[2020-08-19 17:02:59,694] multiqc [DEBUG ] No MultiQC config found: /gscratch/srlab/programs/anaconda3/lib/python3.7/site-packages/multiqc_config.yaml [2020-08-19 17:02:59,712] multiqc [DEBUG ] Loading config settings from: /usr/lusers/samwhite/.multiqc_config.yaml [2020-08-19 17:02:59,712] multiqc [DEBUG ] Added to filename patterns: {'fastp': {'fn': '*report.json'}} [2020-08-19 17:02:59,712] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2020-08-19 17:02:59,712] multiqc [DEBUG ] Command used: /gscratch/srlab/programs/anaconda3/bin/multiqc . [2020-08-19 17:03:05,328] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2020-08-19 17:03:05,328] multiqc [INFO ] This is MultiQC v1.8 [2020-08-19 17:03:05,332] multiqc [DEBUG ] Command : /gscratch/srlab/programs/anaconda3/bin/multiqc . [2020-08-19 17:03:05,332] multiqc [DEBUG ] Working dir : /gscratch/scrubbed/samwhite/outputs/20200818_cgig_wgbs_roberto_fastp_trimming [2020-08-19 17:03:05,332] multiqc [INFO ] Template : default [2020-08-19 17:03:05,332] multiqc [DEBUG ] Running Python 3.7.3 (default, Mar 27 2019, 22:11:17) [GCC 7.3.0] [2020-08-19 17:03:05,332] multiqc [INFO ] Searching : /gscratch/scrubbed/samwhite/outputs/20200818_cgig_wgbs_roberto_fastp_trimming [2020-08-19 17:03:05,333] 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 [2020-08-19 17:03:05,333] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmp6b4p_vrt [2020-08-19 17:03:06,074] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 5902_R2.fastp-trim.20200819_fastqc.html [2020-08-19 17:03:06,075] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 5203_R1.fastp-trim.20200819.report.html [2020-08-19 17:03:06,075] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 3501_R1.fastp-trim.20200819.fq.gz [2020-08-19 17:03:06,076] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 3503_R2.fastp-trim.20200819_fastqc.html [2020-08-19 17:03:06,076] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 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5901_R2.fastp-trim.20200819.fq.gz [2020-08-19 17:03:06,081] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 3502_R2.fastp-trim.20200819.fq.gz [2020-08-19 17:03:06,081] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 0503_R2.fastp-trim.20200819.fq.gz [2020-08-19 17:03:06,081] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 0503_R1.fastp-trim.20200819.report.html [2020-08-19 17:03:06,082] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 5901_R1.fastp-trim.20200819.report.html [2020-08-19 17:03:06,084] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 5203_R1.fastp-trim.20200819.fq.gz [2020-08-19 17:03:06,085] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 5902_R1.fastp-trim.20200819_fastqc.html [2020-08-19 17:03:06,085] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 5201_R1.fastp-trim.20200819.report.html [2020-08-19 17:03:06,085] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 5902_R1.fastp-trim.20200819.fq.gz [2020-08-19 17:03:06,085] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 0501_R1.fastp-trim.20200819.fq.gz [2020-08-19 17:03:06,085] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 3503_R1.fastp-trim.20200819.fq.gz [2020-08-19 17:03:06,085] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 0502_R1.fastp-trim.20200819.report.html [2020-08-19 17:03:06,085] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 5202_R2.fastp-trim.20200819_fastqc.html [2020-08-19 17:03:06,085] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 3503_R1.fastp-trim.20200819.report.html [2020-08-19 17:03:06,085] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 0503_R1.fastp-trim.20200819.fq.gz [2020-08-19 17:03:06,104] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 20200818_cgig_wgbs_roberto_fastp_trimming.sh [2020-08-19 