[2023-01-22 10:31:23,373] multiqc [DEBUG ] No MultiQC config found: /gscratch/srlab/programs/anaconda3/lib/python3.7/site-packages/multiqc_config.yaml [2023-01-22 10:31:23,378] multiqc [DEBUG ] Loading config settings from: /usr/lusers/samwhite/.multiqc_config.yaml [2023-01-22 10:31:23,378] multiqc [DEBUG ] New config 'star': {'fn': '*Log.final.out'} [2023-01-22 10:31:23,378] multiqc [DEBUG ] New config 'star/genecounts': {'fn': '*ReadsPerGene.out.tab'} [2023-01-22 10:31:23,378] multiqc [DEBUG ] Added to filename patterns: {'fastp': {'fn': '*report.json'}} [2023-01-22 10:31:23,378] multiqc [DEBUG ] New config 'hisat2': {'contents': 'HISAT2 summary stats:', 'shared': True} [2023-01-22 10:31:23,379] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-01-22 10:31:23,379] multiqc [DEBUG ] Command used: /gscratch/srlab/programs/anaconda3/bin/multiqc . [2023-01-22 10:31:28,602] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2023-01-22 10:31:28,602] multiqc [INFO ] This is MultiQC v1.8 [2023-01-22 10:31:28,605] multiqc [DEBUG ] Command : /gscratch/srlab/programs/anaconda3/bin/multiqc . [2023-01-22 10:31:28,605] multiqc [DEBUG ] Working dir : /gscratch/scrubbed/samwhite/outputs/20230119-coral-fastqc-fastp-multiqc-PRJNA744403/data/P_grandis/BS-seq [2023-01-22 10:31:28,605] multiqc [INFO ] Template : default [2023-01-22 10:31:28,605] multiqc [DEBUG ] Running Python 3.7.3 (default, Mar 27 2019, 22:11:17) [GCC 7.3.0] [2023-01-22 10:31:28,605] multiqc [INFO ] Searching : /gscratch/scrubbed/samwhite/outputs/20230119-coral-fastqc-fastp-multiqc-PRJNA744403/data/P_grandis/BS-seq [2023-01-22 10:31:28,606] 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 [2023-01-22 10:31:28,606] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpwcwep7b0 [2023-01-22 10:31:29,384] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRR15101744_2.fastq.gz [2023-01-22 10:31:29,384] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRR15101728_2_fastqc.html [2023-01-22 10:31:29,385] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRR15101749_2.fastq.gz [2023-01-22 10:31:29,385] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRR15101727_1.fastq.gz [2023-01-22 10:31:29,386] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRR15101727_2.fastq.gz [2023-01-22 10:31:29,386] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRR15101744_1.fastq.gz [2023-01-22 10:31:29,386] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRR15101732_1_fastqc.html [2023-01-22 10:31:29,386] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRR15101728_1.fastq.gz [2023-01-22 10:31:29,387] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRR15101749_1_fastqc.html [2023-01-22 10:31:29,387] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRR15101732_1.fastq.gz [2023-01-22 10:31:29,387] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRR15101749_1.fastq.gz [2023-01-22 10:31:29,387] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRR15101728_1_fastqc.html [2023-01-22 10:31:29,388] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRR15101727_2_fastqc.html [2023-01-22 10:31:29,388] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRR15101728_2.fastq.gz [2023-01-22 10:31:29,388] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRR15101732_2.fastq.gz [2023-01-22 10:31:29,388] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: input_fastq_checksums.md5 [2023-01-22 10:31:29,388] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRR15101744_2_fastqc.html [2023-01-22 10:31:29,388] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRR15101732_2_fastqc.html [2023-01-22 10:31:29,389] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRR15101727_1_fastqc.html [2023-01-22 10:31:29,389] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRR15101744_1_fastqc.html [2023-01-22 10:31:29,389] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRR15101749_2_fastqc.html [2023-01-22 10:31:33,175] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 2.2.4 [2023-01-22 10:31:33,201] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 2.2.4 [2023-01-22 10:31:33,230] multiqc [DEBUG ] No samples found: custom_content [2023-01-22 10:31:33,280] multiqc [DEBUG ] No samples found: conpair [2023-01-22 10:31:33,374] multiqc [DEBUG ] No samples found: peddy [2023-01-22 10:31:33,429] multiqc [DEBUG ] No samples found: methylQA [2023-01-22 10:31:33,470] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-01-22 10:31:33,562] multiqc [DEBUG ] No samples found: qualimap [2023-01-22 10:31:33,614] multiqc [DEBUG ] No samples found: preseq [2023-01-22 10:31:33,644] multiqc [DEBUG ] No samples found: quast [2023-01-22 10:31:33,663] multiqc [DEBUG ] No samples found: qorts [2023-01-22 10:31:33,711] multiqc [DEBUG ] No samples found: rna_seqc [2023-01-22 10:31:33,758] multiqc [DEBUG ] No samples found: rsem [2023-01-22 10:31:33,844] multiqc [DEBUG ] No samples found: rseqc [2023-01-22 10:31:33,868] multiqc [DEBUG ] No samples found: busco [2023-01-22 10:31:33,911] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-01-22 10:31:33,933] multiqc [DEBUG ] No samples found: disambiguate [2023-01-22 10:31:33,979] multiqc [DEBUG ] No samples found: supernova [2023-01-22 10:31:34,095] multiqc [DEBUG ] No samples found: deeptools [2023-01-22 10:31:34,144] multiqc [DEBUG ] No samples found: sargasso [2023-01-22 10:31:34,218] multiqc [DEBUG ] No samples found: verifybamid [2023-01-22 10:31:34,246] multiqc [DEBUG ] No samples found: mirtrace [2023-01-22 10:31:34,293] multiqc [DEBUG ] No samples found: happy [2023-01-22 10:31:34,315] multiqc [DEBUG ] No samples found: homer [2023-01-22 10:31:34,344] multiqc [DEBUG ] No samples found: macs2 [2023-01-22 10:31:34,366] multiqc [DEBUG ] No samples found: theta2 [2023-01-22 10:31:34,398] multiqc [DEBUG ] No samples found: snpeff [2023-01-22 10:31:34,477] multiqc [DEBUG ] No samples found: gatk [2023-01-22 10:31:34,487] multiqc [DEBUG ] No samples found: htseq [2023-01-22 10:31:34,546] multiqc [DEBUG ] No samples found: bcftools [2023-01-22 10:31:34,556] multiqc [DEBUG ] No samples found: featureCounts [2023-01-22 10:31:34,572] multiqc [DEBUG ] No samples found: fgbio [2023-01-22 10:31:34,581] multiqc [DEBUG ] No samples found: dedup [2023-01-22 10:31:34,601] multiqc [DEBUG ] No samples found: damageprofiler [2023-01-22 10:31:34,728] multiqc [DEBUG ] No samples found: biobambam2 [2023-01-22 10:31:34,758] multiqc [DEBUG ] No samples found: mtnucratio [2023-01-22 10:31:34,762] multiqc [DEBUG ] No samples found: picard [2023-01-22 10:31:34,787] multiqc [DEBUG ] No samples found: prokka [2023-01-22 10:31:34,796] multiqc [DEBUG ] No samples found: samblaster [2023-01-22 10:31:34,830] multiqc [DEBUG ] No samples found: samtools [2023-01-22 10:31:34,846] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-01-22 10:31:34,916] multiqc [DEBUG ] No samples found: bamtools [2023-01-22 10:31:34,929] multiqc [DEBUG ] No samples found: jellyfish [2023-01-22 10:31:34,947] multiqc [DEBUG ] No samples found: vcftools [2023-01-22 10:31:34,981] multiqc [DEBUG ] No samples found: longranger [2023-01-22 10:31:35,003] multiqc [DEBUG ] No samples found: stacks [2023-01-22 10:31:35,079] multiqc [DEBUG ] No samples found: bbmap [2023-01-22 10:31:35,092] multiqc [DEBUG ] No samples found: bismark [2023-01-22 10:31:35,115] multiqc [DEBUG ] No samples found: biscuit [2023-01-22 10:31:35,138] multiqc [DEBUG ] No samples found: hicexplorer [2023-01-22 10:31:35,155] multiqc [DEBUG ] No samples found: hicup [2023-01-22 10:31:35,174] multiqc [DEBUG ] No samples found: hicpro [2023-01-22 10:31:35,182] multiqc [DEBUG ] No samples found: salmon [2023-01-22 10:31:35,196] multiqc [DEBUG ] No samples found: kallisto [2023-01-22 10:31:35,215] multiqc [DEBUG ] No samples found: slamdunk [2023-01-22 10:31:35,249] multiqc [DEBUG ] No samples found: star [2023-01-22 10:31:35,287] multiqc [DEBUG ] No samples found: hisat2 [2023-01-22 10:31:35,311] multiqc [DEBUG ] No samples found: tophat [2023-01-22 10:31:35,321] multiqc [DEBUG ] No samples found: bowtie2 [2023-01-22 10:31:35,348] multiqc [DEBUG ] No samples found: bowtie1 [2023-01-22 10:31:35,358] multiqc [DEBUG ] No samples found: kat [2023-01-22 10:31:35,366] multiqc [DEBUG ] No samples found: leehom [2023-01-22 10:31:35,411] multiqc [DEBUG ] No samples found: adapterRemoval [2023-01-22 10:31:35,423] multiqc [DEBUG ] No samples found: clipandmerge [2023-01-22 10:31:35,452] multiqc [DEBUG ] No samples found: cutadapt [2023-01-22 10:31:35,463] multiqc [DEBUG ] No samples found: flexbar [2023-01-22 10:31:35,486] multiqc [DEBUG ] No samples found: trimmomatic [2023-01-22 10:31:35,522] multiqc [DEBUG ] No samples found: skewer [2023-01-22 10:31:35,534] multiqc [DEBUG ] No samples found: sortmerna [2023-01-22 10:31:35,562] multiqc [DEBUG ] No samples found: biobloomtools [2023-01-22 10:31:35,589] multiqc [DEBUG ] No samples found: fastq_screen [2023-01-22 10:31:35,612] multiqc [DEBUG ] No samples found: afterqc [2023-01-22 10:31:35,638] multiqc [DEBUG ] No samples found: fastp [2023-01-22 10:31:35,731] multiqc.modules.fastqc.fastqc [INFO ] Found 10 reports [2023-01-22 10:31:36,144] multiqc [DEBUG ] No samples found: minionqc [2023-01-22 10:31:36,170] multiqc [DEBUG ] No samples found: mosdepth [2023-01-22 10:31:36,193] multiqc [DEBUG ] No samples found: clusterflow [2023-01-22 10:31:36,219] multiqc [DEBUG ] No samples found: bcl2fastq [2023-01-22 10:31:36,244] multiqc [DEBUG ] No samples found: interop [2023-01-22 10:31:36,263] multiqc [DEBUG ] No samples found: flash [2023-01-22 10:31:36,272] multiqc [DEBUG ] No samples found: seqyclean [2023-01-22 10:31:36,293] multiqc [INFO ] Compressing plot data [2023-01-22 10:31:36,490] multiqc [INFO ] Report : multiqc_report.html [2023-01-22 10:31:36,490] multiqc [INFO ] Data : multiqc_data [2023-01-22 10:31:36,492] multiqc [DEBUG ] Moving data file from '/tmp/tmpwcwep7b0/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/gscratch/scrubbed/samwhite/outputs/20230119-coral-fastqc-fastp-multiqc-PRJNA744403/data/P_grandis/BS-seq/multiqc_data' [2023-01-22 10:31:36,494] multiqc [DEBUG ] Moving data file from '/tmp/tmpwcwep7b0/multiqc_data/multiqc_fastqc.txt' to '/gscratch/scrubbed/samwhite/outputs/20230119-coral-fastqc-fastp-multiqc-PRJNA744403/data/P_grandis/BS-seq/multiqc_data' [2023-01-22 10:31:36,495] multiqc [DEBUG ] Moving data file from '/tmp/tmpwcwep7b0/multiqc_data/multiqc_general_stats.txt' to '/gscratch/scrubbed/samwhite/outputs/20230119-coral-fastqc-fastp-multiqc-PRJNA744403/data/P_grandis/BS-seq/multiqc_data' [2023-01-22 10:31:36,496] multiqc [DEBUG ] Moving data file from '/tmp/tmpwcwep7b0/multiqc_data/multiqc_sources.txt' to '/gscratch/scrubbed/samwhite/outputs/20230119-coral-fastqc-fastp-multiqc-PRJNA744403/data/P_grandis/BS-seq/multiqc_data' [2023-01-22 10:31:36,498] multiqc [DEBUG ] Moving data file from '/tmp/tmpwcwep7b0/multiqc_data/multiqc_data.json' to '/gscratch/scrubbed/samwhite/outputs/20230119-coral-fastqc-fastp-multiqc-PRJNA744403/data/P_grandis/BS-seq/multiqc_data' [2023-01-22 10:31:37,191] multiqc [INFO ] MultiQC complete