[2020-12-16 14:41:50,924] multiqc [DEBUG ] No MultiQC config found: /gscratch/srlab/programs/anaconda3/lib/python3.7/site-packages/multiqc_config.yaml [2020-12-16 14:41:50,953] multiqc [DEBUG ] Loading config settings from: /usr/lusers/samwhite/.multiqc_config.yaml [2020-12-16 14:41:50,953] multiqc [DEBUG ] New config 'star': {'fn': '*Log.final.out'} [2020-12-16 14:41:50,953] multiqc [DEBUG ] New config 'star/genecounts': {'fn': '*ReadsPerGene.out.tab'} [2020-12-16 14:41:50,953] multiqc [DEBUG ] Added to filename patterns: {'fastp': {'fn': '*report.json'}} [2020-12-16 14:41:50,953] multiqc [DEBUG ] New config 'hisat2': {'contents': 'HISAT2 summary stats:', 'shared': True} [2020-12-16 14:41:50,954] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2020-12-16 14:41:50,954] multiqc [DEBUG ] Command used: /gscratch/srlab/programs/anaconda3/bin/multiqc . [2020-12-16 14:41:56,116] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2020-12-16 14:41:56,117] multiqc [INFO ] This is MultiQC v1.8 [2020-12-16 14:41:56,118] multiqc [DEBUG ] Command : /gscratch/srlab/programs/anaconda3/bin/multiqc . [2020-12-16 14:41:56,119] multiqc [DEBUG ] Working dir : /gscratch/scrubbed/samwhite/outputs/20201211_mmag_fastqc_multiqc_mbd-bsseq_miseq [2020-12-16 14:41:56,119] multiqc [INFO ] Template : default [2020-12-16 14:41:56,119] multiqc [DEBUG ] Running Python 3.7.3 (default, Mar 27 2019, 22:11:17) [GCC 7.3.0] [2020-12-16 14:41:56,119] multiqc [INFO ] Searching : /gscratch/scrubbed/samwhite/outputs/20201211_mmag_fastqc_multiqc_mbd-bsseq_miseq [2020-12-16 14:41:56,120] 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 [2020-12-16 14:41:56,120] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmp9m88zq12 [2020-12-16 14:41:56,706] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CH01-14_S2_L001_R1_001_fastqc.html [2020-12-16 14:41:56,720] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CH09-13_S16_L001_R1_001_fastqc.html [2020-12-16 14:41:56,722] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CH03-15_S6_L001_R2_001_fastqc.html [2020-12-16 14:41:56,722] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CH05-24_S11_L001_R1_001_fastqc.html [2020-12-16 14:41:56,723] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CH05-24_S11_L001_R2_001_fastqc.html [2020-12-16 14:41:56,742] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CH05-01_S8_L001_R1_001_fastqc.html [2020-12-16 14:41:56,742] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CH05-06_S9_L001_R2_001_fastqc.html [2020-12-16 14:41:56,743] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CH05-01_S8_L001_R2_001_fastqc.html [2020-12-16 14:41:56,743] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CH05-21_S10_L001_R2_001_fastqc.html [2020-12-16 14:41:56,748] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CH09-28_S17_L001_R2_001_fastqc.html [2020-12-16 14:41:56,802] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CH01-38_S4_L001_R1_001_fastqc.html [2020-12-16 14:41:56,802] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CH10-08_S19_L001_R2_001_fastqc.html [2020-12-16 14:41:56,802] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CH01-14_S2_L001_R2_001_fastqc.html [2020-12-16 14:41:56,803] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CH10-11_S20_L001_R1_001_fastqc.html [2020-12-16 14:41:56,804] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CH07-24_S14_L001_R2_001_fastqc.html [2020-12-16 