[2023-06-21 15:44:35,320] multiqc [DEBUG ] No MultiQC config found: /gscratch/srlab/programs/anaconda3/lib/python3.7/site-packages/multiqc_config.yaml [2023-06-21 15:44:35,324] multiqc [DEBUG ] Loading config settings from: /usr/lusers/samwhite/.multiqc_config.yaml [2023-06-21 15:44:35,324] multiqc [DEBUG ] New config 'star': {'fn': '*Log.final.out'} [2023-06-21 15:44:35,324] multiqc [DEBUG ] New config 'star/genecounts': {'fn': '*ReadsPerGene.out.tab'} [2023-06-21 15:44:35,324] multiqc [DEBUG ] Added to filename patterns: {'fastp': {'fn': '*report.json'}} [2023-06-21 15:44:35,324] multiqc [DEBUG ] New config 'hisat2': {'contents': 'HISAT2 summary stats:', 'shared': True} [2023-06-21 15:44:35,325] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-06-21 15:44:35,325] multiqc [DEBUG ] Command used: /gscratch/srlab/programs/anaconda3/bin/multiqc . [2023-06-21 15:44:40,343] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2023-06-21 15:44:40,343] multiqc [INFO ] This is MultiQC v1.8 [2023-06-21 15:44:40,346] multiqc [DEBUG ] Command : /gscratch/srlab/programs/anaconda3/bin/multiqc . [2023-06-21 15:44:40,346] multiqc [DEBUG ] Working dir : /gscratch/scrubbed/samwhite/outputs/20230620-E5_coral-fastqc-flexbar-multiqc-sRNAseq/A_pulchra/trimmed [2023-06-21 15:44:40,346] multiqc [INFO ] Template : default [2023-06-21 15:44:40,347] multiqc [DEBUG ] Running Python 3.7.3 (default, Mar 27 2019, 22:11:17) [GCC 7.3.0] [2023-06-21 15:44:40,347] multiqc [INFO ] Searching : /gscratch/scrubbed/samwhite/outputs/20230620-E5_coral-fastqc-flexbar-multiqc-sRNAseq/A_pulchra/trimmed [2023-06-21 15:44:40,348] 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 15:44:40,348] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpv3t6vtag [2023-06-21 15:44:40,981] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-178-S1-TP2.flexbar_trim.20230621_2_fastqc.html [2023-06-21 15:44:40,991] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-178-S1-TP2.flexbar_trim.20230621_2.fastq.gz [2023-06-21 15:44:40,992] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1_fastqc.html [2023-06-21 15:44:40,992] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-145-S1-TP2.flexbar_trim.20230621_2_fastqc.html [2023-06-21 15:44:41,016] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: sRNA-ACR-145-S1-TP2.flexbar_trim.20230621.log [2023-06-21 15:44:41,038] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: sRNA-ACR-140-S1-TP2.flexbar_trim.20230621.log [2023-06-21 15:44:41,046] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-173-S1-TP2.flexbar_trim.20230621_1_fastqc.html [2023-06-21 15:44:41,046] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-150-S1-TP2.flexbar_trim.20230621_2.fastq.gz [2023-06-21 15:44:41,047] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_2_fastqc.html [2023-06-21 15:44:41,052] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: sRNA-ACR-150-S1-TP2.flexbar_trim.20230621.log [2023-06-21 15:44:41,060] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-173-S1-TP2.flexbar_trim.20230621_2.fastq.gz [2023-06-21 15:44:41,060] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-178-S1-TP2.flexbar_trim.20230621_1.fastq.gz [2023-06-21 15:44:41,060] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-145-S1-TP2.flexbar_trim.20230621_2.fastq.gz [2023-06-21 15:44:41,060] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-145-S1-TP2.flexbar_trim.20230621_1.fastq.gz [2023-06-21 15:44:41,060] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-150-S1-TP2.flexbar_trim.20230621_1.fastq.gz [2023-06-21 15:44:41,060] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-173-S1-TP2.flexbar_trim.20230621_1.fastq.gz [2023-06-21 15:44:41,060] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-145-S1-TP2.flexbar_trim.20230621_1_fastqc.html [2023-06-21 15:44:41,060] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.fastq.gz [2023-06-21 15:44:41,061] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: trimmed_fastq_checksums.md5 [2023-06-21 15:44:41,061] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-178-S1-TP2.flexbar_trim.20230621_1_fastqc.html [2023-06-21 15:44:41,066] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: sRNA-ACR-178-S1-TP2.flexbar_trim.20230621.log [2023-06-21 15:44:41,073] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-173-S1-TP2.flexbar_trim.20230621_2_fastqc.html [2023-06-21 15:44:41,073] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-150-S1-TP2.flexbar_trim.20230621_2_fastqc.html [2023-06-21 15:44:41,074] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-150-S1-TP2.flexbar_trim.20230621_1_fastqc.html [2023-06-21 15:44:41,074] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_2.fastq.gz [2023-06-21 15:44:41,079] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: sRNA-ACR-173-S1-TP2.flexbar_trim.20230621.log [2023-06-21 15:44:44,664] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 2.2.4 [2023-06-21 15:44:44,665] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 2.2.4 [2023-06-21 15:44:44,706] multiqc [DEBUG ] No samples found: custom_content [2023-06-21 15:44:44,728] multiqc [DEBUG ] No samples found: conpair [2023-06-21 15:44:44,819] multiqc [DEBUG ] No samples found: peddy [2023-06-21 15:44:44,890] multiqc [DEBUG ] No samples found: methylQA [2023-06-21 15:44:44,906] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-06-21 15:44:44,986] multiqc [DEBUG ] No samples found: qualimap [2023-06-21 15:44:45,002] multiqc [DEBUG ] No samples found: preseq [2023-06-21 15:44:45,010] multiqc [DEBUG ] No samples found: quast [2023-06-21 15:44:45,034] multiqc [DEBUG ] No samples found: qorts [2023-06-21 15:44:45,041] multiqc [DEBUG ] No samples found: rna_seqc [2023-06-21 15:44:45,075] multiqc [DEBUG ] No samples found: rsem [2023-06-21 15:44:45,108] multiqc [DEBUG ] No samples found: rseqc [2023-06-21 15:44:45,113] multiqc [DEBUG ] No samples found: busco [2023-06-21 15:44:45,133] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-06-21 15:44:45,174] multiqc [DEBUG ] No samples found: disambiguate [2023-06-21 15:44:45,179] multiqc [DEBUG ] No samples found: supernova [2023-06-21 15:44:45,226] multiqc [DEBUG ] No samples found: deeptools [2023-06-21 15:44:45,273] multiqc [DEBUG ] No samples found: sargasso [2023-06-21 15:44:45,396] multiqc [DEBUG ] No samples found: verifybamid [2023-06-21 15:44:45,405] multiqc [DEBUG ] No samples found: mirtrace [2023-06-21 15:44:45,423] multiqc [DEBUG ] No samples found: happy [2023-06-21 15:44:45,463] multiqc [DEBUG ] No samples found: homer [2023-06-21 15:44:45,470] multiqc [DEBUG ] No samples found: macs2 [2023-06-21 15:44:45,491] multiqc [DEBUG ] No samples found: theta2 [2023-06-21 15:44:45,498] multiqc [DEBUG ] No samples found: snpeff [2023-06-21 15:44:45,524] multiqc [DEBUG ] No samples found: gatk [2023-06-21 15:44:45,614] multiqc [DEBUG ] No samples found: htseq [2023-06-21 15:44:45,624] multiqc [DEBUG ] No samples found: bcftools [2023-06-21 15:44:45,646] multiqc [DEBUG ] No samples found: featureCounts [2023-06-21 15:44:45,654] multiqc [DEBUG ] No samples found: fgbio [2023-06-21 15:44:45,661] multiqc [DEBUG ] No samples found: dedup [2023-06-21 15:44:45,669] multiqc [DEBUG ] No samples found: damageprofiler [2023-06-21 15:44:45,716] multiqc [DEBUG ] No samples found: biobambam2 [2023-06-21 15:44:45,724] multiqc [DEBUG ] No samples found: mtnucratio [2023-06-21 15:44:45,729] multiqc [DEBUG ] No samples found: picard [2023-06-21 15:44:45,737] multiqc [DEBUG ] No samples found: prokka [2023-06-21 15:44:45,757] multiqc [DEBUG ] No samples found: samblaster [2023-06-21 15:44:45,815] multiqc [DEBUG ] No samples found: samtools [2023-06-21 15:44:45,833] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-06-21 15:44:45,847] multiqc [DEBUG ] No samples found: bamtools [2023-06-21 15:44:45,864] multiqc [DEBUG ] No samples found: jellyfish [2023-06-21 15:44:45,893] multiqc [DEBUG ] No samples found: vcftools [2023-06-21 15:44:45,906] multiqc [DEBUG ] No samples found: longranger [2023-06-21 15:44:45,926] multiqc [DEBUG ] No samples found: stacks [2023-06-21 15:44:45,939] multiqc [DEBUG ] No samples found: bbmap [2023-06-21 