[2023-05-22 16:48:13,519] multiqc [DEBUG ] No MultiQC config found: /gscratch/srlab/programs/anaconda3/lib/python3.7/site-packages/multiqc_config.yaml [2023-05-22 16:48:13,521] multiqc [DEBUG ] Loading config settings from: /usr/lusers/samwhite/.multiqc_config.yaml [2023-05-22 16:48:13,521] multiqc [DEBUG ] New config 'star': {'fn': '*Log.final.out'} [2023-05-22 16:48:13,522] multiqc [DEBUG ] New config 'star/genecounts': {'fn': '*ReadsPerGene.out.tab'} [2023-05-22 16:48:13,522] multiqc [DEBUG ] Added to filename patterns: {'fastp': {'fn': '*report.json'}} [2023-05-22 16:48:13,522] multiqc [DEBUG ] New config 'hisat2': {'contents': 'HISAT2 summary stats:', 'shared': True} [2023-05-22 16:48:13,522] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-05-22 16:48:13,522] multiqc [DEBUG ] Command used: /gscratch/srlab/programs/anaconda3/bin/multiqc . [2023-05-22 16:48:18,611] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2023-05-22 16:48:18,612] multiqc [INFO ] This is MultiQC v1.8 [2023-05-22 16:48:18,614] multiqc [DEBUG ] Command : /gscratch/srlab/programs/anaconda3/bin/multiqc . [2023-05-22 16:48:18,614] multiqc [DEBUG ] Working dir : /gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-sRNAseq/P_evermanni/trimmed [2023-05-22 16:48:18,614] multiqc [INFO ] Template : default [2023-05-22 16:48:18,614] multiqc [DEBUG ] Running Python 3.7.3 (default, Mar 27 2019, 22:11:17) [GCC 7.3.0] [2023-05-22 16:48:18,614] multiqc [INFO ] Searching : /gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-sRNAseq/P_evermanni/trimmed [2023-05-22 16:48:18,615] 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 16:48:18,615] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpv5gba0ij [2023-05-22 16:48:18,790] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POR-79-S1-TP2_R1_001.fastp-trim.20230522_fastqc.html [2023-05-22 16:48:18,796] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POR-79-S1-TP2_R2_001.fastp-trim.20230522_fastqc.html [2023-05-22 16:48:18,797] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POR-79-S1-TP2_R1_001.fastp-trim.20230522.fastq.gz [2023-05-22 16:48:18,797] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POR-82-S1-TP2_R1_001.fastp-trim.20230522_fastqc.html [2023-05-22 16:48:18,798] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POR-82-S1-TP2_R2_001.fastp-trim.20230522_fastqc.html [2023-05-22 16:48:18,798] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POR-73-S1-TP2_R2_001.fastp-trim.20230522_fastqc.html [2023-05-22 16:48:18,798] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: trimmed_fastq_checksums.md5 [2023-05-22 16:48:18,799] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POR-79-S1-TP2.fastp-trim.20230522.report.html [2023-05-22 16:48:18,799] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POR-73-S1-TP2_R1_001.fastp-trim.20230522_fastqc.html [2023-05-22 16:48:18,799] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POR-73-S1-TP2_R1_001.fastp-trim.20230522.fastq.gz [2023-05-22 16:48:18,799] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POR-82-S1-TP2.fastp-trim.20230522.report.html [2023-05-22 16:48:18,799] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POR-82-S1-TP2_R1_001.fastp-trim.20230522.fastq.gz [2023-05-22 16:48:18,799] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POR-73-S1-TP2_R2_001.fastp-trim.20230522.fastq.gz [2023-05-22 16:48:18,800] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POR-82-S1-TP2_R2_001.fastp-trim.20230522.fastq.gz [2023-05-22 16:48:18,800] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POR-73-S1-TP2.fastp-trim.20230522.report.html [2023-05-22 16:48:18,800] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POR-79-S1-TP2_R2_001.fastp-trim.20230522.fastq.gz [2023-05-22 