14:41:56,804] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CH03-04_S5_L001_R1_001_fastqc.html [2020-12-16 14:41:56,806] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CH01-06_S1_L001_R2_001_fastqc.html [2020-12-16 14:41:56,806] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CH09-02_S15_L001_R1_001_fastqc.html [2020-12-16 14:41:56,807] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CH01-38_S4_L001_R2_001_fastqc.html [2020-12-16 14:41:56,848] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CH03-04_S5_L001_R2_001_fastqc.html [2020-12-16 14:41:56,849] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CH03-33_S7_L001_R2_001_fastqc.html [2020-12-16 14:41:56,889] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 20201211_mmag_fastqc_multiqc_mbd-bsseq_miseq.sh [2020-12-16 14:41:56,905] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CH10-01_S18_L001_R1_001_fastqc.html [2020-12-16 14:41:56,906] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CH07-06_S12_L001_R2_001_fastqc.html [2020-12-16 14:41:56,906] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CH07-24_S14_L001_R1_001_fastqc.html [2020-12-16 14:41:56,906] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CH01-22_S3_L001_R2_001_fastqc.html [2020-12-16 14:41:56,907] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CH09-13_S16_L001_R2_001_fastqc.html [2020-12-16 14:41:56,907] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CH05-21_S10_L001_R1_001_fastqc.html [2020-12-16 14:41:56,915] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: slurm-616043.out [2020-12-16 14:41:56,918] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: slurm-616043.out [2020-12-16 14:41:56,974] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CH10-11_S20_L001_R2_001_fastqc.html [2020-12-16 14:41:56,974] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CH01-06_S1_L001_R1_001_fastqc.html [2020-12-16 14:41:56,974] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CH03-33_S7_L001_R1_001_fastqc.html [2020-12-16 14:41:56,974] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CH09-28_S17_L001_R1_001_fastqc.html [2020-12-16 14:41:56,975] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CH10-08_S19_L001_R1_001_fastqc.html [2020-12-16 14:41:56,975] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: fastq_checksums.md5 [2020-12-16 14:41:56,975] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CH09-02_S15_L001_R2_001_fastqc.html [2020-12-16 14:41:56,975] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CH01-22_S3_L001_R1_001_fastqc.html [2020-12-16 14:41:56,975] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CH07-11_S13_L001_R1_001_fastqc.html [2020-12-16 14:41:56,976] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CH07-11_S13_L001_R2_001_fastqc.html [2020-12-16 14:41:56,976] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CH07-06_S12_L001_R1_001_fastqc.html [2020-12-16 14:41:56,976] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CH05-06_S9_L001_R1_001_fastqc.html [2020-12-16 14:41:56,976] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CH03-15_S6_L001_R1_001_fastqc.html [2020-12-16 14:41:56,976] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CH10-01_S18_L001_R2_001_fastqc.html [2020-12-16 14:42:04,610] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 2.2.4 [2020-12-16 14:42:04,632] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 2.2.4 [2020-12-16 