[2023-05-22 16:59:50,714] multiqc [DEBUG ] No MultiQC config found: /gscratch/srlab/programs/anaconda3/lib/python3.7/site-packages/multiqc_config.yaml [2023-05-22 16:59:50,717] multiqc [DEBUG ] Loading config settings from: /usr/lusers/samwhite/.multiqc_config.yaml [2023-05-22 16:59:50,717] multiqc [DEBUG ] New config 'star': {'fn': '*Log.final.out'} [2023-05-22 16:59:50,717] multiqc [DEBUG ] New config 'star/genecounts': {'fn': '*ReadsPerGene.out.tab'} [2023-05-22 16:59:50,717] multiqc [DEBUG ] Added to filename patterns: {'fastp': {'fn': '*report.json'}} [2023-05-22 16:59:50,717] multiqc [DEBUG ] New config 'hisat2': {'contents': 'HISAT2 summary stats:', 'shared': True} [2023-05-22 16:59:50,717] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-05-22 16:59:50,717] multiqc [DEBUG ] Command used: /gscratch/srlab/programs/anaconda3/bin/multiqc . [2023-05-22 16:59:55,736] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2023-05-22 16:59:55,737] multiqc [INFO ] This is MultiQC v1.8 [2023-05-22 16:59:55,739] multiqc [DEBUG ] Command : /gscratch/srlab/programs/anaconda3/bin/multiqc . [2023-05-22 16:59:55,739] multiqc [DEBUG ] Working dir : /gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-sRNAseq/P_meandrina/trimmed [2023-05-22 16:59:55,739] multiqc [INFO ] Template : default [2023-05-22 16:59:55,739] multiqc [DEBUG ] Running Python 3.7.3 (default, Mar 27 2019, 22:11:17) [GCC 7.3.0] [2023-05-22 16:59:55,739] multiqc [INFO ] Searching : /gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-sRNAseq/P_meandrina/trimmed [2023-05-22 16:59:55,740] 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 16:59:55,740] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpuml_7nqh [2023-05-22 16:59:55,917] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-48-S1-TP2_R2_001.fastp-trim.20230522_fastqc.html [2023-05-22 16:59:55,917] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-48-S1-TP2_R2_001.fastp-trim.20230522.fastq.gz [2023-05-22 16:59:55,917] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-48-S1-TP2_R1_001.fastp-trim.20230522_fastqc.html [2023-05-22 16:59:55,918] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-57-S1-TP2_R1_001.fastp-trim.20230522_fastqc.html [2023-05-22 16:59:55,918] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-53-S1-TP2_R1_001.fastp-trim.20230522.fastq.gz [2023-05-22 16:59:55,918] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-50-S1-TP2.fastp-trim.20230522.report.html [2023-05-22 16:59:55,918] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-50-S1-TP2_R1_001.fastp-trim.20230522.fastq.gz [2023-05-22 16:59:55,918] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-57-S1-TP2_R2_001.fastp-trim.20230522_fastqc.html [2023-05-22 16:59:55,918] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-47-S1-TP2_R1_001.fastp-trim.20230522_fastqc.html [2023-05-22 16:59:55,918] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-48-S1-TP2_R1_001.fastp-trim.20230522.fastq.gz [2023-05-22 16:59:55,919] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-50-S1-TP2_R2_001.fastp-trim.20230522_fastqc.html [2023-05-22 16:59:55,919] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-48-S1-TP2.fastp-trim.20230522.report.html [2023-05-22 16:59:55,919] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-47-S1-TP2_R1_001.fastp-trim.20230522.fastq.gz [2023-05-22 16:59:55,919] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-50-S1-TP2_R1_001.fastp-trim.20230522_fastqc.html [2023-05-22 16:59:55,919] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-47-S1-TP2_R2_001.fastp-trim.20230522.fastq.gz [2023-05-22 16:59:55,919] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-47-S1-TP2_R2_001.fastp-trim.20230522_fastqc.html [2023-05-22 16:59:55,919] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-53-S1-TP2_R2_001.fastp-trim.20230522.fastq.gz [2023-05-22 16:59:55,919] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-57-S1-TP2_R2_001.fastp-trim.20230522.fastq.gz [2023-05-22 16:59:55,919] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-57-S1-TP2_R1_001.fastp-trim.20230522.fastq.gz [2023-05-22 16:59:55,920] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-50-S1-TP2_R2_001.fastp-trim.20230522.fastq.gz [2023-05-22 