[2023-05-22 16:44:07,735] multiqc [DEBUG ] No MultiQC config found: /gscratch/srlab/programs/anaconda3/lib/python3.7/site-packages/multiqc_config.yaml [2023-05-22 16:44:07,737] multiqc [DEBUG ] Loading config settings from: /usr/lusers/samwhite/.multiqc_config.yaml [2023-05-22 16:44:07,737] multiqc [DEBUG ] New config 'star': {'fn': '*Log.final.out'} [2023-05-22 16:44:07,738] multiqc [DEBUG ] New config 'star/genecounts': {'fn': '*ReadsPerGene.out.tab'} [2023-05-22 16:44:07,738] multiqc [DEBUG ] Added to filename patterns: {'fastp': {'fn': '*report.json'}} [2023-05-22 16:44:07,738] multiqc [DEBUG ] New config 'hisat2': {'contents': 'HISAT2 summary stats:', 'shared': True} [2023-05-22 16:44:07,738] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-05-22 16:44:07,738] multiqc [DEBUG ] Command used: /gscratch/srlab/programs/anaconda3/bin/multiqc . [2023-05-22 16:44:12,746] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2023-05-22 16:44:12,746] multiqc [INFO ] This is MultiQC v1.8 [2023-05-22 16:44:12,748] multiqc [DEBUG ] Command : /gscratch/srlab/programs/anaconda3/bin/multiqc . [2023-05-22 16:44:12,748] multiqc [DEBUG ] Working dir : /gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-sRNAseq/P_evermanni/raw_fastqc [2023-05-22 16:44:12,748] multiqc [INFO ] Template : default [2023-05-22 16:44:12,748] multiqc [DEBUG ] Running Python 3.7.3 (default, Mar 27 2019, 22:11:17) [GCC 7.3.0] [2023-05-22 16:44:12,749] multiqc [INFO ] Searching : /gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-sRNAseq/P_evermanni/raw_fastqc [2023-05-22 16:44:12,749] 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 [2023-05-22 16:44:12,750] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpptz42ivk [2023-05-22 16:44:12,922] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POR-73-S1-TP2_R2_001.fastq.gz [2023-05-22 16:44:12,923] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POR-73-S1-TP2_R1_001.fastq.gz [2023-05-22 16:44:12,923] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POR-79-S1-TP2_R1_001.fastq.gz [2023-05-22 16:44:12,923] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POR-82-S1-TP2_R1_001_fastqc.html [2023-05-22 16:44:12,929] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POR-73-S1-TP2_R1_001_fastqc.html [2023-05-22 16:44:12,929] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POR-79-S1-TP2_R1_001_fastqc.html [2023-05-22 16:44:12,929] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POR-73-S1-TP2_R2_001_fastqc.html [2023-05-22 16:44:12,929] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POR-79-S1-TP2_R2_001_fastqc.html [2023-05-22 16:44:12,930] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POR-82-S1-TP2_R1_001.fastq.gz [2023-05-22 16:44:12,930] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POR-82-S1-TP2_R2_001_fastqc.html [2023-05-22 16:44:12,931] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POR-79-S1-TP2_R2_001.fastq.gz [2023-05-22 16:44:12,931] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POR-82-S1-TP2_R2_001.fastq.gz [2023-05-22 16:44:13,216] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 2.2.4 [2023-05-22 16:44:13,216] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 2.2.4 [2023-05-22 16:44:13,217] multiqc [DEBUG ] No samples found: custom_content [2023-05-22 16:44:13,222] multiqc [DEBUG ] No samples found: