[2023-06-21 15:48:19,234] multiqc [DEBUG ] No MultiQC config found: /gscratch/srlab/programs/anaconda3/lib/python3.7/site-packages/multiqc_config.yaml [2023-06-21 15:48:19,236] multiqc [DEBUG ] Loading config settings from: /usr/lusers/samwhite/.multiqc_config.yaml [2023-06-21 15:48:19,236] multiqc [DEBUG ] New config 'star': {'fn': '*Log.final.out'} [2023-06-21 15:48:19,237] multiqc [DEBUG ] New config 'star/genecounts': {'fn': '*ReadsPerGene.out.tab'} [2023-06-21 15:48:19,237] multiqc [DEBUG ] Added to filename patterns: {'fastp': {'fn': '*report.json'}} [2023-06-21 15:48:19,237] multiqc [DEBUG ] New config 'hisat2': {'contents': 'HISAT2 summary stats:', 'shared': True} [2023-06-21 15:48:19,237] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-06-21 15:48:19,237] multiqc [DEBUG ] Command used: /gscratch/srlab/programs/anaconda3/bin/multiqc . [2023-06-21 15:48:24,244] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2023-06-21 15:48:24,245] multiqc [INFO ] This is MultiQC v1.8 [2023-06-21 15:48:24,247] multiqc [DEBUG ] Command : /gscratch/srlab/programs/anaconda3/bin/multiqc . [2023-06-21 15:48:24,247] multiqc [DEBUG ] Working dir : /gscratch/scrubbed/samwhite/outputs/20230620-E5_coral-fastqc-flexbar-multiqc-sRNAseq/P_evermanni/raw_fastqc [2023-06-21 15:48:24,247] multiqc [INFO ] Template : default [2023-06-21 15:48:24,247] multiqc [DEBUG ] Running Python 3.7.3 (default, Mar 27 2019, 22:11:17) [GCC 7.3.0] [2023-06-21 15:48:24,247] multiqc [INFO ] Searching : /gscratch/scrubbed/samwhite/outputs/20230620-E5_coral-fastqc-flexbar-multiqc-sRNAseq/P_evermanni/raw_fastqc [2023-06-21 15:48:24,248] 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 [2023-06-21 15:48:24,248] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmppjef0md5 [2023-06-21 15:48:24,418] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POR-73-S1-TP2_R2_001.fastq.gz [2023-06-21 15:48:24,418] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POR-73-S1-TP2_R1_001.fastq.gz [2023-06-21 15:48:24,418] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POR-79-S1-TP2_R1_001.fastq.gz [2023-06-21 15:48:24,418] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POR-82-S1-TP2_R1_001_fastqc.html [2023-06-21 15:48:24,424] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POR-73-S1-TP2_R1_001_fastqc.html [2023-06-21 15:48:24,424] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POR-79-S1-TP2_R1_001_fastqc.html [2023-06-21 15:48:24,425] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POR-73-S1-TP2_R2_001_fastqc.html [2023-06-21 15:48:24,425] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POR-79-S1-TP2_R2_001_fastqc.html [2023-06-21 15:48:24,425] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POR-82-S1-TP2_R1_001.fastq.gz [2023-06-21 15:48:24,426] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POR-82-S1-TP2_R2_001_fastqc.html [2023-06-21 15:48:24,426] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POR-79-S1-TP2_R2_001.fastq.gz [2023-06-21 15:48:24,426] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POR-82-S1-TP2_R2_001.fastq.gz [2023-06-21 15:48:24,694] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 2.2.4 [2023-06-21 15:48:24,695] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 2.2.4 [2023-06-21 15:48:24,696] multiqc [DEBUG ] No samples found: custom_content [2023-06-21 15:48:24,700] multiqc [DEBUG ] No samples found: conpair [2023-06-21 15:48:24,704] multiqc [DEBUG ] No samples found: peddy [2023-06-21 15:48:24,709] multiqc [DEBUG ] No samples found: methylQA [2023-06-21 15:48:24,714] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-06-21 15:48:24,719] multiqc [DEBUG ] No samples found: qualimap [2023-06-21 15:48:24,723] multiqc [DEBUG ] No samples found: preseq [2023-06-21 15:48:24,728] multiqc [DEBUG ] No samples found: quast [2023-06-21 15:48:24,732] multiqc [DEBUG ] No samples found: qorts [2023-06-21 15:48:24,736] multiqc [DEBUG ] No samples found: rna_seqc [2023-06-21 15:48:24,741] multiqc [DEBUG ] No samples found: rsem [2023-06-21 15:48:24,747] multiqc [DEBUG ] No samples found: rseqc [2023-06-21 15:48:24,751] multiqc [DEBUG ] No samples found: busco [2023-06-21 15:48:24,756] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-06-21 15:48:24,760] multiqc [DEBUG ] No samples found: disambiguate [2023-06-21 15:48:24,764] multiqc [DEBUG ] No samples found: supernova [2023-06-21 15:48:24,771] multiqc [DEBUG ] No samples found: deeptools [2023-06-21 15:48:24,775] multiqc [DEBUG ] No samples found: sargasso [2023-06-21 15:48:24,779] multiqc [DEBUG ] No samples found: verifybamid [2023-06-21 15:48:24,784] multiqc [DEBUG ] No samples found: mirtrace [2023-06-21 15:48:24,788] multiqc [DEBUG ] No samples found: happy [2023-06-21 15:48:24,793] multiqc [DEBUG ] No samples found: homer [2023-06-21 15:48:24,797] multiqc [DEBUG ] No samples found: macs2 [2023-06-21 15:48:24,801] multiqc [DEBUG ] No samples found: theta2 [2023-06-21 15:48:24,806] multiqc [DEBUG ] No samples found: snpeff [2023-06-21 15:48:24,811] multiqc [DEBUG ] No samples found: gatk [2023-06-21 15:48:24,815] multiqc [DEBUG ] No samples found: htseq [2023-06-21 15:48:24,819] multiqc [DEBUG ] No samples found: bcftools [2023-06-21 15:48:24,823] multiqc [DEBUG ] No samples found: featureCounts [2023-06-21 15:48:24,828] multiqc [DEBUG ] No samples found: fgbio [2023-06-21 15:48:24,832] multiqc [DEBUG ] No samples found: dedup [2023-06-21 15:48:24,836] multiqc [DEBUG ] No samples found: damageprofiler [2023-06-21 15:48:24,845] multiqc [DEBUG ] No samples found: biobambam2 [2023-06-21 15:48:24,849] multiqc [DEBUG ] No samples found: mtnucratio [2023-06-21 15:48:24,853] multiqc [DEBUG ] No samples found: picard [2023-06-21 15:48:24,857] multiqc [DEBUG ] No samples found: prokka [2023-06-21 15:48:24,861] multiqc [DEBUG ] No samples found: samblaster [2023-06-21 15:48:24,866] multiqc [DEBUG ] No samples found: samtools [2023-06-21 15:48:24,871] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-06-21 15:48:24,875] multiqc [DEBUG ] No samples found: bamtools [2023-06-21 15:48:24,879] multiqc [DEBUG ] No samples found: jellyfish [2023-06-21 15:48:24,885] multiqc [DEBUG ] No samples found: vcftools [2023-06-21 15:48:24,889] multiqc [DEBUG ] No samples found: longranger [2023-06-21 15:48:24,893] multiqc [DEBUG ] No samples found: stacks [2023-06-21 15:48:24,899] multiqc [DEBUG ] No samples found: bbmap [2023-06-21 15:48:24,903] multiqc [DEBUG ] No samples found: bismark [2023-06-21 15:48:24,908] multiqc [DEBUG ] No samples found: biscuit [2023-06-21 15:48:24,911] multiqc [DEBUG ] No samples found: hicexplorer [2023-06-21 15:48:24,915] multiqc [DEBUG ] No samples found: hicup [2023-06-21 15:48:24,919] multiqc [DEBUG ] No samples found: hicpro [2023-06-21 15:48:24,922] multiqc [DEBUG ] No samples found: salmon [2023-06-21 15:48:24,926] multiqc [DEBUG ] No samples found: kallisto [2023-06-21 15:48:24,930] multiqc [DEBUG ] No samples found: slamdunk [2023-06-21 15:48:24,933] multiqc [DEBUG ] No samples found: star [2023-06-21 15:48:24,937] multiqc [DEBUG ] No samples found: hisat2 [2023-06-21 15:48:24,940] multiqc [DEBUG ] No samples found: tophat [2023-06-21 15:48:24,944] multiqc [DEBUG ] No samples found: bowtie2 [2023-06-21 15:48:24,947] multiqc [DEBUG ] No samples found: bowtie1 [2023-06-21 15:48:24,951] multiqc [DEBUG ] No samples found: kat [2023-06-21 15:48:24,954] multiqc [DEBUG ] No samples found: leehom [2023-06-21 15:48:24,958] multiqc [DEBUG ] No samples found: adapterRemoval [2023-06-21 15:48:24,961] multiqc [DEBUG ] No samples found: clipandmerge [2023-06-21 15:48:24,965] multiqc [DEBUG ] No samples found: cutadapt [2023-06-21 15:48:24,968] multiqc [DEBUG ] No samples found: flexbar [2023-06-21 15:48:24,972] multiqc [DEBUG ] No samples found: trimmomatic [2023-06-21 15:48:24,975] multiqc [DEBUG ] No samples found: skewer [2023-06-21 15:48:24,979] multiqc [DEBUG ] No samples found: sortmerna [2023-06-21 15:48:24,982] multiqc [DEBUG ] No samples found: biobloomtools [2023-06-21 15:48:24,986] multiqc [DEBUG ] No samples found: fastq_screen [2023-06-21 15:48:24,992] multiqc [DEBUG ] No samples found: afterqc [2023-06-21 15:48:24,996] multiqc [DEBUG ] No samples found: fastp [2023-06-21 15:48:25,874] multiqc.modules.fastqc.fastqc [INFO ] Found 6 reports [2023-06-21 15:48:26,036] multiqc [DEBUG ] No samples found: minionqc [2023-06-21 15:48:26,040] multiqc [DEBUG ] No samples found: mosdepth [2023-06-21 15:48:26,043] multiqc [DEBUG ] No samples found: clusterflow [2023-06-21 15:48:26,047] multiqc [DEBUG ] No samples found: bcl2fastq [2023-06-21 15:48:26,051] multiqc [DEBUG ] No samples found: interop [2023-06-21 15:48:26,054] multiqc [DEBUG ] No samples found: flash [2023-06-21 15:48:26,058] multiqc [DEBUG ] No samples found: seqyclean [2023-06-21 15:48:26,067] multiqc [INFO ] Compressing plot data [2023-06-21 15:48:26,164] multiqc [INFO ] Report : multiqc_report.html [2023-06-21 15:48:26,164] multiqc [INFO ] Data : multiqc_data [2023-06-21 15:48:26,165] multiqc [DEBUG ] Moving data file from '/tmp/tmppjef0md5/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/gscratch/scrubbed/samwhite/outputs/20230620-E5_coral-fastqc-flexbar-multiqc-sRNAseq/P_evermanni/raw_fastqc/multiqc_data' [2023-06-21 15:48:26,167] multiqc [DEBUG ] Moving data file from '/tmp/tmppjef0md5/multiqc_data/multiqc_fastqc.txt' to '/gscratch/scrubbed/samwhite/outputs/20230620-E5_coral-fastqc-flexbar-multiqc-sRNAseq/P_evermanni/raw_fastqc/multiqc_data' [2023-06-21 15:48:26,168] multiqc [DEBUG ] Moving data file from '/tmp/tmppjef0md5/multiqc_data/multiqc_general_stats.txt' to '/gscratch/scrubbed/samwhite/outputs/20230620-E5_coral-fastqc-flexbar-multiqc-sRNAseq/P_evermanni/raw_fastqc/multiqc_data' [2023-06-21 15:48:26,170] multiqc [DEBUG ] Moving data file from '/tmp/tmppjef0md5/multiqc_data/multiqc_sources.txt' to '/gscratch/scrubbed/samwhite/outputs/20230620-E5_coral-fastqc-flexbar-multiqc-sRNAseq/P_evermanni/raw_fastqc/multiqc_data' [2023-06-21 15:48:26,172] multiqc [DEBUG ] Moving data file from '/tmp/tmppjef0md5/multiqc_data/multiqc_data.json' to '/gscratch/scrubbed/samwhite/outputs/20230620-E5_coral-fastqc-flexbar-multiqc-sRNAseq/P_evermanni/raw_fastqc/multiqc_data' [2023-06-21 15:48:26,314] multiqc [INFO ] MultiQC complete