[2020-11-30 11:05:08,352] multiqc [DEBUG ] No MultiQC config found: /gscratch/srlab/programs/anaconda3/lib/python3.7/site-packages/multiqc_config.yaml [2020-11-30 11:05:08,354] multiqc [DEBUG ] Loading config settings from: /usr/lusers/samwhite/.multiqc_config.yaml [2020-11-30 11:05:08,354] multiqc [DEBUG ] Added to filename patterns: {'fastp': {'fn': '*report.json'}} [2020-11-30 11:05:08,355] multiqc [DEBUG ] New config 'hisat2': {'contents': 'HISAT2 summary stats:', 'shared': True} [2020-11-30 11:05:08,355] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2020-11-30 11:05:08,355] multiqc [DEBUG ] Command used: /gscratch/srlab/programs/anaconda3/bin/multiqc . [2020-11-30 11:05:13,509] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2020-11-30 11:05:13,509] multiqc [INFO ] This is MultiQC v1.8 [2020-11-30 11:05:13,737] multiqc [DEBUG ] Command : /gscratch/srlab/programs/anaconda3/bin/multiqc . [2020-11-30 11:05:13,737] multiqc [DEBUG ] Working dir : /gscratch/scrubbed/samwhite/outputs/20201130_cgig_fastp_ronit-ploidy-wgbs [2020-11-30 11:05:13,737] multiqc [INFO ] Template : default [2020-11-30 11:05:13,737] multiqc [DEBUG ] Running Python 3.7.3 (default, Mar 27 2019, 22:11:17) [GCC 7.3.0] [2020-11-30 11:05:13,737] multiqc [INFO ] Searching : /gscratch/scrubbed/samwhite/outputs/20201130_cgig_fastp_ronit-ploidy-wgbs [2020-11-30 11:05:13,738] 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 [2020-11-30 11:05:13,738] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpkr383wf6 [2020-11-30 11:05:15,954] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_1_R1.fastp-trim.20201130.report.html [2020-11-30 11:05:15,954] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_7_R2.fastp-trim.20201130.fq.gz [2020-11-30 11:05:15,954] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_1_R1.fastp-trim.20201130.fq.gz [2020-11-30 11:05:15,966] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_8_R2.fastp-trim.20201130.fq.gz [2020-11-30 11:05:16,282] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_4_R2.fastp-trim.20201130.fq.gz [2020-11-30 11:05:16,282] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_1_R2.fastp-trim.20201130.fq.gz [2020-11-30 11:05:16,282] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_6_R1.fastp-trim.20201130.fq.gz [2020-11-30 11:05:16,283] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: raw_fastq_checksums.md5 [2020-11-30 11:05:16,283] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_5_R1.fastp-trim.20201130.fq.gz [2020-11-30 11:05:16,283] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_6_R1.fastp-trim.20201130.report.html [2020-11-30 11:05:16,283] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_7_R1.fastp-trim.20201130.fq.gz [2020-11-30 11:05:16,283] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_8_R1.fastp-trim.20201130.report.html [2020-11-30 11:05:16,283] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_8_R1.fastp-trim.20201130.fq.gz [2020-11-30 11:05:16,284] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_4_R1.fastp-trim.20201130.report.html [2020-11-30 11:05:16,284] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_9_R1.fastp-trim.20201130.fq.gz [2020-11-30 11:05:16,284] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_3_R1.fastp-trim.20201130.fq.gz [2020-11-30 11:05:16,285] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_10_R1.fastp-trim.20201130.report.html [2020-11-30 11:05:16,285] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_2_R1.fastp-trim.20201130.fq.gz [2020-11-30 11:05:16,285] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_3_R1.fastp-trim.20201130.report.html [2020-11-30 11:05:16,285] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: trimmed_fastq_checksums.md5 [2020-11-30 11:05:16,285] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_2_R2.fastp-trim.20201130.fq.gz [2020-11-30 11:05:16,286] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_6_R2.fastp-trim.20201130.fq.gz [2020-11-30 11:05:16,286] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_10_R1.fastp-trim.20201130.fq.gz [2020-11-30 11:05:16,286] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_9_R1.fastp-trim.20201130.report.html [2020-11-30 11:05:16,286] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_9_R2.fastp-trim.20201130.fq.gz [2020-11-30 11:05:16,287] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_2_R1.fastp-trim.20201130.report.html [2020-11-30 11:05:16,287] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_3_R2.fastp-trim.20201130.fq.gz [2020-11-30 11:05:16,288] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_5_R2.fastp-trim.20201130.fq.gz [2020-11-30 11:05:16,822] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 20201130_cgig_fastp_ronit-ploidy-wgbs.sh [2020-11-30 11:05:16,824] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 20201130_cgig_fastp_ronit-ploidy-wgbs.sh [2020-11-30 11:05:16,841] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_7_R1.fastp-trim.20201130.report.html [2020-11-30 11:05:16,842] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_5_R1.fastp-trim.20201130.report.html [2020-11-30 11:05:16,842] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_10_R2.fastp-trim.20201130.fq.gz [2020-11-30 11:05:16,842] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_4_R1.fastp-trim.20201130.fq.gz [2020-11-30 11:05:16,850] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: slurm-512206.out [2020-11-30 11:05:16,852] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: slurm-512206.out [2020-11-30 11:05:38,765] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 2.2.4 [2020-11-30 11:05:38,841] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 2.2.4 [2020-11-30 11:05:38,982] multiqc [DEBUG ] No samples found: custom_content [2020-11-30 11:05:39,379] multiqc [DEBUG ] No samples found: conpair [2020-11-30 11:05:39,662] multiqc [DEBUG ] No samples found: peddy [2020-11-30 11:05:39,863] multiqc [DEBUG ] No samples found: methylQA [2020-11-30 11:05:40,104] multiqc [DEBUG ] No samples found: phantompeakqualtools [2020-11-30 11:05:40,612] multiqc [DEBUG ] No samples found: qualimap [2020-11-30 11:05:40,753] multiqc [DEBUG ] No samples found: preseq [2020-11-30 11:05:41,075] multiqc [DEBUG ] No samples found: quast [2020-11-30 11:05:41,083] multiqc [DEBUG ] No samples found: qorts [2020-11-30 11:05:41,220] multiqc [DEBUG ] No samples found: rna_seqc [2020-11-30 11:05:41,330] multiqc [DEBUG ] No samples found: rsem [2020-11-30 11:05:41,503] multiqc [DEBUG ] No samples found: rseqc [2020-11-30 11:05:41,852] multiqc [DEBUG ] No samples found: busco [2020-11-30 11:05:41,935] multiqc [DEBUG ] No samples found: goleft_indexcov [2020-11-30 11:05:41,943] multiqc [DEBUG ] No samples found: disambiguate [2020-11-30 11:05:41,951] multiqc [DEBUG ] No samples found: supernova [2020-11-30 11:05:42,181] multiqc [DEBUG ] No samples found: deeptools [2020-11-30 11:05:42,270] multiqc [DEBUG ] No samples found: sargasso [2020-11-30 11:05:42,551] multiqc [DEBUG ] No samples found: verifybamid [2020-11-30 11:05:42,559] multiqc [DEBUG ] No samples found: mirtrace [2020-11-30 11:05:42,568] multiqc [DEBUG ] No samples found: happy [2020-11-30 11:05:42,645] multiqc [DEBUG ] No samples found: homer [2020-11-30 11:05:42,652] multiqc [DEBUG ] No samples found: macs2 [2020-11-30 11:05:42,659] multiqc [DEBUG ] No samples found: theta2 [2020-11-30 11:05:42,670] multiqc [DEBUG ] No samples found: snpeff [2020-11-30 11:05:42,870] multiqc [DEBUG ] No samples found: gatk [2020-11-30 11:05:42,877] multiqc [DEBUG ] No samples found: htseq [2020-11-30 11:05:42,885] multiqc [DEBUG ] No samples found: bcftools [2020-11-30 11:05:42,892] multiqc [DEBUG ] No samples found: featureCounts [2020-11-30 11:05:42,899] multiqc [DEBUG ] No samples found: fgbio [2020-11-30 11:05:42,906] multiqc [DEBUG ] No samples found: dedup [2020-11-30 11:05:42,914] multiqc [DEBUG ] No samples found: damageprofiler [2020-11-30 11:05:43,497] multiqc [DEBUG ] No samples found: biobambam2 [2020-11-30 11:05:43,504] multiqc [DEBUG ] No samples found: mtnucratio [2020-11-30 11:05:43,510] multiqc [DEBUG ] No samples found: picard [2020-11-30 11:05:43,517] multiqc [DEBUG ] No samples found: prokka [2020-11-30 11:05:43,524] multiqc [DEBUG ] No samples found: samblaster [2020-11-30 11:05:43,533] multiqc [DEBUG ] No samples found: samtools [2020-11-30 