conpair [2023-05-22 16:44:13,226] multiqc [DEBUG ] No samples found: peddy [2023-05-22 16:44:13,230] multiqc [DEBUG ] No samples found: methylQA [2023-05-22 16:44:13,235] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-05-22 16:44:13,241] multiqc [DEBUG ] No samples found: qualimap [2023-05-22 16:44:13,245] multiqc [DEBUG ] No samples found: preseq [2023-05-22 16:44:13,249] multiqc [DEBUG ] No samples found: quast [2023-05-22 16:44:13,253] multiqc [DEBUG ] No samples found: qorts [2023-05-22 16:44:13,258] multiqc [DEBUG ] No samples found: rna_seqc [2023-05-22 16:44:13,262] multiqc [DEBUG ] No samples found: rsem [2023-05-22 16:44:13,268] multiqc [DEBUG ] No samples found: rseqc [2023-05-22 16:44:13,273] multiqc [DEBUG ] No samples found: busco [2023-05-22 16:44:13,277] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-05-22 16:44:13,281] multiqc [DEBUG ] No samples found: disambiguate [2023-05-22 16:44:13,285] multiqc [DEBUG ] No samples found: supernova [2023-05-22 16:44:13,292] multiqc [DEBUG ] No samples found: deeptools [2023-05-22 16:44:13,296] multiqc [DEBUG ] No samples found: sargasso [2023-05-22 16:44:13,301] multiqc [DEBUG ] No samples found: verifybamid [2023-05-22 16:44:13,305] multiqc [DEBUG ] No samples found: mirtrace [2023-05-22 16:44:13,309] multiqc [DEBUG ] No samples found: happy [2023-05-22 16:44:13,314] multiqc [DEBUG ] No samples found: homer [2023-05-22 16:44:13,318] multiqc [DEBUG ] No samples found: macs2 [2023-05-22 16:44:13,323] multiqc [DEBUG ] No samples found: theta2 [2023-05-22 16:44:13,327] multiqc [DEBUG ] No samples found: snpeff [2023-05-22 16:44:13,332] multiqc [DEBUG ] No samples found: gatk [2023-05-22 16:44:13,336] multiqc [DEBUG ] No samples found: htseq [2023-05-22 16:44:13,340] multiqc [DEBUG ] No samples found: bcftools [2023-05-22 16:44:13,344] multiqc [DEBUG ] No samples found: featureCounts [2023-05-22 16:44:13,349] multiqc [DEBUG ] No samples found: fgbio [2023-05-22 16:44:13,353] multiqc [DEBUG ] No samples found: dedup [2023-05-22 16:44:13,357] multiqc [DEBUG ] No samples found: damageprofiler [2023-05-22 16:44:13,365] multiqc [DEBUG ] No samples found: biobambam2 [2023-05-22 16:44:13,370] multiqc [DEBUG ] No samples found: mtnucratio [2023-05-22 16:44:13,373] multiqc [DEBUG ] No samples found: picard [2023-05-22 16:44:13,377] multiqc [DEBUG ] No samples found: prokka [2023-05-22 16:44:13,382] multiqc [DEBUG ] No samples found: samblaster [2023-05-22 16:44:13,387] multiqc [DEBUG ] No samples found: samtools [2023-05-22 16:44:13,391] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-05-22 16:44:13,396] multiqc [DEBUG ] No samples found: bamtools [2023-05-22 16:44:13,400] multiqc [DEBUG ] No samples found: jellyfish [2023-05-22 16:44:13,405] multiqc [DEBUG ] No samples found: vcftools [2023-05-22 16:44:13,409] multiqc [DEBUG ] No samples found: longranger [2023-05-22 16:44:13,413] multiqc [DEBUG ] No samples found: stacks [2023-05-22 16:44:13,420] multiqc [DEBUG ] No samples found: bbmap [2023-05-22 16:44:13,425] multiqc [DEBUG ] No samples found: bismark [2023-05-22 16:44:13,430] multiqc [DEBUG ] No samples found: biscuit [2023-05-22 16:44:13,434] multiqc [DEBUG ] No samples found: hicexplorer [2023-05-22 16:44:13,439] multiqc [DEBUG ] No samples found: hicup [2023-05-22 16:44:13,443] multiqc [DEBUG ] No samples found: hicpro [2023-05-22 16:44:13,447] multiqc [DEBUG ] No samples found: salmon [2023-05-22 16:44:13,451] multiqc [DEBUG ] No samples found: kallisto [2023-05-22 16:44:13,456] multiqc [DEBUG ] No samples found: slamdunk [2023-05-22 16:44:13,460] multiqc [DEBUG ] No samples found: star [2023-05-22 16:44:13,464] multiqc [DEBUG ] No samples found: hisat2 [2023-05-22 16:44:13,472] multiqc [DEBUG ] No samples found: tophat [2023-05-22 16:44:13,480] multiqc [DEBUG ] No samples found: bowtie2 [2023-05-22 16:44:13,484] multiqc [DEBUG ] No samples found: bowtie1 [2023-05-22 16:44:13,488] multiqc [DEBUG ] No samples found: kat [2023-05-22 16:44:13,492] multiqc [DEBUG ] No samples found: leehom [2023-05-22 16:44:13,495] multiqc [DEBUG ] No samples found: adapterRemoval [2023-05-22 16:44:13,499] multiqc [DEBUG ] No samples found: clipandmerge [2023-05-22 16:44:13,502] multiqc [DEBUG ] No samples found: cutadapt [2023-05-22 16:44:13,506] multiqc [DEBUG ] No samples found: flexbar [2023-05-22 16:44:13,509] multiqc [DEBUG ] No samples found: trimmomatic [2023-05-22 16:44:13,513] multiqc [DEBUG ] No samples found: skewer [2023-05-22 16:44:13,517] multiqc [DEBUG ] No samples found: sortmerna [2023-05-22 16:44:13,520] multiqc [DEBUG ] No samples found: biobloomtools [2023-05-22 16:44:13,524] multiqc [DEBUG ] No samples found: fastq_screen [2023-05-22 16:44:13,527] multiqc [DEBUG ] No samples found: afterqc [2023-05-22 16:44:13,531] multiqc [DEBUG ] No samples found: fastp [2023-05-22 16:44:14,418] multiqc.modules.fastqc.fastqc [INFO ] Found 6 reports [2023-05-22 16:44:14,577] multiqc [DEBUG ] No samples found: minionqc [2023-05-22 16:44:14,580] multiqc [DEBUG ] No samples found: mosdepth [2023-05-22 16:44:14,584] multiqc [DEBUG ] No samples found: clusterflow [2023-05-22 16:44:14,588] multiqc [DEBUG ] No samples found: bcl2fastq [2023-05-22 16:44:14,591] multiqc [DEBUG ] No samples found: interop [2023-05-22 16:44:14,595] multiqc [DEBUG ] No samples found: flash [2023-05-22 16:44:14,598] multiqc [DEBUG ] No samples found: seqyclean [2023-05-22 16:44:14,607] multiqc [INFO ] Compressing plot data [2023-05-22 16:44:14,703] multiqc [INFO ] Report : multiqc_report.html [2023-05-22 16:44:14,703] multiqc [INFO ] Data : multiqc_data [2023-05-22 16:44:14,704] multiqc [DEBUG ] Moving data file from '/tmp/tmpptz42ivk/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-sRNAseq/P_evermanni/raw_fastqc/multiqc_data' [2023-05-22 16:44:14,706] multiqc [DEBUG ] Moving data file from '/tmp/tmpptz42ivk/multiqc_data/multiqc_fastqc.txt' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-sRNAseq/P_evermanni/raw_fastqc/multiqc_data' [2023-05-22 16:44:14,708] multiqc [DEBUG ] Moving data file from '/tmp/tmpptz42ivk/multiqc_data/multiqc_general_stats.txt' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-sRNAseq/P_evermanni/raw_fastqc/multiqc_data' [2023-05-22 16:44:14,709] multiqc [DEBUG ] Moving data file from '/tmp/tmpptz42ivk/multiqc_data/multiqc_sources.txt' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-sRNAseq/P_evermanni/raw_fastqc/multiqc_data' [2023-05-22 16:44:14,711] multiqc [DEBUG ] Moving data file from '/tmp/tmpptz42ivk/multiqc_data/multiqc_data.json' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-sRNAseq/P_evermanni/raw_fastqc/multiqc_data' [2023-05-22 16:44:14,849] multiqc [INFO ] MultiQC complete