[2020-12-02 14:20:26,068] multiqc [DEBUG ] No MultiQC config found: /gscratch/srlab/programs/anaconda3/lib/python3.7/site-packages/multiqc_config.yaml [2020-12-02 14:20:26,094] multiqc [DEBUG ] Loading config settings from: /usr/lusers/samwhite/.multiqc_config.yaml [2020-12-02 14:20:26,094] multiqc [DEBUG ] Added to filename patterns: {'fastp': {'fn': '*report.json'}} [2020-12-02 14:20:26,095] multiqc [DEBUG ] New config 'hisat2': {'contents': 'HISAT2 summary stats:', 'shared': True} [2020-12-02 14:20:26,095] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2020-12-02 14:20:26,095] multiqc [DEBUG ] Command used: /gscratch/srlab/programs/anaconda3/bin/multiqc . [2020-12-02 14:20:31,396] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2020-12-02 14:20:31,396] multiqc [INFO ] This is MultiQC v1.8 [2020-12-02 14:20:31,421] multiqc [DEBUG ] Command : /gscratch/srlab/programs/anaconda3/bin/multiqc . [2020-12-02 14:20:31,421] multiqc [DEBUG ] Working dir : /gscratch/scrubbed/samwhite/outputs/20201202_cgig_fastp-10bp-5-3-prime_ronit-ploidy-wgbs [2020-12-02 14:20:31,421] multiqc [INFO ] Template : default [2020-12-02 14:20:31,422] multiqc [DEBUG ] Running Python 3.7.3 (default, Mar 27 2019, 22:11:17) [GCC 7.3.0] [2020-12-02 14:20:31,422] multiqc [INFO ] Searching : /gscratch/scrubbed/samwhite/outputs/20201202_cgig_fastp-10bp-5-3-prime_ronit-ploidy-wgbs [2020-12-02 14:20:31,423] 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 [2020-12-02 14:20:31,423] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpo8a6fpfi [2020-12-02 14:20:33,058] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: slurm-517395.out [2020-12-02 14:20:33,060] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: slurm-517395.out [2020-12-02 14:20:33,077] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_1_R1.fastp-trim.20201202.fq.gz [2020-12-02 14:20:33,077] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_9_R1.fastp-trim.20201202.fq.gz [2020-12-02 14:20:33,077] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_4_R1.fastp-trim.20201202.fq.gz [2020-12-02 14:20:33,077] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: raw_fastq_checksums.md5 [2020-12-02 14:20:33,077] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_6_R1.fastp-trim.20201202.report.html [2020-12-02 14:20:33,077] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_9_R1.fastp-trim.20201202.report.html [2020-12-02 14:20:33,078] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_3_R1.fastp-trim.20201202.report.html [2020-12-02 14:20:33,078] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_6_R2.fastp-trim.20201202.fq.gz [2020-12-02 14:20:33,078] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_3_R2.fastp-trim.20201202.fq.gz [2020-12-02 14:20:33,078] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_3_R1.fastp-trim.20201202.fq.gz [2020-12-02 14:20:33,078] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_4_R2.fastp-trim.20201202.fq.gz [2020-12-02 14:20:33,078] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_5_R2.fastp-trim.20201202.fq.gz [2020-12-02 14:20:33,180] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 20201202_cgig_fastp-10bp-5-3-prime_ronit-ploidy-wgbs.sh [2020-12-02 14:20:33,183] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 20201202_cgig_fastp-10bp-5-3-prime_ronit-ploidy-wgbs.sh [2020-12-02 14:20:33,193] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_9_R2.fastp-trim.20201202.fq.gz [2020-12-02 14:20:33,194] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_7_R1.fastp-trim.20201202.report.html [2020-12-02 14:20:33,194] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_2_R2.fastp-trim.20201202.fq.gz [2020-12-02 14:20:33,194] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_7_R1.fastp-trim.20201202.fq.gz [2020-12-02 14:20:33,194] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_10_R1.fastp-trim.20201202.fq.gz [2020-12-02 14:20:33,194] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: trimmed_fastq_checksums.md5 [2020-12-02 14:20:33,194] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_8_R2.fastp-trim.20201202.fq.gz [2020-12-02 14:20:33,195] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_7_R2.fastp-trim.20201202.fq.gz [2020-12-02 14:20:33,195] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_4_R1.fastp-trim.20201202.report.html [2020-12-02 14:20:33,195] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_5_R1.fastp-trim.20201202.report.html [2020-12-02 14:20:33,195] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_2_R1.fastp-trim.20201202.report.html [2020-12-02 14:20:33,195] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_8_R1.fastp-trim.20201202.fq.gz [2020-12-02 14:20:33,195] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_6_R1.fastp-trim.20201202.fq.gz [2020-12-02 14:20:33,196] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_2_R1.fastp-trim.20201202.fq.gz [2020-12-02 14:20:33,196] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_5_R1.fastp-trim.20201202.fq.gz [2020-12-02 14:20:33,196] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_1_R1.fastp-trim.20201202.report.html [2020-12-02 14:20:33,196] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_1_R2.fastp-trim.20201202.fq.gz [2020-12-02 14:20:33,196] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_10_R2.fastp-trim.20201202.fq.gz [2020-12-02 14:20:33,196] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_8_R1.fastp-trim.20201202.report.html [2020-12-02 14:20:33,196] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_10_R1.fastp-trim.20201202.report.html [2020-12-02 14:20:41,860] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 2.2.4 [2020-12-02 14:20:41,871] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 2.2.4 [2020-12-02 14:20:41,973] multiqc [DEBUG ] No samples found: custom_content [2020-12-02 14:20:42,194] multiqc [DEBUG ] No samples found: conpair [2020-12-02 14:20:42,428] multiqc [DEBUG ] No samples found: peddy [2020-12-02 14:20:42,598] multiqc [DEBUG ] No samples found: methylQA [2020-12-02 14:20:42,662] multiqc [DEBUG ] No samples found: phantompeakqualtools [2020-12-02 14:20:42,993] multiqc [DEBUG ] No samples found: qualimap [2020-12-02 14:20:43,040] multiqc [DEBUG ] No samples found: preseq [2020-12-02 14:20:43,081] multiqc [DEBUG ] No samples found: quast [2020-12-02 14:20:43,117] multiqc [DEBUG ] No samples found: qorts [2020-12-02 14:20:43,253] multiqc [DEBUG ] No samples found: rna_seqc [2020-12-02 14:20:43,404] multiqc [DEBUG ] No samples found: rsem [2020-12-02 14:20:43,649] multiqc [DEBUG ] No samples found: rseqc [2020-12-02 14:20:43,677] multiqc [DEBUG ] No samples found: busco [2020-12-02 14:20:43,768] multiqc [DEBUG ] No samples found: goleft_indexcov [2020-12-02 14:20:43,827] multiqc [DEBUG ] No samples found: disambiguate [2020-12-02 14:20:43,913] multiqc [DEBUG ] No samples found: supernova [2020-12-02 14:20:44,122] multiqc [DEBUG ] No samples found: deeptools [2020-12-02 14:20:44,175] multiqc [DEBUG ] No samples found: sargasso [2020-12-02 14:20:44,227] multiqc [DEBUG ] No samples found: verifybamid [2020-12-02 14:20:44,299] multiqc [DEBUG ] No samples found: mirtrace [2020-12-02 14:20:44,360] multiqc [DEBUG ] No samples found: happy [2020-12-02 14:20:44,406] multiqc [DEBUG ] No samples found: homer [2020-12-02 14:20:44,464] multiqc [DEBUG ] No samples found: macs2 [2020-12-02 14:20:44,470] multiqc [DEBUG ] No samples found: theta2 [2020-12-02 14:20:44,522] multiqc [DEBUG ] No samples found: snpeff [2020-12-02 14:20:44,602] multiqc [DEBUG ] No samples found: gatk [2020-12-02 14:20:44,616] multiqc [DEBUG ] No samples found: htseq [2020-12-02 14:20:44,690] multiqc [DEBUG ] No samples found: bcftools [2020-12-02 14:20:44,703] multiqc [DEBUG ] No samples found: featureCounts [2020-12-02 14:20:44,713] multiqc [DEBUG ] No samples found: fgbio [2020-12-02 14:20:44,721] multiqc [DEBUG ] No samples found: dedup [2020-12-02 14:20:44,825] multiqc [DEBUG ] No samples found: damageprofiler [2020-12-02 14:20:45,151] multiqc [DEBUG ] No samples found: biobambam2 [2020-12-02 14:20:45,219] multiqc [DEBUG ] No samples found: mtnucratio [2020-12-02 14:20:45,227] multiqc [DEBUG ] No samples found: picard [2020-12-02 14:20:45,251] multiqc [DEBUG ] No samples found: prokka [2020-12-02 14:20:45,264] multiqc [DEBUG ] No samples found: samblaster [2020-12-02 14:20:45,354] multiqc [DEBUG ] No samples found: samtools [2020-12-02 14:20:45,419] multiqc [DEBUG ] No samples found: sexdeterrmine [2020-12-02 14:20:45,470] multiqc [DEBUG ] No samples found: bamtools [2020-12-02 14:20:45,481] multiqc [DEBUG ] No samples found: jellyfish [2020-12-02 14:20:45,512] multiqc [DEBUG ] No samples found: vcftools [2020-12-02 14:20:45,555] multiqc [DEBUG ] No samples found: longranger [2020-12-02 14:20:45,599] multiqc [DEBUG ] No samples found: stacks [2020-12-02 14:20:45,745] multiqc [DEBUG ] No samples found: bbmap [2020-12-02 14:20:45,789] multiqc [DEBUG ] No samples found: bismark [2020-12-02 14:20:45,856] multiqc [DEBUG ] No samples found: biscuit [2020-12-02 14:20:45,886] multiqc [DEBUG ] No samples found: hicexplorer [2020-12-02 14:20:45,919] multiqc [DEBUG ] No samples found: hicup [2020-12-02 14:20:45,949] multiqc [DEBUG ] No samples found: hicpro [2020-12-02 14:20:45,962] multiqc [DEBUG ] No samples found: salmon [2020-12-02 14:20:45,985] multiqc [DEBUG ] No samples found: kallisto [2020-12-02 14:20:46,029] multiqc [DEBUG ] No samples found: slamdunk [2020-12-02 14:20:46,047] multiqc [DEBUG ] No samples found: star [2020-12-02 14:20:46,084] multiqc [DEBUG ] No samples found: hisat2 [2020-12-02 14:20:46,108] multiqc [DEBUG ] No samples found: tophat [2020-12-02 14:20:46,156] multiqc [DEBUG ] No samples found: bowtie2 [2020-12-02 14:20:46,200] multiqc [DEBUG ] No samples found: bowtie1 [2020-12-02 14:20:46,213] multiqc [DEBUG ] No samples found: kat [2020-12-02 14:20:46,221] multiqc [DEBUG ] No samples found: leehom [2020-12-02 14:20:46,272] multiqc [DEBUG ] No samples found: adapterRemoval [2020-12-02 14:20:46,292] multiqc [DEBUG ] No samples found: clipandmerge [2020-12-02 14:20:46,323] multiqc [DEBUG ] No samples found: cutadapt [2020-12-02 14:20:46,338] multiqc [DEBUG ] No samples found: flexbar [2020-12-02 14:20:46,368] multiqc [DEBUG ] No samples found: trimmomatic [2020-12-02 14:20:46,412] multiqc [DEBUG ] No samples found: skewer [2020-12-02 14:20:46,425] multiqc [DEBUG ] No samples found: sortmerna [2020-12-02 14:20:46,449] multiqc [DEBUG ] No samples found: biobloomtools [2020-12-02 14:20:46,482] multiqc [DEBUG ] No samples found: fastq_screen [2020-12-02 14:20:46,513] multiqc [DEBUG ] No samples found: afterqc [2020-12-02 14:20:47,163] multiqc.modules.fastp.fastp [INFO ] Found 10 reports [2020-12-02 14:20:47,217] multiqc [DEBUG ] No samples found: fastqc [2020-12-02 14:20:47,255] multiqc [DEBUG ] No samples found: minionqc [2020-12-02 14:20:47,305] multiqc [DEBUG ] No samples found: mosdepth [2020-12-02 14:20:47,388] multiqc [DEBUG ] No samples found: clusterflow [2020-12-02 14:20:47,449] multiqc [DEBUG ] No samples found: bcl2fastq [2020-12-02 14:20:47,487] multiqc [DEBUG ] No samples found: interop [2020-12-02 14:20:47,509] multiqc [DEBUG ] No samples found: flash [2020-12-02 14:20:47,531] multiqc [DEBUG ] No samples found: seqyclean [2020-12-02 14:20:47,558] multiqc [INFO ] Compressing plot data [2020-12-02 14:20:47,998] multiqc [INFO ] Report : multiqc_report.html [2020-12-02 14:20:48,000] multiqc [INFO ] Data : multiqc_data [2020-12-02 14:20:48,001] multiqc [DEBUG ] Moving data file from '/tmp/tmpo8a6fpfi/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/gscratch/scrubbed/samwhite/outputs/20201202_cgig_fastp-10bp-5-3-prime_ronit-ploidy-wgbs/multiqc_data' [2020-12-02 14:20:48,002] multiqc [DEBUG ] Moving data file from '/tmp/tmpo8a6fpfi/multiqc_data/multiqc_fastp.txt' to '/gscratch/scrubbed/samwhite/outputs/20201202_cgig_fastp-10bp-5-3-prime_ronit-ploidy-wgbs/multiqc_data' [2020-12-02 14:20:48,004] multiqc [DEBUG ] Moving data file from '/tmp/tmpo8a6fpfi/multiqc_data/multiqc_general_stats.txt' to '/gscratch/scrubbed/samwhite/outputs/20201202_cgig_fastp-10bp-5-3-prime_ronit-ploidy-wgbs/multiqc_data' [2020-12-02 14:20:48,005] multiqc [DEBUG ] Moving data file from '/tmp/tmpo8a6fpfi/multiqc_data/multiqc_sources.txt' to '/gscratch/scrubbed/samwhite/outputs/20201202_cgig_fastp-10bp-5-3-prime_ronit-ploidy-wgbs/multiqc_data' [2020-12-02 14:20:48,006] multiqc [DEBUG ] Moving data file from '/tmp/tmpo8a6fpfi/multiqc_data/multiqc_data.json' to '/gscratch/scrubbed/samwhite/outputs/20201202_cgig_fastp-10bp-5-3-prime_ronit-ploidy-wgbs/multiqc_data' [2020-12-02 14:20:49,464] multiqc [INFO ] MultiQC complete