[2023-06-21 16:08:43,800] multiqc [DEBUG ] No MultiQC config found: /gscratch/srlab/programs/anaconda3/lib/python3.7/site-packages/multiqc_config.yaml [2023-06-21 16:08:43,803] multiqc [DEBUG ] Loading config settings from: /usr/lusers/samwhite/.multiqc_config.yaml [2023-06-21 16:08:43,804] multiqc [DEBUG ] New config 'star': {'fn': '*Log.final.out'} [2023-06-21 16:08:43,804] multiqc [DEBUG ] New config 'star/genecounts': {'fn': '*ReadsPerGene.out.tab'} [2023-06-21 16:08:43,804] multiqc [DEBUG ] Added to filename patterns: {'fastp': {'fn': '*report.json'}} [2023-06-21 16:08:43,804] multiqc [DEBUG ] New config 'hisat2': {'contents': 'HISAT2 summary stats:', 'shared': True} [2023-06-21 16:08:43,804] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-06-21 16:08:43,805] multiqc [DEBUG ] Command used: /gscratch/srlab/programs/anaconda3/bin/multiqc . [2023-06-21 16:08:48,814] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2023-06-21 16:08:48,814] multiqc [INFO ] This is MultiQC v1.8 [2023-06-21 16:08:48,816] multiqc [DEBUG ] Command : /gscratch/srlab/programs/anaconda3/bin/multiqc . [2023-06-21 16:08:48,817] multiqc [DEBUG ] Working dir : /gscratch/scrubbed/samwhite/outputs/20230620-E5_coral-fastqc-flexbar-multiqc-sRNAseq/P_meandrina/raw_fastqc [2023-06-21 16:08:48,817] multiqc [INFO ] Template : default [2023-06-21 16:08:48,817] multiqc [DEBUG ] Running Python 3.7.3 (default, Mar 27 2019, 22:11:17) [GCC 7.3.0] [2023-06-21 16:08:48,817] multiqc [INFO ] Searching : /gscratch/scrubbed/samwhite/outputs/20230620-E5_coral-fastqc-flexbar-multiqc-sRNAseq/P_meandrina/raw_fastqc [2023-06-21 16:08:48,818] 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 16:08:48,818] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpcpavfglt [2023-06-21 16:08:48,983] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-47-S1-TP2_R1_001.fastq.gz [2023-06-21 16:08:48,990] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-53-S1-TP2_R2_001_fastqc.html [2023-06-21 16:08:48,990] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-53-S1-TP2_R1_001.fastq.gz [2023-06-21 16:08:48,990] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-57-S1-TP2_R1_001_fastqc.html [2023-06-21 16:08:48,990] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-47-S1-TP2_R2_001_fastqc.html [2023-06-21 16:08:48,990] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-48-S1-TP2_R2_001.fastq.gz [2023-06-21 16:08:48,991] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-47-S1-TP2_R2_001.fastq.gz [2023-06-21 16:08:48,991] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-48-S1-TP2_R1_001_fastqc.html [2023-06-21 16:08:48,991] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-57-S1-TP2_R2_001_fastqc.html [2023-06-21 16:08:48,992] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-48-S1-TP2_R2_001_fastqc.html [2023-06-21 16:08:48,992] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-50-S1-TP2_R2_001.fastq.gz [2023-06-21 16:08:48,992] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-48-S1-TP2_R1_001.fastq.gz [2023-06-21 16:08:48,992] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-53-S1-TP2_R1_001_fastqc.html [2023-06-21 16:08:48,992] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-47-S1-TP2_R1_001_fastqc.html [2023-06-21 16:08:48,992] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-57-S1-TP2_R1_001.fastq.gz [2023-06-21 16:08:48,992] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-53-S1-TP2_R2_001.fastq.gz [2023-06-21 16:08:48,993] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-50-S1-TP2_R1_001_fastqc.html [2023-06-21 16:08:48,993] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-57-S1-TP2_R2_001.fastq.gz [2023-06-21 