16:59:55,920] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: trimmed_fastq_checksums.md5 [2023-05-22 16:59:55,920] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-53-S1-TP2_R1_001.fastp-trim.20230522_fastqc.html [2023-05-22 16:59:55,922] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-53-S1-TP2_R2_001.fastp-trim.20230522_fastqc.html [2023-05-22 16:59:55,922] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-47-S1-TP2.fastp-trim.20230522.report.html [2023-05-22 16:59:55,922] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-53-S1-TP2.fastp-trim.20230522.report.html [2023-05-22 16:59:55,922] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-57-S1-TP2.fastp-trim.20230522.report.html [2023-05-22 16:59:56,241] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 2.2.4 [2023-05-22 16:59:56,243] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 2.2.4 [2023-05-22 16:59:56,246] multiqc [DEBUG ] No samples found: custom_content [2023-05-22 16:59:56,252] multiqc [DEBUG ] No samples found: conpair [2023-05-22 16:59:56,259] multiqc [DEBUG ] No samples found: peddy [2023-05-22 16:59:56,265] multiqc [DEBUG ] No samples found: methylQA [2023-05-22 16:59:56,271] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-05-22 16:59:56,278] multiqc [DEBUG ] No samples found: qualimap [2023-05-22 16:59:56,283] multiqc [DEBUG ] No samples found: preseq [2023-05-22 16:59:56,288] multiqc [DEBUG ] No samples found: quast [2023-05-22 16:59:56,294] multiqc [DEBUG ] No samples found: qorts [2023-05-22 16:59:56,299] multiqc [DEBUG ] No samples found: rna_seqc [2023-05-22 16:59:56,303] multiqc [DEBUG ] No samples found: rsem [2023-05-22 16:59:56,310] multiqc [DEBUG ] No samples found: rseqc [2023-05-22 16:59:56,315] multiqc [DEBUG ] No samples found: busco [2023-05-22 16:59:56,319] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-05-22 16:59:56,324] multiqc [DEBUG ] No samples found: disambiguate [2023-05-22 16:59:56,328] multiqc [DEBUG ] No samples found: supernova [2023-05-22 16:59:56,336] multiqc [DEBUG ] No samples found: deeptools [2023-05-22 16:59:56,340] multiqc [DEBUG ] No samples found: sargasso [2023-05-22 16:59:56,345] multiqc [DEBUG ] No samples found: verifybamid [2023-05-22 16:59:56,350] multiqc [DEBUG ] No samples found: mirtrace [2023-05-22 16:59:56,354] multiqc [DEBUG ] No samples found: happy [2023-05-22 16:59:56,362] multiqc [DEBUG ] No samples found: homer [2023-05-22 16:59:56,366] multiqc [DEBUG ] No samples found: macs2 [2023-05-22 16:59:56,370] multiqc [DEBUG ] No samples found: theta2 [2023-05-22 16:59:56,374] multiqc [DEBUG ] No samples found: snpeff [2023-05-22 16:59:56,380] multiqc [DEBUG ] No samples found: gatk [2023-05-22 16:59:56,385] multiqc [DEBUG ] No samples found: htseq [2023-05-22 16:59:56,389] multiqc [DEBUG ] No samples found: bcftools [2023-05-22 16:59:56,394] multiqc [DEBUG ] No samples found: featureCounts [2023-05-22 16:59:56,398] multiqc [DEBUG ] No samples found: fgbio [2023-05-22 16:59:56,402] multiqc [DEBUG ] No samples found: dedup [2023-05-22 16:59:56,406] multiqc [DEBUG ] No samples found: damageprofiler [2023-05-22 16:59:56,416] multiqc [DEBUG ] No samples found: biobambam2 [2023-05-22 16:59:56,420] multiqc [DEBUG ] No samples found: mtnucratio [2023-05-22 16:59:56,424] multiqc [DEBUG ] No samples found: picard [2023-05-22 16:59:56,428] multiqc [DEBUG ] No samples found: prokka [2023-05-22 16:59:56,432] multiqc [DEBUG ] No samples found: samblaster [2023-05-22 16:59:56,438] multiqc [DEBUG ] No samples found: samtools [2023-05-22 16:59:56,443] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-05-22 16:59:56,448] multiqc [DEBUG ] No samples found: bamtools [2023-05-22 16:59:56,452] multiqc [DEBUG ] No samples found: jellyfish [2023-05-22 16:59:56,459] multiqc [DEBUG ] No samples found: vcftools [2023-05-22 16:59:56,463] multiqc [DEBUG ] No samples found: longranger [2023-05-22 16:59:56,467] multiqc [DEBUG ] No samples found: stacks [2023-05-22 16:59:56,475] multiqc [DEBUG ] No samples found: bbmap [2023-05-22 16:59:56,479] multiqc [DEBUG ] No samples found: bismark [2023-05-22 16:59:56,484] multiqc [DEBUG ] No samples found: biscuit [2023-05-22 16:59:56,489] multiqc [DEBUG ] No samples found: hicexplorer [2023-05-22 16:59:56,493] multiqc [DEBUG ] No samples found: hicup [2023-05-22 16:59:56,497] multiqc [DEBUG ] No samples found: hicpro [2023-05-22 16:59:56,501] multiqc [DEBUG ] No samples found: salmon [2023-05-22 16:59:56,506] multiqc [DEBUG ] No samples found: kallisto [2023-05-22 16:59:56,511] multiqc [DEBUG ] No samples found: slamdunk [2023-05-22 16:59:56,515] multiqc [DEBUG ] No samples found: star [2023-05-22 16:59:56,519] multiqc [DEBUG ] No samples found: hisat2 [2023-05-22 16:59:56,523] multiqc [DEBUG ] No samples found: tophat [2023-05-22 16:59:56,528] multiqc [DEBUG ] No samples found: bowtie2 [2023-05-22 16:59:56,532] multiqc [DEBUG ] No samples found: bowtie1 [2023-05-22 16:59:56,540] multiqc [DEBUG ] No samples found: kat [2023-05-22 16:59:56,545] multiqc [DEBUG ] No samples found: leehom [2023-05-22 16:59:56,549] multiqc [DEBUG ] No samples found: adapterRemoval [2023-05-22 16:59:56,554] multiqc [DEBUG ] No samples found: clipandmerge [2023-05-22 16:59:56,558] multiqc [DEBUG ] No samples found: cutadapt [2023-05-22 16:59:56,562] multiqc [DEBUG ] No samples found: flexbar [2023-05-22 16:59:56,566] multiqc [DEBUG ] No samples found: trimmomatic [2023-05-22 16:59:56,570] multiqc [DEBUG ] No samples found: skewer [2023-05-22 16:59:56,574] multiqc [DEBUG ] No samples found: sortmerna [2023-05-22 16:59:56,579] multiqc [DEBUG ] No samples found: biobloomtools [2023-05-22 16:59:56,583] multiqc [DEBUG ] No samples found: fastq_screen [2023-05-22 16:59:56,587] multiqc [DEBUG ] No samples found: afterqc [2023-05-22 16:59:56,597] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: sRNA-POC-53-S1-TP2.fastp-trim.20230522.report.json [2023-05-22 16:59:56,601] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: sRNA-POC-47-S1-TP2.fastp-trim.20230522.report.json [2023-05-22 16:59:56,605] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: sRNA-POC-50-S1-TP2.fastp-trim.20230522.report.json [2023-05-22 16:59:56,610] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: sRNA-POC-48-S1-TP2.fastp-trim.20230522.report.json [2023-05-22 16:59:56,614] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: sRNA-POC-57-S1-TP2.fastp-trim.20230522.report.json [2023-05-22 16:59:56,615] multiqc.modules.fastp.fastp [INFO ] Found 5 reports [2023-05-22 16:59:57,872] multiqc.modules.fastqc.fastqc [INFO ] Found 10 reports [2023-05-22 16:59:58,112] multiqc [DEBUG ] No samples found: minionqc [2023-05-22 16:59:58,116] multiqc [DEBUG ] No samples found: mosdepth [2023-05-22 16:59:58,119] multiqc [DEBUG ] No samples found: clusterflow [2023-05-22 16:59:58,123] multiqc [DEBUG ] No samples found: bcl2fastq [2023-05-22 16:59:58,126] multiqc [DEBUG ] No samples found: interop [2023-05-22 16:59:58,130] multiqc [DEBUG ] No samples found: flash [2023-05-22 16:59:58,133] multiqc [DEBUG ] No samples found: seqyclean [2023-05-22 16:59:58,155] multiqc [INFO ] Compressing plot data [2023-05-22 16:59:58,652] multiqc [INFO ] Report : multiqc_report.html [2023-05-22 16:59:58,654] multiqc [INFO ] Data : multiqc_data [2023-05-22 16:59:58,655] multiqc [DEBUG ] Moving data file from '/tmp/tmpuml_7nqh/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-sRNAseq/P_meandrina/trimmed/multiqc_data' [2023-05-22 16:59:58,656] multiqc [DEBUG ] Moving data file from '/tmp/tmpuml_7nqh/multiqc_data/multiqc_fastp.txt' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-sRNAseq/P_meandrina/trimmed/multiqc_data' [2023-05-22 16:59:58,657] multiqc [DEBUG ] Moving data file from '/tmp/tmpuml_7nqh/multiqc_data/multiqc_fastqc.txt' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-sRNAseq/P_meandrina/trimmed/multiqc_data' [2023-05-22 16:59:58,658] multiqc [DEBUG ] Moving data file from '/tmp/tmpuml_7nqh/multiqc_data/multiqc_general_stats.txt' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-sRNAseq/P_meandrina/trimmed/multiqc_data' [2023-05-22 16:59:58,659] multiqc [DEBUG ] Moving data file from '/tmp/tmpuml_7nqh/multiqc_data/multiqc_sources.txt' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-sRNAseq/P_meandrina/trimmed/multiqc_data' [2023-05-22 16:59:58,660] multiqc [DEBUG ] Moving data file from '/tmp/tmpuml_7nqh/multiqc_data/multiqc_data.json' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-sRNAseq/P_meandrina/trimmed/multiqc_data' [2023-05-22 16:59:58,760] multiqc [INFO ] MultiQC complete