[2023-06-21 15:13:27,183] multiqc [DEBUG ] No MultiQC config found: /gscratch/srlab/programs/anaconda3/lib/python3.7/site-packages/multiqc_config.yaml [2023-06-21 15:13:27,216] multiqc [DEBUG ] Loading config settings from: /usr/lusers/samwhite/.multiqc_config.yaml [2023-06-21 15:13:27,217] multiqc [DEBUG ] New config 'star': {'fn': '*Log.final.out'} [2023-06-21 15:13:27,217] multiqc [DEBUG ] New config 'star/genecounts': {'fn': '*ReadsPerGene.out.tab'} [2023-06-21 15:13:27,217] multiqc [DEBUG ] Added to filename patterns: {'fastp': {'fn': '*report.json'}} [2023-06-21 15:13:27,218] multiqc [DEBUG ] New config 'hisat2': {'contents': 'HISAT2 summary stats:', 'shared': True} [2023-06-21 15:13:27,218] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-06-21 15:13:27,218] multiqc [DEBUG ] Command used: /gscratch/srlab/programs/anaconda3/bin/multiqc . [2023-06-21 15:13:32,321] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2023-06-21 15:13:32,321] multiqc [INFO ] This is MultiQC v1.8 [2023-06-21 15:13:32,323] multiqc [DEBUG ] Command : /gscratch/srlab/programs/anaconda3/bin/multiqc . [2023-06-21 15:13:32,324] multiqc [DEBUG ] Working dir : /gscratch/scrubbed/samwhite/outputs/20230620-E5_coral-fastqc-flexbar-multiqc-sRNAseq/A_pulchra/raw_fastqc [2023-06-21 15:13:32,324] multiqc [INFO ] Template : default [2023-06-21 15:13:32,324] multiqc [DEBUG ] Running Python 3.7.3 (default, Mar 27 2019, 22:11:17) [GCC 7.3.0] [2023-06-21 15:13:32,324] multiqc [INFO ] Searching : /gscratch/scrubbed/samwhite/outputs/20230620-E5_coral-fastqc-flexbar-multiqc-sRNAseq/A_pulchra/raw_fastqc [2023-06-21 15:13:32,325] 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 15:13:32,325] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmp9qszyi97 [2023-06-21 15:13:33,139] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-178-S1-TP2_R2_001_fastqc.html [2023-06-21 15:13:33,139] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-150-S1-TP2_R1_001_fastqc.html [2023-06-21 15:13:33,139] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-150-S1-TP2_R2_001_fastqc.html [2023-06-21 15:13:33,140] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-178-S1-TP2_R1_001.fastq.gz [2023-06-21 15:13:33,140] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-173-S1-TP2_R2_001.fastq.gz [2023-06-21 15:13:33,141] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-140-S1-TP2_R1_001_fastqc.html [2023-06-21 15:13:33,141] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-145-S1-TP2_R2_001_fastqc.html [2023-06-21 15:13:33,141] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-145-S1-TP2_R2_001.fastq.gz [2023-06-21 15:13:33,141] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-145-S1-TP2_R1_001_fastqc.html [2023-06-21 15:13:33,141] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-173-S1-TP2_R2_001_fastqc.html [2023-06-21 15:13:33,142] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-173-S1-TP2_R1_001.fastq.gz [2023-06-21 15:13:33,142] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-173-S1-TP2_R1_001_fastqc.html [2023-06-21 15:13:33,142] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-140-S1-TP2_R2_001_fastqc.html [2023-06-21 15:13:33,142] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-150-S1-TP2_R1_001.fastq.gz [2023-06-21 15:13:33,142] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-178-S1-TP2_R2_001.fastq.gz [2023-06-21 15:13:33,142] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-145-S1-TP2_R1_001.fastq.gz [2023-06-21 15:13:33,143] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-140-S1-TP2_R1_001.fastq.gz [2023-06-21 15:13:33,144] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-178-S1-TP2_R1_001_fastqc.html [2023-06-21 15:13:33,144] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-150-S1-TP2_R2_001.fastq.gz [2023-06-21 15:13:33,144] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-140-S1-TP2_R2_001.fastq.gz [2023-06-21 15:13:37,854] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 2.2.4 [2023-06-21 15:13:37,914] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 2.2.4 [2023-06-21 15:13:37,963] multiqc [DEBUG ] No samples found: custom_content [2023-06-21 15:13:38,032] multiqc [DEBUG ] No samples found: conpair [2023-06-21 15:13:38,074] multiqc [DEBUG ] No samples found: peddy [2023-06-21 15:13:38,147] multiqc [DEBUG ] No samples found: methylQA [2023-06-21 15:13:38,217] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-06-21 15:13:38,339] multiqc [DEBUG ] No samples found: qualimap [2023-06-21 15:13:38,420] multiqc [DEBUG ] No samples found: preseq [2023-06-21 15:13:38,454] multiqc [DEBUG ] No samples found: quast [2023-06-21 15:13:38,476] multiqc [DEBUG ] No samples found: qorts [2023-06-21 15:13:38,645] multiqc [DEBUG ] No samples found: rna_seqc [2023-06-21 15:13:38,735] multiqc [DEBUG ] No samples found: rsem [2023-06-21 15:13:38,887] multiqc [DEBUG ] No samples found: rseqc [2023-06-21 15:13:38,962] multiqc [DEBUG ] No samples found: busco [2023-06-21 15:13:39,022] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-06-21 15:13:39,120] multiqc [DEBUG ] No samples found: disambiguate [2023-06-21 15:13:39,207] multiqc [DEBUG ] No samples found: supernova [2023-06-21 15:13:39,325] multiqc [DEBUG ] No samples found: deeptools [2023-06-21 15:13:39,392] multiqc [DEBUG ] No samples found: sargasso [2023-06-21 15:13:39,442] multiqc [DEBUG ] No samples found: verifybamid [2023-06-21 15:13:39,458] multiqc [DEBUG ] No samples found: mirtrace [2023-06-21 15:13:39,498] multiqc [DEBUG ] No samples found: happy [2023-06-21 15:13:39,548] multiqc [DEBUG ] No samples found: homer [2023-06-21 15:13:39,600] multiqc [DEBUG ] No samples found: macs2 [2023-06-21 15:13:39,611] multiqc [DEBUG ] No samples found: theta2 [2023-06-21 15:13:39,634] multiqc [DEBUG ] No samples found: snpeff [2023-06-21 15:13:39,713] multiqc [DEBUG ] No samples found: gatk [2023-06-21 15:13:39,734] multiqc [DEBUG ] No samples found: htseq [2023-06-21 15:13:39,743] multiqc [DEBUG ] No samples found: bcftools [2023-06-21 15:13:39,753] multiqc [DEBUG ] No samples found: featureCounts [2023-06-21 15:13:39,763] multiqc [DEBUG ] No samples found: fgbio [2023-06-21 15:13:39,771] multiqc [DEBUG ] No samples found: dedup [2023-06-21 15:13:39,795] multiqc [DEBUG ] No samples found: damageprofiler [2023-06-21 15:13:39,834] multiqc [DEBUG ] No samples found: biobambam2 [2023-06-21 15:13:39,842] multiqc [DEBUG ] No samples found: mtnucratio [2023-06-21 15:13:39,847] multiqc [DEBUG ] No samples found: picard [2023-06-21 15:13:39,869] multiqc [DEBUG ] No samples found: prokka [2023-06-21 15:13:39,876] multiqc [DEBUG ] No samples found: samblaster [2023-06-21 15:13:39,919] multiqc [DEBUG ] No samples found: samtools [2023-06-21 15:13:39,946] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-06-21 15:13:40,001] multiqc [DEBUG ] No samples found: bamtools [2023-06-21 15:13:40,011] multiqc [DEBUG ] No samples found: jellyfish [2023-06-21 15:13:40,042] multiqc [DEBUG ] No samples found: vcftools [2023-06-21 15:13:40,074] multiqc [DEBUG ] No samples found: longranger [2023-06-21 15:13:40,084] multiqc [DEBUG ] No samples found: stacks [2023-06-21 15:13:40,155] multiqc [DEBUG ] No samples found: bbmap [2023-06-21 15:13:40,174] multiqc [DEBUG ] No samples found: bismark [2023-06-21 15:13:40,223] multiqc [DEBUG ] No samples found: biscuit [2023-06-21 15:13:40,262] multiqc [DEBUG ] No samples found: hicexplorer [2023-06-21 15:13:40,272] multiqc [DEBUG ] No samples found: hicup [2023-06-21 15:13:40,281] multiqc [DEBUG ] No samples found: hicpro [2023-06-21 15:13:40,292] multiqc [DEBUG ] No samples found: salmon [2023-06-21 15:13:40,300] multiqc [DEBUG ] No samples found: kallisto [2023-06-21 15:13:40,317] multiqc [DEBUG ] No samples found: slamdunk [2023-06-21 15:13:40,339] multiqc [DEBUG ] No samples found: star [2023-06-21 15:13:40,346] multiqc [DEBUG ] No samples found: hisat2 [2023-06-21 15:13:40,368] multiqc [DEBUG ] No samples found: tophat [2023-06-21 15:13:40,392] multiqc [DEBUG ] No samples found: bowtie2 [2023-06-21 15:13:40,434] multiqc [DEBUG ] No samples found: bowtie1 [2023-06-21 15:13:40,445] multiqc [DEBUG ] No samples found: kat [2023-06-21 15:13:40,455] multiqc [DEBUG ] No samples found: leehom [2023-06-21 15:13:40,464] multiqc [DEBUG ] No samples found: adapterRemoval [2023-06-21 15:13:40,473] multiqc [DEBUG ] No samples found: clipandmerge [2023-06-21 15:13:40,480] multiqc [DEBUG ] No samples found: cutadapt [2023-06-21 15:13:40,489] multiqc [DEBUG ] No samples found: flexbar [2023-06-21 15:13:40,497] multiqc [DEBUG ] No samples found: trimmomatic [2023-06-21 15:13:40,524] multiqc [DEBUG ] No samples found: skewer [2023-06-21 15:13:40,531] multiqc [DEBUG ] No samples found: sortmerna [2023-06-21 15:13:40,538] multiqc [DEBUG ] No samples found: biobloomtools [2023-06-21 15:13:40,558] multiqc [DEBUG ] No samples found: fastq_screen [2023-06-21 15:13:40,564] multiqc [DEBUG ] No samples found: afterqc [2023-06-21 15:13:40,573] multiqc [DEBUG ] No samples found: fastp [2023-06-21 15:13:41,987] multiqc.modules.fastqc.fastqc [INFO ] Found 10 reports [2023-06-21 15:13:42,309] multiqc [DEBUG ] No samples found: minionqc [2023-06-21 15:13:42,326] multiqc [DEBUG ] No samples found: mosdepth [2023-06-21 15:13:42,353] multiqc [DEBUG ] No samples found: clusterflow [2023-06-21 15:13:42,370] multiqc [DEBUG ] No samples found: bcl2fastq [2023-06-21 15:13:42,395] multiqc [DEBUG ] No samples found: interop [2023-06-21 15:13:42,418] multiqc [DEBUG ] No samples found: flash [2023-06-21 15:13:42,437] multiqc [DEBUG ] No samples found: seqyclean [2023-06-21 15:13:42,459] multiqc [INFO ] Compressing plot data [2023-06-21 15:13:42,623] multiqc [INFO ] Report : multiqc_report.html [2023-06-21 15:13:42,623] multiqc [INFO ] Data : multiqc_data [2023-06-21 15:13:42,624] multiqc [DEBUG ] Moving data file from '/tmp/tmp9qszyi97/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/gscratch/scrubbed/samwhite/outputs/20230620-E5_coral-fastqc-flexbar-multiqc-sRNAseq/A_pulchra/raw_fastqc/multiqc_data' [2023-06-21 15:13:42,626] multiqc [DEBUG ] Moving data file from '/tmp/tmp9qszyi97/multiqc_data/multiqc_fastqc.txt' to '/gscratch/scrubbed/samwhite/outputs/20230620-E5_coral-fastqc-flexbar-multiqc-sRNAseq/A_pulchra/raw_fastqc/multiqc_data' [2023-06-21 15:13:42,627] multiqc [DEBUG ] Moving data file from '/tmp/tmp9qszyi97/multiqc_data/multiqc_general_stats.txt' to '/gscratch/scrubbed/samwhite/outputs/20230620-E5_coral-fastqc-flexbar-multiqc-sRNAseq/A_pulchra/raw_fastqc/multiqc_data' [2023-06-21 15:13:42,629] multiqc [DEBUG ] Moving data file from '/tmp/tmp9qszyi97/multiqc_data/multiqc_sources.txt' to '/gscratch/scrubbed/samwhite/outputs/20230620-E5_coral-fastqc-flexbar-multiqc-sRNAseq/A_pulchra/raw_fastqc/multiqc_data' [2023-06-21 15:13:42,630] multiqc [DEBUG ] Moving data file from '/tmp/tmp9qszyi97/multiqc_data/multiqc_data.json' to '/gscratch/scrubbed/samwhite/outputs/20230620-E5_coral-fastqc-flexbar-multiqc-sRNAseq/A_pulchra/raw_fastqc/multiqc_data' [2023-06-21 15:13:43,224] multiqc [INFO ] MultiQC complete