17:03:06,111] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 5202_R1.fastp-trim.20200819.fq.gz [2020-08-19 17:03:06,112] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 5201_R2.fastp-trim.20200819_fastqc.html [2020-08-19 17:03:06,112] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 5902_R1.fastp-trim.20200819.report.html [2020-08-19 17:03:06,112] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 0502_R1.fastp-trim.20200819_fastqc.html [2020-08-19 17:03:06,113] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 5903_R1.fastp-trim.20200819_fastqc.html [2020-08-19 17:03:06,113] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: trimmed_fastq_checksums.md5 [2020-08-19 17:03:06,113] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 3501_R2.fastp-trim.20200819.fq.gz [2020-08-19 17:03:06,113] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 5203_R2.fastp-trim.20200819_fastqc.html [2020-08-19 17:03:06,113] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 3502_R2.fastp-trim.20200819_fastqc.html [2020-08-19 17:03:06,113] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 0501_R1.fastp-trim.20200819.report.html [2020-08-19 17:03:06,113] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 5901_R1.fastp-trim.20200819_fastqc.html [2020-08-19 17:03:06,116] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: slurm-200209.out [2020-08-19 17:03:06,117] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: slurm-200209.out [2020-08-19 17:03:06,138] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 3502_R1.fastp-trim.20200819.report.html [2020-08-19 17:03:06,138] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 3501_R1.fastp-trim.20200819_fastqc.html [2020-08-19 17:03:06,138] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 3501_R2.fastp-trim.20200819_fastqc.html [2020-08-19 17:03:06,138] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 3501_R1.fastp-trim.20200819.report.html [2020-08-19 17:03:06,138] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 5901_R2.fastp-trim.20200819_fastqc.html [2020-08-19 17:03:06,138] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 0501_R2.fastp-trim.20200819_fastqc.html [2020-08-19 17:03:06,138] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 5201_R2.fastp-trim.20200819.fq.gz [2020-08-19 17:03:06,138] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 0503_R2.fastp-trim.20200819_fastqc.html [2020-08-19 17:03:06,139] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 5202_R2.fastp-trim.20200819.fq.gz [2020-08-19 17:03:06,139] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 5203_R1.fastp-trim.20200819_fastqc.html [2020-08-19 17:03:06,139] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 5203_R2.fastp-trim.20200819.fq.gz [2020-08-19 17:03:06,139] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 3503_R2.fastp-trim.20200819.fq.gz [2020-08-19 17:03:06,139] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 5902_R2.fastp-trim.20200819.fq.gz [2020-08-19 17:03:06,139] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 5202_R1.fastp-trim.20200819_fastqc.html [2020-08-19 17:03:06,139] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 5903_R2.fastp-trim.20200819_fastqc.html [2020-08-19 17:03:06,139] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 3502_R1.fastp-trim.20200819_fastqc.html [2020-08-19 17:03:06,139] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 0502_R2.fastp-trim.20200819_fastqc.html [2020-08-19 17:03:06,139] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 0502_R2.fastp-trim.20200819.fq.gz [2020-08-19 17:03:06,140] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 3503_R1.fastp-trim.20200819_fastqc.html [2020-08-19 17:03:06,140] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 0501_R1.fastp-trim.20200819_fastqc.html [2020-08-19 17:03:06,140] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 5903_R2.fastp-trim.20200819.fq.gz [2020-08-19 17:03:06,140] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 5903_R1.fastp-trim.20200819.fq.gz [2020-08-19 17:03:06,140] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 5202_R1.fastp-trim.20200819.report.html [2020-08-19 17:03:10,687] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 2.2.4 [2020-08-19 17:03:10,698] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 2.2.4 [2020-08-19 17:03:10,729] multiqc [DEBUG ] No samples found: custom_content [2020-08-19 17:03:10,807] multiqc [DEBUG ] No samples found: conpair [2020-08-19 17:03:10,905] multiqc [DEBUG ] No samples found: peddy [2020-08-19 17:03:10,996] multiqc [DEBUG ] No samples found: methylQA [2020-08-19 17:03:11,028] multiqc [DEBUG ] No samples found: phantompeakqualtools [2020-08-19 17:03:11,178] multiqc [DEBUG ] No samples found: qualimap [2020-08-19 17:03:11,238] multiqc [DEBUG ] No samples found: preseq [2020-08-19 17:03:11,294] multiqc [DEBUG ] No samples found: quast [2020-08-19 17:03:11,314] multiqc [DEBUG ] No samples found: qorts [2020-08-19 17:03:11,399] multiqc [DEBUG ] No samples found: rna_seqc [2020-08-19 17:03:11,455] multiqc [DEBUG ] No samples found: rsem [2020-08-19 17:03:11,562] multiqc [DEBUG ] No samples found: rseqc [2020-08-19 17:03:11,603] multiqc [DEBUG ] No samples found: busco [2020-08-19 17:03:11,652] multiqc [DEBUG ] No samples found: goleft_indexcov [2020-08-19 17:03:11,680] multiqc [DEBUG ] No samples found: disambiguate [2020-08-19 17:03:11,724] multiqc [DEBUG ] No samples found: supernova [2020-08-19 17:03:11,851] multiqc [DEBUG ] No samples found: deeptools [2020-08-19 17:03:11,900] multiqc [DEBUG ] No samples found: sargasso [2020-08-19 17:03:11,935] multiqc [DEBUG ] No samples found: verifybamid [2020-08-19 17:03:11,965] multiqc [DEBUG ] No samples found: mirtrace [2020-08-19 17:03:12,004] multiqc [DEBUG ] No samples found: happy [2020-08-19 17:03:12,063] multiqc [DEBUG ] No samples found: homer [2020-08-19 17:03:12,091] multiqc [DEBUG ] No samples found: macs2 [2020-08-19 17:03:12,105] multiqc [DEBUG ] No samples found: theta2 [2020-08-19 17:03:12,139] multiqc [DEBUG ] No samples found: snpeff [2020-08-19 17:03:12,184] multiqc [DEBUG ] No samples found: gatk [2020-08-19 17:03:12,207] multiqc [DEBUG ] No samples found: htseq [2020-08-19 17:03:12,243] multiqc [DEBUG ] No samples found: bcftools [2020-08-19 17:03:12,256] multiqc [DEBUG ] No samples found: featureCounts [2020-08-19 17:03:12,267] multiqc [DEBUG ] No samples found: fgbio [2020-08-19 17:03:12,274] multiqc [DEBUG ] No samples found: dedup [2020-08-19 17:03:12,300] multiqc [DEBUG ] No samples found: damageprofiler [2020-08-19 17:03:12,526] multiqc [DEBUG ] No samples found: biobambam2 [2020-08-19 17:03:12,553] multiqc [DEBUG ] No samples found: mtnucratio [2020-08-19 17:03:12,561] multiqc [DEBUG ] No samples found: picard [2020-08-19 17:03:12,593] multiqc [DEBUG ] No samples found: prokka [2020-08-19 17:03:12,607] multiqc [DEBUG ] No samples found: samblaster [2020-08-19 17:03:12,709] multiqc [DEBUG ] No samples found: samtools [2020-08-19 17:03:12,749] multiqc [DEBUG ] No samples found: sexdeterrmine [2020-08-19 17:03:12,808] multiqc [DEBUG ] No samples found: bamtools [2020-08-19 17:03:12,821] multiqc [DEBUG ] No samples found: jellyfish [2020-08-19 17:03:12,837] multiqc [DEBUG ] No samples found: vcftools [2020-08-19 17:03:12,863] multiqc [DEBUG ] No samples found: longranger [2020-08-19 17:03:12,893] multiqc [DEBUG ] No samples found: stacks [2020-08-19 17:03:12,959] multiqc [DEBUG ] No samples found: bbmap [2020-08-19 17:03:13,023] multiqc [DEBUG ] No samples found: bismark [2020-08-19 17:03:13,059] multiqc [DEBUG ] No samples found: biscuit [2020-08-19 17:03:13,077] multiqc [DEBUG ] No samples found: hicexplorer [2020-08-19 17:03:13,094] multiqc [DEBUG ] No samples found: hicup [2020-08-19 17:03:13,114] multiqc [DEBUG ] No samples found: hicpro [2020-08-19 17:03:13,126] multiqc [DEBUG ] No samples found: salmon [2020-08-19 17:03:13,147] multiqc [DEBUG ] No samples found: kallisto [2020-08-19 17:03:13,171] multiqc [DEBUG ] No samples found: slamdunk [2020-08-19 17:03:13,193] multiqc [DEBUG ] No samples found: star [2020-08-19 17:03:13,219] multiqc [DEBUG ] No samples found: hisat2 [2020-08-19 17:03:13,249] multiqc [DEBUG ] No samples found: tophat [2020-08-19 17:03:13,273] multiqc [DEBUG ] No samples found: bowtie2 [2020-08-19 17:03:13,304] multiqc [DEBUG ] No samples found: bowtie1 [2020-08-19 17:03:13,317] multiqc [DEBUG ] No samples found: kat [2020-08-19 17:03:13,327] multiqc [DEBUG ] No samples found: leehom [2020-08-19 17:03:13,375] multiqc [DEBUG ] No samples found: adapterRemoval [2020-08-19 17:03:13,389] multiqc [DEBUG ] No samples found: clipandmerge [2020-08-19 17:03:13,426] multiqc [DEBUG ] No samples found: cutadapt [2020-08-19 17:03:13,441] multiqc [DEBUG ] No samples found: flexbar [2020-08-19 17:03:13,468] multiqc [DEBUG ] No samples found: trimmomatic [2020-08-19 17:03:13,510] multiqc [DEBUG ] No samples found: skewer [2020-08-19 17:03:13,525] multiqc [DEBUG ] No samples found: sortmerna [2020-08-19 17:03:13,545] multiqc [DEBUG ] No samples found: biobloomtools [2020-08-19 17:03:13,570] multiqc [DEBUG ] No samples found: fastq_screen [2020-08-19 17:03:13,610] multiqc [DEBUG ] No samples found: afterqc [2020-08-19 17:03:13,973] multiqc.modules.fastp.fastp [INFO ] Found 12 reports [2020-08-19 17:03:17,255] multiqc.modules.fastqc.fastqc [INFO ] Found 24 reports [2020-08-19 17:03:17,644] multiqc [DEBUG ] No samples found: minionqc [2020-08-19 17:03:17,669] multiqc [DEBUG ] No samples found: mosdepth [2020-08-19 17:03:17,708] multiqc [DEBUG ] No samples found: clusterflow [2020-08-19 17:03:17,747] multiqc [DEBUG ] No samples found: bcl2fastq [2020-08-19 17:03:17,781] multiqc [DEBUG ] No samples found: interop [2020-08-19 17:03:17,824] multiqc [DEBUG ] No samples found: flash [2020-08-19 17:03:17,870] multiqc [DEBUG ] No samples found: seqyclean [2020-08-19 17:03:17,916] multiqc [INFO ] Compressing plot data [2020-08-19 17:03:18,707] multiqc [INFO ] Report : multiqc_report.html [2020-08-19 17:03:18,707] multiqc [INFO ] Data : multiqc_data [2020-08-19 17:03:18,708] multiqc [DEBUG ] Moving data file from '/tmp/tmp6b4p_vrt/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/gscratch/scrubbed/samwhite/outputs/20200818_cgig_wgbs_roberto_fastp_trimming/multiqc_data' [2020-08-19 17:03:18,709] multiqc [DEBUG ] Moving data file from '/tmp/tmp6b4p_vrt/multiqc_data/multiqc_fastp.txt' to '/gscratch/scrubbed/samwhite/outputs/20200818_cgig_wgbs_roberto_fastp_trimming/multiqc_data' [2020-08-19 17:03:18,710] multiqc [DEBUG ] Moving data file from '/tmp/tmp6b4p_vrt/multiqc_data/multiqc_fastqc.txt' to '/gscratch/scrubbed/samwhite/outputs/20200818_cgig_wgbs_roberto_fastp_trimming/multiqc_data' [2020-08-19 17:03:18,711] multiqc [DEBUG ] Moving data file from '/tmp/tmp6b4p_vrt/multiqc_data/multiqc_general_stats.txt' to '/gscratch/scrubbed/samwhite/outputs/20200818_cgig_wgbs_roberto_fastp_trimming/multiqc_data' [2020-08-19 17:03:18,711] multiqc [DEBUG ] Moving data file from '/tmp/tmp6b4p_vrt/multiqc_data/multiqc_sources.txt' to '/gscratch/scrubbed/samwhite/outputs/20200818_cgig_wgbs_roberto_fastp_trimming/multiqc_data' [2020-08-19 17:03:18,712] multiqc [DEBUG ] Moving data file from '/tmp/tmp6b4p_vrt/multiqc_data/multiqc_data.json' to '/gscratch/scrubbed/samwhite/outputs/20200818_cgig_wgbs_roberto_fastp_trimming/multiqc_data' [2020-08-19 17:03:19,499] multiqc [INFO ] MultiQC complete