16:08:48,993] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-50-S1-TP2_R2_001_fastqc.html [2023-06-21 16:08:48,993] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-50-S1-TP2_R1_001.fastq.gz [2023-06-21 16:08:49,500] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 2.2.4 [2023-06-21 16:08:49,501] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 2.2.4 [2023-06-21 16:08:49,503] multiqc [DEBUG ] No samples found: custom_content [2023-06-21 16:08:49,511] multiqc [DEBUG ] No samples found: conpair [2023-06-21 16:08:49,518] multiqc [DEBUG ] No samples found: peddy [2023-06-21 16:08:49,525] multiqc [DEBUG ] No samples found: methylQA [2023-06-21 16:08:49,533] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-06-21 16:08:49,541] multiqc [DEBUG ] No samples found: qualimap [2023-06-21 16:08:49,547] multiqc [DEBUG ] No samples found: preseq [2023-06-21 16:08:49,553] multiqc [DEBUG ] No samples found: quast [2023-06-21 16:08:49,558] multiqc [DEBUG ] No samples found: qorts [2023-06-21 16:08:49,564] multiqc [DEBUG ] No samples found: rna_seqc [2023-06-21 16:08:49,569] multiqc [DEBUG ] No samples found: rsem [2023-06-21 16:08:49,577] multiqc [DEBUG ] No samples found: rseqc [2023-06-21 16:08:49,582] multiqc [DEBUG ] No samples found: busco [2023-06-21 16:08:49,587] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-06-21 16:08:49,601] multiqc [DEBUG ] No samples found: disambiguate [2023-06-21 16:08:49,606] multiqc [DEBUG ] No samples found: supernova [2023-06-21 16:08:49,613] multiqc [DEBUG ] No samples found: deeptools [2023-06-21 16:08:49,618] multiqc [DEBUG ] No samples found: sargasso [2023-06-21 16:08:49,622] multiqc [DEBUG ] No samples found: verifybamid [2023-06-21 16:08:49,627] multiqc [DEBUG ] No samples found: mirtrace [2023-06-21 16:08:49,631] multiqc [DEBUG ] No samples found: happy [2023-06-21 16:08:49,639] multiqc [DEBUG ] No samples found: homer [2023-06-21 16:08:49,644] multiqc [DEBUG ] No samples found: macs2 [2023-06-21 16:08:49,648] multiqc [DEBUG ] No samples found: theta2 [2023-06-21 16:08:49,653] multiqc [DEBUG ] No samples found: snpeff [2023-06-21 16:08:49,674] multiqc [DEBUG ] No samples found: gatk [2023-06-21 16:08:49,678] multiqc [DEBUG ] No samples found: htseq [2023-06-21 16:08:49,683] multiqc [DEBUG ] No samples found: bcftools [2023-06-21 16:08:49,687] multiqc [DEBUG ] No samples found: featureCounts [2023-06-21 16:08:49,692] multiqc [DEBUG ] No samples found: fgbio [2023-06-21 16:08:49,712] multiqc [DEBUG ] No samples found: dedup [2023-06-21 16:08:49,733] multiqc [DEBUG ] No samples found: damageprofiler [2023-06-21 16:08:49,742] multiqc [DEBUG ] No samples found: biobambam2 [2023-06-21 16:08:49,746] multiqc [DEBUG ] No samples found: mtnucratio [2023-06-21 16:08:49,750] multiqc [DEBUG ] No samples found: picard [2023-06-21 16:08:49,754] multiqc [DEBUG ] No samples found: prokka [2023-06-21 16:08:49,758] multiqc [DEBUG ] No samples found: samblaster [2023-06-21 16:08:49,764] multiqc [DEBUG ] No samples found: samtools [2023-06-21 16:08:49,768] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-06-21 16:08:49,772] multiqc [DEBUG ] No samples found: bamtools [2023-06-21 16:08:49,777] multiqc [DEBUG ] No samples found: jellyfish [2023-06-21 16:08:49,782] multiqc [DEBUG ] No samples found: vcftools [2023-06-21 16:08:49,786] multiqc [DEBUG ] No samples found: longranger [2023-06-21 16:08:49,791] multiqc [DEBUG ] No samples found: stacks [2023-06-21 16:08:49,808] multiqc [DEBUG ] No samples found: bbmap [2023-06-21 16:08:49,813] multiqc [DEBUG ] No samples found: bismark [2023-06-21 16:08:49,818] multiqc [DEBUG ] No samples found: biscuit [2023-06-21 16:08:49,823] multiqc [DEBUG ] No