16:48:19,094] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 2.2.4 [2023-05-22 16:48:19,095] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 2.2.4 [2023-05-22 16:48:19,097] multiqc [DEBUG ] No samples found: custom_content [2023-05-22 16:48:19,105] multiqc [DEBUG ] No samples found: conpair [2023-05-22 16:48:19,112] multiqc [DEBUG ] No samples found: peddy [2023-05-22 16:48:19,120] multiqc [DEBUG ] No samples found: methylQA [2023-05-22 16:48:19,128] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-05-22 16:48:19,136] multiqc [DEBUG ] No samples found: qualimap [2023-05-22 16:48:19,142] multiqc [DEBUG ] No samples found: preseq [2023-05-22 16:48:19,149] multiqc [DEBUG ] No samples found: quast [2023-05-22 16:48:19,155] multiqc [DEBUG ] No samples found: qorts [2023-05-22 16:48:19,160] multiqc [DEBUG ] No samples found: rna_seqc [2023-05-22 16:48:19,166] multiqc [DEBUG ] No samples found: rsem [2023-05-22 16:48:19,174] multiqc [DEBUG ] No samples found: rseqc [2023-05-22 16:48:19,179] multiqc [DEBUG ] No samples found: busco [2023-05-22 16:48:19,184] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-05-22 16:48:19,190] multiqc [DEBUG ] No samples found: disambiguate [2023-05-22 16:48:19,194] multiqc [DEBUG ] No samples found: supernova [2023-05-22 16:48:19,202] multiqc [DEBUG ] No samples found: deeptools [2023-05-22 16:48:19,206] multiqc [DEBUG ] No samples found: sargasso [2023-05-22 16:48:19,211] multiqc [DEBUG ] No samples found: verifybamid [2023-05-22 16:48:19,215] multiqc [DEBUG ] No samples found: mirtrace [2023-05-22 16:48:19,220] multiqc [DEBUG ] No samples found: happy [2023-05-22 16:48:19,225] multiqc [DEBUG ] No samples found: homer [2023-05-22 16:48:19,229] multiqc [DEBUG ] No samples found: macs2 [2023-05-22 16:48:19,233] multiqc [DEBUG ] No samples found: theta2 [2023-05-22 16:48:19,237] multiqc [DEBUG ] No samples found: snpeff [2023-05-22 16:48:19,242] multiqc [DEBUG ] No samples found: gatk [2023-05-22 16:48:19,247] multiqc [DEBUG ] No samples found: htseq [2023-05-22 16:48:19,251] multiqc [DEBUG ] No samples found: bcftools [2023-05-22 16:48:19,255] multiqc [DEBUG ] No samples found: featureCounts [2023-05-22 16:48:19,259] multiqc [DEBUG ] No samples found: fgbio [2023-05-22 16:48:19,264] multiqc [DEBUG ] No samples found: dedup [2023-05-22 16:48:19,268] multiqc [DEBUG ] No samples found: damageprofiler [2023-05-22 16:48:19,277] multiqc [DEBUG ] No samples found: biobambam2 [2023-05-22 16:48:19,281] multiqc [DEBUG ] No samples found: mtnucratio [2023-05-22 16:48:19,285] multiqc [DEBUG ] No samples found: picard [2023-05-22 16:48:19,289] multiqc [DEBUG ] No samples found: prokka [2023-05-22 16:48:19,293] multiqc [DEBUG ] No samples found: samblaster [2023-05-22 16:48:19,298] multiqc [DEBUG ] No samples found: samtools [2023-05-22 16:48:19,303] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-05-22 16:48:19,307] multiqc [DEBUG ] No samples found: bamtools [2023-05-22 16:48:19,311] multiqc [DEBUG ] No samples found: jellyfish [2023-05-22 16:48:19,316] multiqc [DEBUG ] No samples found: vcftools [2023-05-22 16:48:19,321] multiqc [DEBUG ] No samples found: longranger [2023-05-22 16:48:19,325] multiqc [DEBUG ] No samples found: stacks [2023-05-22 16:48:19,332] multiqc [DEBUG ] No samples found: bbmap [2023-05-22 16:48:19,336] multiqc [DEBUG ] No samples found: bismark [2023-05-22 16:48:19,342] multiqc [DEBUG ] No samples found: biscuit [2023-05-22 16:48:19,346] multiqc [DEBUG ] No samples found: hicexplorer [2023-05-22 16:48:19,351] multiqc [DEBUG ] No samples found: hicup [2023-05-22 16:48:19,355] multiqc [DEBUG ] No samples found: hicpro [2023-05-22 16:48:19,359] multiqc [DEBUG ] No samples found: salmon [2023-05-22 16:48:19,363] multiqc [DEBUG ] No samples found: kallisto [2023-05-22 