14:42:04,636] multiqc [DEBUG ] No samples found: custom_content [2020-12-16 14:42:04,647] multiqc [DEBUG ] No samples found: conpair [2020-12-16 14:42:04,791] multiqc [DEBUG ] No samples found: peddy [2020-12-16 14:42:04,852] multiqc [DEBUG ] No samples found: methylQA [2020-12-16 14:42:04,862] multiqc [DEBUG ] No samples found: phantompeakqualtools [2020-12-16 14:42:05,041] multiqc [DEBUG ] No samples found: qualimap [2020-12-16 14:42:05,062] multiqc [DEBUG ] No samples found: preseq [2020-12-16 14:42:05,118] multiqc [DEBUG ] No samples found: quast [2020-12-16 14:42:05,179] multiqc [DEBUG ] No samples found: qorts [2020-12-16 14:42:05,206] multiqc [DEBUG ] No samples found: rna_seqc [2020-12-16 14:42:05,249] multiqc [DEBUG ] No samples found: rsem [2020-12-16 14:42:05,319] multiqc [DEBUG ] No samples found: rseqc [2020-12-16 14:42:05,331] multiqc [DEBUG ] No samples found: busco [2020-12-16 14:42:05,357] multiqc [DEBUG ] No samples found: goleft_indexcov [2020-12-16 14:42:05,367] multiqc [DEBUG ] No samples found: disambiguate [2020-12-16 14:42:05,407] multiqc [DEBUG ] No samples found: supernova [2020-12-16 14:42:05,525] multiqc [DEBUG ] No samples found: deeptools [2020-12-16 14:42:05,567] multiqc [DEBUG ] No samples found: sargasso [2020-12-16 14:42:05,614] multiqc [DEBUG ] No samples found: verifybamid [2020-12-16 14:42:05,643] multiqc [DEBUG ] No samples found: mirtrace [2020-12-16 14:42:05,679] multiqc [DEBUG ] No samples found: happy [2020-12-16 14:42:05,714] multiqc [DEBUG ] No samples found: homer [2020-12-16 14:42:05,775] multiqc [DEBUG ] No samples found: macs2 [2020-12-16 14:42:05,785] multiqc [DEBUG ] No samples found: theta2 [2020-12-16 14:42:05,811] multiqc [DEBUG ] No samples found: snpeff [2020-12-16 14:42:05,881] multiqc [DEBUG ] No samples found: gatk [2020-12-16 14:42:05,892] multiqc [DEBUG ] No samples found: htseq [2020-12-16 14:42:05,919] multiqc [DEBUG ] No samples found: bcftools [2020-12-16 14:42:05,930] multiqc [DEBUG ] No samples found: featureCounts [2020-12-16 14:42:05,942] multiqc [DEBUG ] No samples found: fgbio [2020-12-16 14:42:05,953] multiqc [DEBUG ] No samples found: dedup [2020-12-16 14:42:05,980] multiqc [DEBUG ] No samples found: damageprofiler [2020-12-16 14:42:06,384] multiqc [DEBUG ] No samples found: biobambam2 [2020-12-16 14:42:06,395] multiqc [DEBUG ] No samples found: mtnucratio [2020-12-16 14:42:06,401] multiqc [DEBUG ] No samples found: picard [2020-12-16 14:42:06,460] multiqc [DEBUG ] No samples found: prokka [2020-12-16 14:42:06,472] multiqc [DEBUG ] No samples found: samblaster [2020-12-16 14:42:06,623] multiqc [DEBUG ] No samples found: samtools [2020-12-16 14:42:06,656] multiqc [DEBUG ] No samples found: sexdeterrmine [2020-12-16 14:42:06,669] multiqc [DEBUG ] No samples found: bamtools [2020-12-16 14:42:06,679] multiqc [DEBUG ] No samples found: jellyfish [2020-12-16 14:42:06,696] multiqc [DEBUG ] No samples found: vcftools [2020-12-16 14:42:06,761] multiqc [DEBUG ] No samples found: longranger [2020-12-16 14:42:06,866] multiqc [DEBUG ] No samples found: stacks [2020-12-16 14:42:06,977] multiqc [DEBUG ] No samples found: bbmap [2020-12-16 14:42:07,057] multiqc [DEBUG ] No samples found: bismark [2020-12-16 14:42:07,096] multiqc [DEBUG ] No samples found: biscuit [2020-12-16 14:42:07,128] multiqc [DEBUG ] No samples found: hicexplorer [2020-12-16 14:42:07,155] multiqc [DEBUG ] No samples found: hicup [2020-12-16 14:42:07,206] multiqc [DEBUG ] No samples found: hicpro [2020-12-16 14:42:07,217] multiqc [DEBUG ] No samples found: salmon [2020-12-16 14:42:07,240] multiqc [DEBUG ] No samples found: kallisto [2020-12-16 14:42:07,333] multiqc [DEBUG ] No samples found: slamdunk [2020-12-16 14:42:07,350] multiqc [DEBUG ] No samples found: star [2020-12-16 14:42:07,403] multiqc [DEBUG ] No samples found: hisat2 [2020-12-16 14:42:07,460] multiqc [DEBUG ] No samples found: tophat [2020-12-16 14:42:07,510] multiqc [DEBUG ] No samples found: bowtie2 [2020-12-16 14:42:07,550] multiqc [DEBUG ] No samples found: bowtie1 [2020-12-16 14:42:07,561] multiqc [DEBUG ] No samples found: kat [2020-12-16 14:42:07,571] multiqc [DEBUG ] No samples found: leehom [2020-12-16 14:42:07,596] multiqc [DEBUG ] No samples found: adapterRemoval [2020-12-16 14:42:07,606] multiqc [DEBUG ] No samples found: clipandmerge [2020-12-16 14:42:07,692] multiqc [DEBUG ] No samples found: cutadapt [2020-12-16 14:42:07,703] multiqc [DEBUG ] No samples found: flexbar [2020-12-16 14:42:07,775] multiqc [DEBUG ] No samples found: trimmomatic [2020-12-16 14:42:07,840] multiqc [DEBUG ] No samples found: skewer [2020-12-16 14:42:07,850] multiqc [DEBUG ] No samples found: sortmerna [2020-12-16 14:42:07,861] multiqc [DEBUG ] No samples found: biobloomtools [2020-12-16 14:42:07,882] multiqc [DEBUG ] No samples found: fastq_screen [2020-12-16 14:42:07,905] multiqc [DEBUG ] No samples found: afterqc [2020-12-16 14:42:07,939] multiqc [DEBUG ] No samples found: fastp [2020-12-16 14:42:08,887] multiqc.modules.fastqc.fastqc [INFO ] Found 40 reports [2020-12-16 14:42:09,795] multiqc [DEBUG ] No samples found: minionqc [2020-12-16 14:42:09,863] multiqc [DEBUG ] No samples found: mosdepth [2020-12-16 14:42:09,897] multiqc [DEBUG ] No samples found: clusterflow [2020-12-16 14:42:10,075] multiqc [DEBUG ] No samples found: bcl2fastq [2020-12-16 14:42:10,115] multiqc [DEBUG ] No samples found: interop [2020-12-16 14:42:10,163] multiqc [DEBUG ] No samples found: flash [2020-12-16 14:42:10,201] multiqc [DEBUG ] No samples found: seqyclean [2020-12-16 14:42:10,322] multiqc [INFO ] Compressing plot data [2020-12-16 14:42:10,918] multiqc [INFO ] Report : multiqc_report.html [2020-12-16 14:42:10,918] multiqc [INFO ] Data : multiqc_data [2020-12-16 14:42:10,934] multiqc [DEBUG ] Moving data file from '/tmp/tmp9m88zq12/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/gscratch/scrubbed/samwhite/outputs/20201211_mmag_fastqc_multiqc_mbd-bsseq_miseq/multiqc_data' [2020-12-16 14:42:10,935] multiqc [DEBUG ] Moving data file from '/tmp/tmp9m88zq12/multiqc_data/multiqc_fastqc.txt' to '/gscratch/scrubbed/samwhite/outputs/20201211_mmag_fastqc_multiqc_mbd-bsseq_miseq/multiqc_data' [2020-12-16 14:42:10,937] multiqc [DEBUG ] Moving data file from '/tmp/tmp9m88zq12/multiqc_data/multiqc_general_stats.txt' to '/gscratch/scrubbed/samwhite/outputs/20201211_mmag_fastqc_multiqc_mbd-bsseq_miseq/multiqc_data' [2020-12-16 14:42:10,937] multiqc [DEBUG ] Moving data file from '/tmp/tmp9m88zq12/multiqc_data/multiqc_sources.txt' to '/gscratch/scrubbed/samwhite/outputs/20201211_mmag_fastqc_multiqc_mbd-bsseq_miseq/multiqc_data' [2020-12-16 14:42:10,938] multiqc [DEBUG ] Moving data file from '/tmp/tmp9m88zq12/multiqc_data/multiqc_data.json' to '/gscratch/scrubbed/samwhite/outputs/20201211_mmag_fastqc_multiqc_mbd-bsseq_miseq/multiqc_data' [2020-12-16 14:42:13,237] multiqc [INFO ] MultiQC complete