samples found: hicexplorer [2023-06-21 16:08:49,827] multiqc [DEBUG ] No samples found: hicup [2023-06-21 16:08:49,831] multiqc [DEBUG ] No samples found: hicpro [2023-06-21 16:08:49,835] multiqc [DEBUG ] No samples found: salmon [2023-06-21 16:08:49,839] multiqc [DEBUG ] No samples found: kallisto [2023-06-21 16:08:49,876] multiqc [DEBUG ] No samples found: slamdunk [2023-06-21 16:08:49,884] multiqc [DEBUG ] No samples found: star [2023-06-21 16:08:49,892] multiqc [DEBUG ] No samples found: hisat2 [2023-06-21 16:08:49,899] multiqc [DEBUG ] No samples found: tophat [2023-06-21 16:08:49,906] multiqc [DEBUG ] No samples found: bowtie2 [2023-06-21 16:08:49,913] multiqc [DEBUG ] No samples found: bowtie1 [2023-06-21 16:08:49,920] multiqc [DEBUG ] No samples found: kat [2023-06-21 16:08:49,926] multiqc [DEBUG ] No samples found: leehom [2023-06-21 16:08:49,932] multiqc [DEBUG ] No samples found: adapterRemoval [2023-06-21 16:08:49,938] multiqc [DEBUG ] No samples found: clipandmerge [2023-06-21 16:08:49,944] multiqc [DEBUG ] No samples found: cutadapt [2023-06-21 16:08:49,950] multiqc [DEBUG ] No samples found: flexbar [2023-06-21 16:08:49,955] multiqc [DEBUG ] No samples found: trimmomatic [2023-06-21 16:08:49,960] multiqc [DEBUG ] No samples found: skewer [2023-06-21 16:08:49,965] multiqc [DEBUG ] No samples found: sortmerna [2023-06-21 16:08:49,970] multiqc [DEBUG ] No samples found: biobloomtools [2023-06-21 16:08:49,975] multiqc [DEBUG ] No samples found: fastq_screen [2023-06-21 16:08:49,980] multiqc [DEBUG ] No samples found: afterqc [2023-06-21 16:08:49,985] multiqc [DEBUG ] No samples found: fastp [2023-06-21 16:08:51,280] multiqc.modules.fastqc.fastqc [INFO ] Found 10 reports [2023-06-21 16:08:51,525] multiqc [DEBUG ] No samples found: minionqc [2023-06-21 16:08:51,528] multiqc [DEBUG ] No samples found: mosdepth [2023-06-21 16:08:51,532] multiqc [DEBUG ] No samples found: clusterflow [2023-06-21 16:08:51,535] multiqc [DEBUG ] No samples found: bcl2fastq [2023-06-21 16:08:51,539] multiqc [DEBUG ] No samples found: interop [2023-06-21 16:08:51,542] multiqc [DEBUG ] No samples found: flash [2023-06-21 16:08:51,546] multiqc [DEBUG ] No samples found: seqyclean [2023-06-21 16:08:51,559] multiqc [INFO ] Compressing plot data [2023-06-21 16:08:51,718] multiqc [INFO ] Report : multiqc_report.html [2023-06-21 16:08:51,718] multiqc [INFO ] Data : multiqc_data [2023-06-21 16:08:51,720] multiqc [DEBUG ] Moving data file from '/tmp/tmpcpavfglt/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/gscratch/scrubbed/samwhite/outputs/20230620-E5_coral-fastqc-flexbar-multiqc-sRNAseq/P_meandrina/raw_fastqc/multiqc_data' [2023-06-21 16:08:51,721] multiqc [DEBUG ] Moving data file from '/tmp/tmpcpavfglt/multiqc_data/multiqc_fastqc.txt' to '/gscratch/scrubbed/samwhite/outputs/20230620-E5_coral-fastqc-flexbar-multiqc-sRNAseq/P_meandrina/raw_fastqc/multiqc_data' [2023-06-21 16:08:51,723] multiqc [DEBUG ] Moving data file from '/tmp/tmpcpavfglt/multiqc_data/multiqc_general_stats.txt' to '/gscratch/scrubbed/samwhite/outputs/20230620-E5_coral-fastqc-flexbar-multiqc-sRNAseq/P_meandrina/raw_fastqc/multiqc_data' [2023-06-21 16:08:51,725] multiqc [DEBUG ] Moving data file from '/tmp/tmpcpavfglt/multiqc_data/multiqc_sources.txt' to '/gscratch/scrubbed/samwhite/outputs/20230620-E5_coral-fastqc-flexbar-multiqc-sRNAseq/P_meandrina/raw_fastqc/multiqc_data' [2023-06-21 16:08:51,726] multiqc [DEBUG ] Moving data file from '/tmp/tmpcpavfglt/multiqc_data/multiqc_data.json' to '/gscratch/scrubbed/samwhite/outputs/20230620-E5_coral-fastqc-flexbar-multiqc-sRNAseq/P_meandrina/raw_fastqc/multiqc_data' [2023-06-21 16:08:51,826] multiqc [INFO ] MultiQC complete