11:05:43,540] multiqc [DEBUG ] No samples found: sexdeterrmine [2020-11-30 11:05:43,600] multiqc [DEBUG ] No samples found: bamtools [2020-11-30 11:05:43,607] multiqc [DEBUG ] No samples found: jellyfish [2020-11-30 11:05:43,616] multiqc [DEBUG ] No samples found: vcftools [2020-11-30 11:05:43,623] multiqc [DEBUG ] No samples found: longranger [2020-11-30 11:05:43,630] multiqc [DEBUG ] No samples found: stacks [2020-11-30 11:05:43,659] multiqc [DEBUG ] No samples found: bbmap [2020-11-30 11:05:43,666] multiqc [DEBUG ] No samples found: bismark [2020-11-30 11:05:43,767] multiqc [DEBUG ] No samples found: biscuit [2020-11-30 11:05:43,775] multiqc [DEBUG ] No samples found: hicexplorer [2020-11-30 11:05:43,782] multiqc [DEBUG ] No samples found: hicup [2020-11-30 11:05:43,790] multiqc [DEBUG ] No samples found: hicpro [2020-11-30 11:05:43,797] multiqc [DEBUG ] No samples found: salmon [2020-11-30 11:05:43,804] multiqc [DEBUG ] No samples found: kallisto [2020-11-30 11:05:43,935] multiqc [DEBUG ] No samples found: slamdunk [2020-11-30 11:05:43,943] multiqc [DEBUG ] No samples found: star [2020-11-30 11:05:43,950] multiqc [DEBUG ] No samples found: hisat2 [2020-11-30 11:05:43,957] multiqc [DEBUG ] No samples found: tophat [2020-11-30 11:05:43,964] multiqc [DEBUG ] No samples found: bowtie2 [2020-11-30 11:05:43,971] multiqc [DEBUG ] No samples found: bowtie1 [2020-11-30 11:05:43,977] multiqc [DEBUG ] No samples found: kat [2020-11-30 11:05:43,984] multiqc [DEBUG ] No samples found: leehom [2020-11-30 11:05:43,991] multiqc [DEBUG ] No samples found: adapterRemoval [2020-11-30 11:05:43,998] multiqc [DEBUG ] No samples found: clipandmerge [2020-11-30 11:05:44,005] multiqc [DEBUG ] No samples found: cutadapt [2020-11-30 11:05:44,013] multiqc [DEBUG ] No samples found: flexbar [2020-11-30 11:05:44,020] multiqc [DEBUG ] No samples found: trimmomatic [2020-11-30 11:05:44,027] multiqc [DEBUG ] No samples found: skewer [2020-11-30 11:05:44,034] multiqc [DEBUG ] No samples found: sortmerna [2020-11-30 11:05:44,040] multiqc [DEBUG ] No samples found: biobloomtools [2020-11-30 11:05:44,046] multiqc [DEBUG ] No samples found: fastq_screen [2020-11-30 11:05:44,052] multiqc [DEBUG ] No samples found: afterqc [2020-11-30 11:05:45,422] multiqc.modules.fastp.fastp [INFO ] Found 10 reports [2020-11-30 11:05:45,704] multiqc [DEBUG ] No samples found: fastqc [2020-11-30 11:05:45,711] multiqc [DEBUG ] No samples found: minionqc [2020-11-30 11:05:45,718] multiqc [DEBUG ] No samples found: mosdepth [2020-11-30 11:05:45,726] multiqc [DEBUG ] No samples found: clusterflow [2020-11-30 11:05:45,733] multiqc [DEBUG ] No samples found: bcl2fastq [2020-11-30 11:05:45,740] multiqc [DEBUG ] No samples found: interop [2020-11-30 11:05:45,747] multiqc [DEBUG ] No samples found: flash [2020-11-30 11:05:45,754] multiqc [DEBUG ] No samples found: seqyclean [2020-11-30 11:05:45,792] multiqc [INFO ] Compressing plot data [2020-11-30 11:05:46,540] multiqc [INFO ] Report : multiqc_report.html [2020-11-30 11:05:46,540] multiqc [INFO ] Data : multiqc_data [2020-11-30 11:05:49,620] multiqc [DEBUG ] Moving data file from '/tmp/tmpkr383wf6/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/gscratch/scrubbed/samwhite/outputs/20201130_cgig_fastp_ronit-ploidy-wgbs/multiqc_data' [2020-11-30 11:05:49,796] multiqc [DEBUG ] Moving data file from '/tmp/tmpkr383wf6/multiqc_data/multiqc_fastp.txt' to '/gscratch/scrubbed/samwhite/outputs/20201130_cgig_fastp_ronit-ploidy-wgbs/multiqc_data' [2020-11-30 11:05:49,803] multiqc [DEBUG ] Moving data file from '/tmp/tmpkr383wf6/multiqc_data/multiqc_general_stats.txt' to '/gscratch/scrubbed/samwhite/outputs/20201130_cgig_fastp_ronit-ploidy-wgbs/multiqc_data' [2020-11-30 11:05:49,805] multiqc [DEBUG ] Moving data file from '/tmp/tmpkr383wf6/multiqc_data/multiqc_sources.txt' to '/gscratch/scrubbed/samwhite/outputs/20201130_cgig_fastp_ronit-ploidy-wgbs/multiqc_data' [2020-11-30 11:05:49,807] multiqc [DEBUG ] Moving data file from '/tmp/tmpkr383wf6/multiqc_data/multiqc_data.json' to '/gscratch/scrubbed/samwhite/outputs/20201130_cgig_fastp_ronit-ploidy-wgbs/multiqc_data' [2020-11-30 11:05:52,386] multiqc [INFO ] MultiQC complete