16:48:19,368] multiqc [DEBUG ] No samples found: slamdunk [2023-05-22 16:48:19,372] multiqc [DEBUG ] No samples found: star [2023-05-22 16:48:19,376] multiqc [DEBUG ] No samples found: hisat2 [2023-05-22 16:48:19,380] multiqc [DEBUG ] No samples found: tophat [2023-05-22 16:48:19,384] multiqc [DEBUG ] No samples found: bowtie2 [2023-05-22 16:48:19,389] multiqc [DEBUG ] No samples found: bowtie1 [2023-05-22 16:48:19,393] multiqc [DEBUG ] No samples found: kat [2023-05-22 16:48:19,397] multiqc [DEBUG ] No samples found: leehom [2023-05-22 16:48:19,401] multiqc [DEBUG ] No samples found: adapterRemoval [2023-05-22 16:48:19,406] multiqc [DEBUG ] No samples found: clipandmerge [2023-05-22 16:48:19,410] multiqc [DEBUG ] No samples found: cutadapt [2023-05-22 16:48:19,414] multiqc [DEBUG ] No samples found: flexbar [2023-05-22 16:48:19,418] multiqc [DEBUG ] No samples found: trimmomatic [2023-05-22 16:48:19,423] multiqc [DEBUG ] No samples found: skewer [2023-05-22 16:48:19,427] multiqc [DEBUG ] No samples found: sortmerna [2023-05-22 16:48:19,431] multiqc [DEBUG ] No samples found: biobloomtools [2023-05-22 16:48:19,435] multiqc [DEBUG ] No samples found: fastq_screen [2023-05-22 16:48:19,439] multiqc [DEBUG ] No samples found: afterqc [2023-05-22 16:48:19,450] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: sRNA-POR-79-S1-TP2.fastp-trim.20230522.report.json [2023-05-22 16:48:19,455] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: sRNA-POR-73-S1-TP2.fastp-trim.20230522.report.json [2023-05-22 16:48:19,459] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: sRNA-POR-82-S1-TP2.fastp-trim.20230522.report.json [2023-05-22 16:48:19,460] multiqc.modules.fastp.fastp [INFO ] Found 3 reports [2023-05-22 16:48:20,267] multiqc.modules.fastqc.fastqc [INFO ] Found 6 reports [2023-05-22 16:48:20,419] multiqc [DEBUG ] No samples found: minionqc [2023-05-22 16:48:20,422] multiqc [DEBUG ] No samples found: mosdepth [2023-05-22 16:48:20,426] multiqc [DEBUG ] No samples found: clusterflow [2023-05-22 16:48:20,429] multiqc [DEBUG ] No samples found: bcl2fastq [2023-05-22 16:48:20,433] multiqc [DEBUG ] No samples found: interop [2023-05-22 16:48:20,436] multiqc [DEBUG ] No samples found: flash [2023-05-22 16:48:20,440] multiqc [DEBUG ] No samples found: seqyclean [2023-05-22 16:48:20,454] multiqc [INFO ] Compressing plot data [2023-05-22 16:48:20,759] multiqc [INFO ] Report : multiqc_report.html [2023-05-22 16:48:20,760] multiqc [INFO ] Data : multiqc_data [2023-05-22 16:48:20,762] multiqc [DEBUG ] Moving data file from '/tmp/tmpv5gba0ij/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-sRNAseq/P_evermanni/trimmed/multiqc_data' [2023-05-22 16:48:20,763] multiqc [DEBUG ] Moving data file from '/tmp/tmpv5gba0ij/multiqc_data/multiqc_fastp.txt' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-sRNAseq/P_evermanni/trimmed/multiqc_data' [2023-05-22 16:48:20,765] multiqc [DEBUG ] Moving data file from '/tmp/tmpv5gba0ij/multiqc_data/multiqc_fastqc.txt' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-sRNAseq/P_evermanni/trimmed/multiqc_data' [2023-05-22 16:48:20,765] multiqc [DEBUG ] Moving data file from '/tmp/tmpv5gba0ij/multiqc_data/multiqc_general_stats.txt' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-sRNAseq/P_evermanni/trimmed/multiqc_data' [2023-05-22 16:48:20,767] multiqc [DEBUG ] Moving data file from '/tmp/tmpv5gba0ij/multiqc_data/multiqc_sources.txt' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-sRNAseq/P_evermanni/trimmed/multiqc_data' [2023-05-22 16:48:20,768] multiqc [DEBUG ] Moving data file from '/tmp/tmpv5gba0ij/multiqc_data/multiqc_data.json' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-sRNAseq/P_evermanni/trimmed/multiqc_data' [2023-05-22 16:48:20,865] multiqc [INFO ] MultiQC complete