15:44:45,973] multiqc [DEBUG ] No samples found: bismark [2023-06-21 15:44:45,999] multiqc [DEBUG ] No samples found: biscuit [2023-06-21 15:44:46,004] multiqc [DEBUG ] No samples found: hicexplorer [2023-06-21 15:44:46,009] multiqc [DEBUG ] No samples found: hicup [2023-06-21 15:44:46,016] multiqc [DEBUG ] No samples found: hicpro [2023-06-21 15:44:46,021] multiqc [DEBUG ] No samples found: salmon [2023-06-21 15:44:46,027] multiqc [DEBUG ] No samples found: kallisto [2023-06-21 15:44:46,052] multiqc [DEBUG ] No samples found: slamdunk [2023-06-21 15:44:46,057] multiqc [DEBUG ] No samples found: star [2023-06-21 15:44:46,063] multiqc [DEBUG ] No samples found: hisat2 [2023-06-21 15:44:46,084] multiqc [DEBUG ] No samples found: tophat [2023-06-21 15:44:46,090] multiqc [DEBUG ] No samples found: bowtie2 [2023-06-21 15:44:46,096] multiqc [DEBUG ] No samples found: bowtie1 [2023-06-21 15:44:46,101] multiqc [DEBUG ] No samples found: kat [2023-06-21 15:44:46,107] multiqc [DEBUG ] No samples found: leehom [2023-06-21 15:44:46,113] multiqc [DEBUG ] No samples found: adapterRemoval [2023-06-21 15:44:46,118] multiqc [DEBUG ] No samples found: clipandmerge [2023-06-21 15:44:46,123] multiqc [DEBUG ] No samples found: cutadapt [2023-06-21 15:44:46,135] multiqc.modules.flexbar.flexbar [INFO ] Found 5 logs [2023-06-21 15:44:46,145] multiqc [DEBUG ] No samples found: trimmomatic [2023-06-21 15:44:46,150] multiqc [DEBUG ] No samples found: skewer [2023-06-21 15:44:46,155] multiqc [DEBUG ] No samples found: sortmerna [2023-06-21 15:44:46,160] multiqc [DEBUG ] No samples found: biobloomtools [2023-06-21 15:44:46,165] multiqc [DEBUG ] No samples found: fastq_screen [2023-06-21 15:44:46,171] multiqc [DEBUG ] No samples found: afterqc [2023-06-21 15:44:46,176] multiqc [DEBUG ] No samples found: fastp [2023-06-21 15:44:47,238] multiqc.modules.fastqc.fastqc [INFO ] Found 10 reports [2023-06-21 15:44:47,306] multiqc [DEBUG ] No samples found: minionqc [2023-06-21 15:44:47,310] multiqc [DEBUG ] No samples found: mosdepth [2023-06-21 15:44:47,331] multiqc [DEBUG ] No samples found: clusterflow [2023-06-21 15:44:47,336] multiqc [DEBUG ] No samples found: bcl2fastq [2023-06-21 15:44:47,340] multiqc [DEBUG ] No samples found: interop [2023-06-21 15:44:47,344] multiqc [DEBUG ] No samples found: flash [2023-06-21 15:44:47,374] multiqc [DEBUG ] No samples found: seqyclean [2023-06-21 15:44:47,397] multiqc [INFO ] Compressing plot data [2023-06-21 15:44:47,534] multiqc [INFO ] Report : multiqc_report.html [2023-06-21 15:44:47,534] multiqc [INFO ] Data : multiqc_data [2023-06-21 15:44:47,535] multiqc [DEBUG ] Moving data file from '/tmp/tmpv3t6vtag/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/gscratch/scrubbed/samwhite/outputs/20230620-E5_coral-fastqc-flexbar-multiqc-sRNAseq/A_pulchra/trimmed/multiqc_data' [2023-06-21 15:44:47,537] multiqc [DEBUG ] Moving data file from '/tmp/tmpv3t6vtag/multiqc_data/multiqc_flexbar.txt' to '/gscratch/scrubbed/samwhite/outputs/20230620-E5_coral-fastqc-flexbar-multiqc-sRNAseq/A_pulchra/trimmed/multiqc_data' [2023-06-21 15:44:47,539] multiqc [DEBUG ] Moving data file from '/tmp/tmpv3t6vtag/multiqc_data/multiqc_fastqc.txt' to '/gscratch/scrubbed/samwhite/outputs/20230620-E5_coral-fastqc-flexbar-multiqc-sRNAseq/A_pulchra/trimmed/multiqc_data' [2023-06-21 15:44:47,540] multiqc [DEBUG ] Moving data file from '/tmp/tmpv3t6vtag/multiqc_data/multiqc_general_stats.txt' to '/gscratch/scrubbed/samwhite/outputs/20230620-E5_coral-fastqc-flexbar-multiqc-sRNAseq/A_pulchra/trimmed/multiqc_data' [2023-06-21 15:44:47,541] multiqc [DEBUG ] Moving data file from '/tmp/tmpv3t6vtag/multiqc_data/multiqc_sources.txt' to '/gscratch/scrubbed/samwhite/outputs/20230620-E5_coral-fastqc-flexbar-multiqc-sRNAseq/A_pulchra/trimmed/multiqc_data' [2023-06-21 15:44:47,543] multiqc [DEBUG ] Moving data file from '/tmp/tmpv3t6vtag/multiqc_data/multiqc_data.json' to '/gscratch/scrubbed/samwhite/outputs/20230620-E5_coral-fastqc-flexbar-multiqc-sRNAseq/A_pulchra/trimmed/multiqc_data' [2023-06-21 15:44:48,172] multiqc [INFO ] MultiQC complete