[2023-06-21 16:04:04,860] multiqc [DEBUG ] No MultiQC config found: /gscratch/srlab/programs/anaconda3/lib/python3.7/site-packages/multiqc_config.yaml [2023-06-21 16:04:04,864] multiqc [DEBUG ] Loading config settings from: /usr/lusers/samwhite/.multiqc_config.yaml [2023-06-21 16:04:04,864] multiqc [DEBUG ] New config 'star': {'fn': '*Log.final.out'} [2023-06-21 16:04:04,864] multiqc [DEBUG ] New config 'star/genecounts': {'fn': '*ReadsPerGene.out.tab'} [2023-06-21 16:04:04,864] multiqc [DEBUG ] Added to filename patterns: {'fastp': {'fn': '*report.json'}} [2023-06-21 16:04:04,864] multiqc [DEBUG ] New config 'hisat2': {'contents': 'HISAT2 summary stats:', 'shared': True} [2023-06-21 16:04:04,865] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-06-21 16:04:04,865] multiqc [DEBUG ] Command used: /gscratch/srlab/programs/anaconda3/bin/multiqc . [2023-06-21 16:04:09,992] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2023-06-21 16:04:09,992] multiqc [INFO ] This is MultiQC v1.8 [2023-06-21 16:04:09,994] multiqc [DEBUG ] Command : /gscratch/srlab/programs/anaconda3/bin/multiqc . [2023-06-21 16:04:09,994] multiqc [DEBUG ] Working dir : /gscratch/scrubbed/samwhite/outputs/20230620-E5_coral-fastqc-flexbar-multiqc-sRNAseq/P_evermanni/trimmed [2023-06-21 16:04:09,994] multiqc [INFO ] Template : default [2023-06-21 16:04:09,994] multiqc [DEBUG ] Running Python 3.7.3 (default, Mar 27 2019, 22:11:17) [GCC 7.3.0] [2023-06-21 16:04:09,995] multiqc [INFO ] Searching : /gscratch/scrubbed/samwhite/outputs/20230620-E5_coral-fastqc-flexbar-multiqc-sRNAseq/P_evermanni/trimmed [2023-06-21 16:04:09,995] 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 16:04:09,996] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpnoajc_sz [2023-06-21 16:04:10,267] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POR-73-S1-TP2.flexbar_trim.20230621_2_fastqc.html [2023-06-21 16:04:10,290] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: sRNA-POR-82-S1-TP2.flexbar_trim.20230621.log [2023-06-21 16:04:10,302] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POR-79-S1-TP2.flexbar_trim.20230621_1.fastq.gz [2023-06-21 16:04:10,303] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POR-73-S1-TP2.flexbar_trim.20230621_2.fastq.gz [2023-06-21 16:04:10,308] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: sRNA-POR-73-S1-TP2.flexbar_trim.20230621.log [2023-06-21 16:04:10,314] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POR-82-S1-TP2.flexbar_trim.20230621_2.fastq.gz [2023-06-21 16:04:10,314] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POR-79-S1-TP2.flexbar_trim.20230621_2_fastqc.html [2023-06-21 16:04:10,315] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: trimmed_fastq_checksums.md5 [2023-06-21 16:04:10,315] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POR-79-S1-TP2.flexbar_trim.20230621_1_fastqc.html [2023-06-21 16:04:10,315] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POR-73-S1-TP2.flexbar_trim.20230621_1.fastq.gz [2023-06-21 16:04:10,315] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POR-82-S1-TP2.flexbar_trim.20230621_1.fastq.gz [2023-06-21 16:04:10,315] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POR-82-S1-TP2.flexbar_trim.20230621_2_fastqc.html [2023-06-21 16:04:10,315] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POR-82-S1-TP2.flexbar_trim.20230621_1_fastqc.html [2023-06-21 16:04:10,315] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POR-79-S1-TP2.flexbar_trim.20230621_2.fastq.gz [2023-06-21 16:04:10,319] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: sRNA-POR-79-S1-TP2.flexbar_trim.20230621.log [2023-06-21 16:04:10,326] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POR-73-S1-TP2.flexbar_trim.20230621_1_fastqc.html [2023-06-21 16:04:11,012] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 2.2.4 [2023-06-21 16:04:11,032] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 2.2.4 [2023-06-21 16:04:11,034] multiqc [DEBUG ] No samples found: custom_content [2023-06-21 16:04:11,041] multiqc [DEBUG ] No samples found: conpair [2023-06-21 16:04:11,046] multiqc [DEBUG ] No samples found: peddy [2023-06-21 16:04:11,052] multiqc [DEBUG ] No samples found: methylQA [2023-06-21 16:04:11,058] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-06-21 16:04:11,064] multiqc [DEBUG ] No samples found: qualimap [2023-06-21 16:04:11,087] multiqc [DEBUG ] No samples found: preseq [2023-06-21 16:04:11,092] multiqc [DEBUG ] No samples found: quast [2023-06-21 16:04:11,096] multiqc [DEBUG ] No samples found: qorts [2023-06-21 16:04:11,114] multiqc [DEBUG ] No samples found: rna_seqc [2023-06-21 16:04:11,131] multiqc [DEBUG ] No samples found: rsem [2023-06-21 16:04:11,154] multiqc [DEBUG ] No samples found: rseqc [2023-06-21 16:04:11,159] multiqc [DEBUG ] No samples found: busco [2023-06-21 16:04:11,163] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-06-21 16:04:11,168] multiqc [DEBUG ] No samples found: disambiguate [2023-06-21 16:04:11,188] multiqc [DEBUG ] No samples found: supernova [2023-06-21 16:04:11,228] multiqc [DEBUG ] No samples found: deeptools [2023-06-21 16:04:11,236] multiqc [DEBUG ] No samples found: sargasso [2023-06-21 16:04:11,260] multiqc [DEBUG ] No samples found: verifybamid [2023-06-21 16:04:11,267] multiqc [DEBUG ] No samples found: mirtrace [2023-06-21 16:04:11,296] multiqc [DEBUG ] No samples found: happy [2023-06-21 16:04:11,306] multiqc [DEBUG ] No samples found: homer [2023-06-21 16:04:11,350] multiqc [DEBUG ] No samples found: macs2 [2023-06-21 16:04:11,359] multiqc [DEBUG ] No samples found: theta2 [2023-06-21 16:04:11,390] multiqc [DEBUG ] No samples found: snpeff [2023-06-21 16:04:11,417] multiqc [DEBUG ] No samples found: gatk [2023-06-21 16:04:11,424] multiqc [DEBUG ] No samples found: htseq [2023-06-21 16:04:11,431] multiqc [DEBUG ] No samples found: bcftools [2023-06-21 16:04:11,438] multiqc [DEBUG ] No samples found: featureCounts [2023-06-21 16:04:11,444] multiqc [DEBUG ] No samples found: fgbio [2023-06-21 16:04:11,450] multiqc [DEBUG ] No samples found: dedup [2023-06-21 16:04:11,466] multiqc [DEBUG ] No samples found: damageprofiler [2023-06-21 16:04:11,537] multiqc [DEBUG ] No samples found: biobambam2 [2023-06-21 16:04:11,542] multiqc [DEBUG ] No samples found: mtnucratio [2023-06-21 16:04:11,547] multiqc [DEBUG ] No samples found: picard [2023-06-21 16:04:11,552] multiqc [DEBUG ] No samples found: prokka [2023-06-21 16:04:11,557] multiqc [DEBUG ] No samples found: samblaster [2023-06-21 16:04:11,637] multiqc [DEBUG ] No samples found: samtools [2023-06-21 16:04:11,644] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-06-21 16:04:11,652] multiqc [DEBUG ] No samples found: bamtools [2023-06-21 16:04:11,660] multiqc [DEBUG ] No samples found: jellyfish [2023-06-21 16:04:11,668] multiqc [DEBUG ] No samples found: vcftools [2023-06-21 16:04:11,675] multiqc [DEBUG ] No samples found: longranger [2023-06-21 16:04:11,681] multiqc [DEBUG ] No samples found: stacks [2023-06-21 16:04:11,706] multiqc [DEBUG ] No samples found: bbmap [2023-06-21 16:04:11,749] multiqc [DEBUG ] No samples found: bismark [2023-06-21 16:04:11,758] multiqc [DEBUG ] No samples found: biscuit [2023-06-21 16:04:11,781] multiqc [DEBUG ] No samples found: hicexplorer [2023-06-21 16:04:11,812] multiqc [DEBUG ] No samples found: hicup [2023-06-21 16:04:11,841] multiqc [DEBUG ] No samples found: hicpro [2023-06-21 16:04:11,849] multiqc [DEBUG ] No samples found: salmon [2023-06-21 16:04:11,876] multiqc [DEBUG ] No samples found: kallisto [2023-06-21 16:04:11,884] multiqc [DEBUG ] No samples found: slamdunk [2023-06-21 16:04:11,907] multiqc [DEBUG ] No samples found: star [2023-06-21 16:04:11,941] multiqc [DEBUG ] No samples found: hisat2 [2023-06-21 16:04:11,949] multiqc [DEBUG ] No samples found: tophat [2023-06-21 16:04:11,990] multiqc [DEBUG ] No samples found: bowtie2 [2023-06-21 16:04:12,013] multiqc [DEBUG ] No samples found: bowtie1 [2023-06-21 16:04:12,020] multiqc [DEBUG ] No samples found: kat [2023-06-21 16:04:12,027] multiqc [DEBUG ] No samples found: leehom [2023-06-21 16:04:12,034] multiqc [DEBUG ] No samples found: adapterRemoval [2023-06-21 16:04:12,040] multiqc [DEBUG ] No samples found: clipandmerge [2023-06-21 16:04:12,046] multiqc [DEBUG ] No samples found: cutadapt [2023-06-21 16:04:12,058] multiqc.modules.flexbar.flexbar [INFO ] Found 3 logs [2023-06-21 16:04:12,069] multiqc [DEBUG ] No samples found: trimmomatic [2023-06-21 16:04:12,094] multiqc [DEBUG ] No samples found: skewer [2023-06-21 16:04:12,099] multiqc [DEBUG ] No samples found: sortmerna [2023-06-21 16:04:12,104] multiqc [DEBUG ] No samples found: biobloomtools [2023-06-21 16:04:12,110] multiqc [DEBUG ] No samples found: fastq_screen [2023-06-21 16:04:12,126] multiqc [DEBUG ] No samples found: afterqc [2023-06-21 16:04:12,131] multiqc [DEBUG ] No samples found: fastp [2023-06-21 16:04:12,861] multiqc.modules.fastqc.fastqc [INFO ] Found 6 reports [2023-06-21 16:04:12,922] multiqc [DEBUG ] No samples found: minionqc [2023-06-21 16:04:12,942] multiqc [DEBUG ] No samples found: mosdepth [2023-06-21 16:04:12,946] multiqc [DEBUG ] No samples found: clusterflow [2023-06-21 16:04:12,951] multiqc [DEBUG ] No samples found: bcl2fastq [2023-06-21 16:04:12,955] multiqc [DEBUG ] No samples found: interop [2023-06-21 16:04:12,969] multiqc [DEBUG ] No samples found: flash [2023-06-21 16:04:12,974] multiqc [DEBUG ] No samples found: seqyclean [2023-06-21 16:04:12,986] multiqc [INFO ] Compressing plot data [2023-06-21 16:04:13,084] multiqc [INFO ] Report : multiqc_report.html [2023-06-21 16:04:13,084] multiqc [INFO ] Data : multiqc_data [2023-06-21 16:04:13,086] multiqc [DEBUG ] Moving data file from '/tmp/tmpnoajc_sz/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/gscratch/scrubbed/samwhite/outputs/20230620-E5_coral-fastqc-flexbar-multiqc-sRNAseq/P_evermanni/trimmed/multiqc_data' [2023-06-21 16:04:13,088] multiqc [DEBUG ] Moving data file from '/tmp/tmpnoajc_sz/multiqc_data/multiqc_flexbar.txt' to '/gscratch/scrubbed/samwhite/outputs/20230620-E5_coral-fastqc-flexbar-multiqc-sRNAseq/P_evermanni/trimmed/multiqc_data' [2023-06-21 16:04:13,090] multiqc [DEBUG ] Moving data file from '/tmp/tmpnoajc_sz/multiqc_data/multiqc_fastqc.txt' to '/gscratch/scrubbed/samwhite/outputs/20230620-E5_coral-fastqc-flexbar-multiqc-sRNAseq/P_evermanni/trimmed/multiqc_data' [2023-06-21 16:04:13,091] multiqc [DEBUG ] Moving data file from '/tmp/tmpnoajc_sz/multiqc_data/multiqc_general_stats.txt' to '/gscratch/scrubbed/samwhite/outputs/20230620-E5_coral-fastqc-flexbar-multiqc-sRNAseq/P_evermanni/trimmed/multiqc_data' [2023-06-21 16:04:13,093] multiqc [DEBUG ] Moving data file from '/tmp/tmpnoajc_sz/multiqc_data/multiqc_sources.txt' to '/gscratch/scrubbed/samwhite/outputs/20230620-E5_coral-fastqc-flexbar-multiqc-sRNAseq/P_evermanni/trimmed/multiqc_data' [2023-06-21 16:04:13,094] multiqc [DEBUG ] Moving data file from '/tmp/tmpnoajc_sz/multiqc_data/multiqc_data.json' to '/gscratch/scrubbed/samwhite/outputs/20230620-E5_coral-fastqc-flexbar-multiqc-sRNAseq/P_evermanni/trimmed/multiqc_data' [2023-06-21 16:04:13,270] multiqc [INFO ] MultiQC complete