/bin/multiqc /Volumes/web/seashell/bu-mox/scrubbed/032820-lambda/lambda_tg/ [2020-04-24 08:53:03,043] multiqc [DEBUG ] Latest MultiQC version is v1.8 [2020-04-24 08:53:03,043] multiqc [INFO ] This is MultiQC v1.8 [2020-04-24 08:53:03,043] multiqc [DEBUG ] Command : /Users/strigg/anaconda3/bin/multiqc /Volumes/web/seashell/bu-mox/scrubbed/032820-lambda/lambda_tg/ [2020-04-24 08:53:03,043] multiqc [DEBUG ] Working dir : /Users/strigg/Desktop/20200416/Mcap [2020-04-24 08:53:03,043] multiqc [INFO ] Template : default [2020-04-24 08:53:03,043] 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)] [2020-04-24 08:53:03,043] multiqc [INFO ] Searching : /Volumes/web/seashell/bu-mox/scrubbed/032820-lambda/lambda_tg [2020-04-24 08:53:03,044] 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 [2020-04-24 08:53:03,044] multiqc [DEBUG ] Using temporary directory for creating report: /var/folders/_v/3qsffc0s69l8d4v9795nknd40000gt/T/tmpj6mw1jyi [2020-04-24 08:53:03,761] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth15_R1_001_val_1_bismark_bt2_pe.bam [2020-04-24 08:53:03,761] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth16_R1_001_val_1_bismark_bt2_pe.bam [2020-04-24 08:53:03,762] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth6_R1_001_val_1_bismark_bt2_pe.bam [2020-04-24 08:53:03,762] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth1_R1_001_val_1_bismark_bt2_pe.bam [2020-04-24 08:53:03,763] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth8_R1_001_val_1_bismark_bt2_pe.bam [2020-04-24 08:53:03,763] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth2_R1_001_val_1_bismark_bt2_pe.bam [2020-04-24 08:53:03,764] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth14_R1_001_val_1_bismark_bt2_pe.bam [2020-04-24 08:53:03,764] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth11_R1_001_val_1_bismark_bt2_pe.bam [2020-04-24 08:53:03,764] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth18_R1_001_val_1_bismark_bt2_pe.bam [2020-04-24 08:53:03,764] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth5_R1_001_val_1_bismark_bt2_pe.bam [2020-04-24 08:53:03,765] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth3_R1_001_val_1_bismark_bt2_pe.bam [2020-04-24 08:53:03,765] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth9_R1_001_val_1_bismark_bt2_pe.bam [2020-04-24 08:53:03,765] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth10_R1_001_val_1_bismark_bt2_pe.bam [2020-04-24 08:53:03,765] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth12_R1_001_val_1_bismark_bt2_pe.bam [2020-04-24 08:53:03,766] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth13_R1_001_val_1_bismark_bt2_pe.bam [2020-04-24 08:53:03,766] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth17_R1_001_val_1_bismark_bt2_pe.bam [2020-04-24 08:53:03,767] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth7_R1_001_val_1_bismark_bt2_pe.bam [2020-04-24 08:53:03,767] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth4_R1_001_val_1_bismark_bt2_pe.bam [2020-04-24 08:53:03,767] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.bam [2020-04-24 08:53:03,772] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam.bai [2020-04-24 08:53:03,774] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam.bai [2020-04-24 08:53:03,776] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam.bai [2020-04-24 08:53:03,777] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam [2020-04-24 08:53:03,777] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth17_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam [2020-04-24 08:53:03,778] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.bam [2020-04-24 08:53:03,778] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.bam [2020-04-24 08:53:03,783] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth16_R1_001_val_1_bismark_bt2_pe.bam [2020-04-24 08:53:04,435] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-24 08:53:04,492] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-24 08:53:04,492] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-24 08:53:04,492] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-24 08:53:04,492] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-24 08:53:04,493] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-24 08:53:04,493] multiqc [DEBUG ] File ignored by snpeff because it exceeded search pattern filesize limit: Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-24 08:53:04,493] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: Meth11_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-24 08:53:19,267] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam [2020-04-24 08:53:19,267] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.bam [2020-04-24 08:53:19,272] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.bam [2020-04-24 08:53:19,277] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam.bai [2020-04-24 08:53:19,292] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth16_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam [2020-04-24 08:53:19,293] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth12_R1_001_val_1_bismark_bt2_pe.deduplicated.bam [2020-04-24 08:53:19,294] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam.bai [2020-04-24 08:53:19,295] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth11_R1_001_val_1_bismark_bt2_pe.bam [2020-04-24 08:53:19,295] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth18_R1_001_val_1_bismark_bt2_pe.bam [2020-04-24 08:53:19,297] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth10_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam.bai [2020-04-24 08:53:19,297] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth10_R1_001_val_1_bismark_bt2_pe.bam [2020-04-24 08:53:19,298] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth12_R1_001_val_1_bismark_bt2_pe.bam [2020-04-24 08:53:19,903] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Meth11_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-24 08:53:19,931] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Meth11_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-24 08:53:19,931] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: Meth11_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-24 08:53:19,931] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: Meth11_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-24 08:53:19,931] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: Meth11_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-24 08:53:19,932] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: Meth11_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-24 08:53:19,932] multiqc [DEBUG ] File ignored by snpeff because it exceeded search pattern filesize limit: Meth11_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-24 08:53:19,932] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: Meth11_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-24 08:53:35,527] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth18_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam [2020-04-24 08:53:35,532] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth17_R1_001_val_1_bismark_bt2_pe.bam [2020-04-24 08:53:35,534] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth11_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam [2020-04-24 08:53:35,540] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth13_R1_001_val_1_bismark_bt2_pe.sorted.bam [2020-04-24 08:53:36,068] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-24 08:53:36,113] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-24 08:53:36,114] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-24 08:53:36,114] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-24 08:53:36,114] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-24 08:53:36,114] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-24 08:53:36,114] multiqc [DEBUG ] File ignored by snpeff because it exceeded search pattern filesize limit: Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-24 08:53:36,114] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: Meth14_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-24 08:53:54,642] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth15_R1_001_val_1_bismark_bt2_pe.bam [2020-04-24 08:53:55,242] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Meth14_R1_001_val_1_bismark_bt2_pe._5x.tab [2020-04-24 08:53:55,271] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Meth14_R1_001_val_1_bismark_bt2_pe._5x.tab [2020-04-24 08:53:55,271] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: Meth14_R1_001_val_1_bismark_bt2_pe._5x.tab [2020-04-24 08:53:55,271] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: Meth14_R1_001_val_1_bismark_bt2_pe._5x.tab [2020-04-24 08:53:55,271] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: Meth14_R1_001_val_1_bismark_bt2_pe._5x.tab [2020-04-24 08:53:55,271] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: Meth14_R1_001_val_1_bismark_bt2_pe._5x.tab [2020-04-24 08:53:55,272] multiqc [DEBUG ] File ignored by snpeff because it exceeded search pattern filesize limit: Meth14_R1_001_val_1_bismark_bt2_pe._5x.tab [2020-04-24 08:53:55,272] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: Meth14_R1_001_val_1_bismark_bt2_pe._5x.tab [2020-04-24 08:54:15,538] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-24 08:54:15,566] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-24 08:54:15,566] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-24 08:54:15,566] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-24 08:54:15,566] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-24 08:54:15,566] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-24 08:54:15,566] multiqc [DEBUG ] File ignored by snpeff because it exceeded search pattern filesize limit: Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-24 08:54:15,566] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: Meth15_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-24 08:54:34,107] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth13_R1_001_val_1_bismark_bt2_pe.sorted.bam.bai [2020-04-24 08:54:34,118] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth14_R1_001_val_1_bismark_bt2_pe.sorted.bam [2020-04-24 08:54:34,138] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth14_R1_001_val_1_bismark_bt2_pe.bam [2020-04-24 08:54:34,670] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-24 08:54:34,701] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-24 08:54:34,701] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-24 08:54:34,702] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-24 08:54:34,702] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-24 08:54:34,702] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-24 08:54:34,702] multiqc [DEBUG ] File ignored by snpeff because it exceeded search pattern filesize limit: Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-24 08:54:34,702] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: Meth14_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-24 08:54:53,284] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-24 08:54:53,367] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-24 08:54:53,367] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-24 08:54:53,367] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-24 08:54:53,367] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-24 08:54:53,367] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-24 08:54:53,367] multiqc [DEBUG ] File ignored by snpeff because it exceeded search pattern filesize limit: Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-24 08:54:53,368] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: Meth15_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-24 08:55:12,259] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth13_R1_001_val_1_bismark_bt2_pe.bam [2020-04-24 08:55:12,266] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth15_R1_001_val_1_bismark_bt2_pe.sorted.bam.bai [2020-04-24 08:55:12,867] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-24 08:55:12,896] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-24 08:55:12,897] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-24 08:55:12,897] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-24 08:55:12,897] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-24 08:55:12,897] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-24 08:55:12,897] multiqc [DEBUG ] File ignored by snpeff because it exceeded search pattern filesize limit: Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-24 08:55:12,897] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: Meth13_R1_001_val_1_bismark_bt2_pe._10x.bedgraph [2020-04-24 08:55:32,232] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Meth14_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-24 08:55:32,366] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Meth14_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-24 08:55:32,366] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: Meth14_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-24 08:55:32,366] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: Meth14_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-24 08:55:32,366] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: Meth14_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-24 08:55:32,366] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: Meth14_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-24 08:55:32,366] multiqc [DEBUG ] File ignored by snpeff because it exceeded search pattern filesize limit: Meth14_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-24 08:55:32,366] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: Meth14_R1_001_val_1_bismark_bt2_pe._10x.tab [2020-04-24 08:55:52,016] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-24 08:55:52,044] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-24 08:55:52,044] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-24 08:55:52,044] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-24 08:55:52,044] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-24 08:55:52,044] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-24 08:55:52,045] multiqc [DEBUG ] File ignored by snpeff because it exceeded search pattern filesize limit: Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-24 08:55:52,045] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: Meth13_R1_001_val_1_bismark_bt2_pe._5x.bedgraph [2020-04-24 08:56:10,930] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth15_R1_001_val_1_bismark_bt2_pe.sorted.bam [2020-04-24 08:56:10,942] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Meth14_R1_001_val_1_bismark_bt2_pe.sorted.bam.bai [2020-04-24 08:56:12,859] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.0.3 [2020-04-24 08:56:12,872] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.0.3 [2020-04-24 08:56:12,888] multiqc [DEBUG ] No samples found: custom_content [2020-04-24 08:56:12,930] multiqc [DEBUG ] No samples found: conpair [2020-04-24 08:56:12,963] multiqc [DEBUG ] No samples found: peddy [2020-04-24 08:56:12,997] multiqc [DEBUG ] No samples found: methylQA [2020-04-24 08:56:13,010] multiqc [DEBUG ] No samples found: phantompeakqualtools [2020-04-24 08:56:13,048] multiqc [DEBUG ] No samples found: qualimap [2020-04-24 08:56:13,062] multiqc [DEBUG ] No samples found: preseq [2020-04-24 08:56:13,083] multiqc [DEBUG ] No samples found: quast [2020-04-24 08:56:13,096] multiqc [DEBUG ] No samples found: qorts [2020-04-24 08:56:13,145] multiqc [DEBUG ] No samples found: rna_seqc [2020-04-24 08:56:13,154] multiqc [DEBUG ] No samples found: rsem [2020-04-24 08:56:13,204] multiqc [DEBUG ] No samples found: rseqc [2020-04-24 08:56:13,211] multiqc [DEBUG ] No samples found: busco [2020-04-24 08:56:13,229] multiqc [DEBUG ] No samples found: goleft_indexcov [2020-04-24 08:56:13,249] multiqc [DEBUG ] No samples found: disambiguate [2020-04-24 08:56:13,269] multiqc [DEBUG ] No samples found: supernova [2020-04-24 08:56:13,306] multiqc [DEBUG ] No samples found: deeptools [2020-04-24 08:56:13,327] multiqc [DEBUG ] No samples found: sargasso [2020-04-24 08:56:13,334] multiqc [DEBUG ] No samples found: verifybamid [2020-04-24 08:56:13,341] multiqc [DEBUG ] No samples found: mirtrace [2020-04-24 08:56:13,369] multiqc [DEBUG ] No samples found: happy [2020-04-24 08:56:13,390] multiqc [DEBUG ] No samples found: homer [2020-04-24 08:56:13,403] multiqc [DEBUG ] No samples found: macs2 [2020-04-24 08:56:13,413] multiqc [DEBUG ] No samples found: theta2 [2020-04-24 08:56:13,421] multiqc [DEBUG ] No samples found: snpeff [2020-04-24 08:56:13,436] multiqc [DEBUG ] No samples found: gatk [2020-04-24 08:56:13,452] multiqc [DEBUG ] No samples found: htseq [2020-04-24 08:56:13,480] multiqc [DEBUG ] No samples found: bcftools [2020-04-24 08:56:13,514] multiqc [DEBUG ] No samples found: featureCounts [2020-04-24 08:56:13,522] multiqc [DEBUG ] No samples found: fgbio [2020-04-24 08:56:13,544] multiqc [DEBUG ] No samples found: dedup [2020-04-24 08:56:13,550] multiqc [DEBUG ] No samples found: damageprofiler [2020-04-24 08:56:13,637] multiqc [DEBUG ] No samples found: biobambam2 [2020-04-24 08:56:13,655] multiqc [DEBUG ] No samples found: mtnucratio [2020-04-24 08:56:13,660] multiqc [DEBUG ] No samples found: picard [2020-04-24 08:56:13,683] multiqc [DEBUG ] No samples found: prokka [2020-04-24 08:56:13,707] multiqc [DEBUG ] No samples found: samblaster [2020-04-24 08:56:13,734] multiqc [DEBUG ] No samples found: samtools [2020-04-24 08:56:13,750] multiqc [DEBUG ] No samples found: sexdeterrmine [2020-04-24 08:56:13,767] multiqc [DEBUG ] No samples found: bamtools [2020-04-24 08:56:13,774] multiqc [DEBUG ] No samples found: jellyfish [2020-04-24 08:56:13,809] multiqc [DEBUG ] No samples found: vcftools [2020-04-24 08:56:13,837] multiqc [DEBUG ] No samples found: longranger [2020-04-24 08:56:13,852] multiqc [DEBUG ] No samples found: stacks [2020-04-24 08:56:13,956] multiqc [DEBUG ] No samples found: bbmap [2020-04-24 08:56:14,412] multiqc.modules.bismark.bismark [INFO ] Found 18 bismark alignment reports [2020-04-24 08:56:14,419] multiqc.modules.bismark.bismark [INFO ] Found 6 bismark dedup reports [2020-04-24 08:56:14,420] multiqc.modules.bismark.bismark [INFO ] Found 9 bismark methextract reports [2020-04-24 08:56:14,489] multiqc [DEBUG ] No samples found: biscuit [2020-04-24 08:56:14,518] multiqc [DEBUG ] No samples found: hicexplorer [2020-04-24 08:56:14,541] multiqc [DEBUG ] No samples found: hicup [2020-04-24 08:56:14,570] multiqc [DEBUG ] No samples found: hicpro [2020-04-24 08:56:14,594] multiqc [DEBUG ] No samples found: salmon [2020-04-24 08:56:14,604] multiqc [DEBUG ] No samples found: kallisto [2020-04-24 08:56:14,631] multiqc [DEBUG ] No samples found: slamdunk [2020-04-24 08:56:14,648] multiqc [DEBUG ] No samples found: star [2020-04-24 08:56:14,662] multiqc [DEBUG ] No samples found: hisat2 [2020-04-24 08:56:14,678] multiqc [DEBUG ] No samples found: tophat [2020-04-24 08:56:14,697] multiqc [DEBUG ] No samples found: bowtie2 [2020-04-24 08:56:14,711] multiqc [DEBUG ] No samples found: bowtie1 [2020-04-24 08:56:14,728] multiqc [DEBUG ] No samples found: kat [2020-04-24 08:56:14,743] multiqc [DEBUG ] No samples found: leehom [2020-04-24 08:56:14,750] multiqc [DEBUG ] No samples found: adapterRemoval [2020-04-24 08:56:14,768] multiqc [DEBUG ] No samples found: clipandmerge [2020-04-24 08:56:14,785] multiqc [DEBUG ] No samples found: cutadapt [2020-04-24 08:56:14,808] multiqc [DEBUG ] No samples found: flexbar [2020-04-24 08:56:14,836] multiqc [DEBUG ] No samples found: trimmomatic [2020-04-24 08:56:14,853] multiqc [DEBUG ] No samples found: skewer [2020-04-24 08:56:14,861] multiqc [DEBUG ] No samples found: sortmerna [2020-04-24 08:56:14,869] multiqc [DEBUG ] No samples found: biobloomtools [2020-04-24 08:56:14,885] multiqc [DEBUG ] No samples found: fastq_screen [2020-04-24 08:56:14,900] multiqc [DEBUG ] No samples found: afterqc [2020-04-24 08:56:14,915] multiqc [DEBUG ] No samples found: fastp [2020-04-24 08:56:14,938] multiqc [DEBUG ] No samples found: fastqc [2020-04-24 08:56:15,016] multiqc [DEBUG ] No samples found: minionqc [2020-04-24 08:56:15,029] multiqc [DEBUG ] No samples found: mosdepth [2020-04-24 08:56:15,052] multiqc [DEBUG ] No samples found: clusterflow [2020-04-24 08:56:15,074] multiqc [DEBUG ] No samples found: bcl2fastq [2020-04-24 08:56:15,093] multiqc [DEBUG ] No samples found: interop [2020-04-24 08:56:15,117] multiqc [DEBUG ] No samples found: flash [2020-04-24 08:56:15,254] multiqc [DEBUG ] No samples found: seqyclean [2020-04-24 08:56:15,297] multiqc [INFO ] Compressing plot data [2020-04-24 08:56:15,596] multiqc [INFO ] Report : multiqc_report.html [2020-04-24 08:56:15,596] multiqc [INFO ] Data : multiqc_data [2020-04-24 08:56:15,596] multiqc [DEBUG ] Moving data file from '/var/folders/_v/3qsffc0s69l8d4v9795nknd40000gt/T/tmpj6mw1jyi/multiqc_data/multiqc_bismark_alignment.txt' to '/Users/strigg/Desktop/20200416/Mcap/multiqc_data' [2020-04-24 08:56:15,597] multiqc [DEBUG ] Moving data file from '/var/folders/_v/3qsffc0s69l8d4v9795nknd40000gt/T/tmpj6mw1jyi/multiqc_data/multiqc_bismark_dedup.txt' to '/Users/strigg/Desktop/20200416/Mcap/multiqc_data' [2020-04-24 08:56:15,597] multiqc [DEBUG ] Moving data file from '/var/folders/_v/3qsffc0s69l8d4v9795nknd40000gt/T/tmpj6mw1jyi/multiqc_data/multiqc_bismark_methextract.txt' to '/Users/strigg/Desktop/20200416/Mcap/multiqc_data' [2020-04-24 08:56:15,597] multiqc [DEBUG ] Moving data file from '/var/folders/_v/3qsffc0s69l8d4v9795nknd40000gt/T/tmpj6mw1jyi/multiqc_data/multiqc_data.json' to '/Users/strigg/Desktop/20200416/Mcap/multiqc_data' [2020-04-24 08:56:15,597] multiqc [DEBUG ] Moving data file from '/var/folders/_v/3qsffc0s69l8d4v9795nknd40000gt/T/tmpj6mw1jyi/multiqc_data/multiqc_general_stats.txt' to '/Users/strigg/Desktop/20200416/Mcap/multiqc_data' [2020-04-24 08:56:15,598] multiqc [DEBUG ] Moving data file from '/var/folders/_v/3qsffc0s69l8d4v9795nknd40000gt/T/tmpj6mw1jyi/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/Users/strigg/Desktop/20200416/Mcap/multiqc_data' [2020-04-24 08:56:15,598] multiqc [DEBUG ] Moving data file from '/var/folders/_v/3qsffc0s69l8d4v9795nknd40000gt/T/tmpj6mw1jyi/multiqc_data/multiqc_sources.txt' to '/Users/strigg/Desktop/20200416/Mcap/multiqc_data' [2020-04-24 08:56:15,959] multiqc [INFO ] MultiQC complete