[2023-05-19 13:08:17,175] multiqc [DEBUG ] No MultiQC config found: /gscratch/srlab/programs/anaconda3/lib/python3.7/site-packages/multiqc_config.yaml [2023-05-19 13:08:17,178] multiqc [DEBUG ] Loading config settings from: /usr/lusers/samwhite/.multiqc_config.yaml [2023-05-19 13:08:17,179] multiqc [DEBUG ] New config 'star': {'fn': '*Log.final.out'} [2023-05-19 13:08:17,179] multiqc [DEBUG ] New config 'star/genecounts': {'fn': '*ReadsPerGene.out.tab'} [2023-05-19 13:08:17,179] multiqc [DEBUG ] Added to filename patterns: {'fastp': {'fn': '*report.json'}} [2023-05-19 13:08:17,179] multiqc [DEBUG ] New config 'hisat2': {'contents': 'HISAT2 summary stats:', 'shared': True} [2023-05-19 13:08:17,179] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-05-19 13:08:17,180] multiqc [DEBUG ] Command used: /gscratch/srlab/programs/anaconda3/bin/multiqc . [2023-05-19 13:08:22,487] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2023-05-19 13:08:22,488] multiqc [INFO ] This is MultiQC v1.8 [2023-05-19 13:08:22,488] multiqc [DEBUG ] Command : /gscratch/srlab/programs/anaconda3/bin/multiqc . [2023-05-19 13:08:22,488] multiqc [DEBUG ] Working dir : /gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_evermanni/raw_fastqc [2023-05-19 13:08:22,488] multiqc [INFO ] Template : default [2023-05-19 13:08:22,488] multiqc [DEBUG ] Running Python 3.7.3 (default, Mar 27 2019, 22:11:17) [GCC 7.3.0] [2023-05-19 13:08:22,489] multiqc [INFO ] Searching : /gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_evermanni/raw_fastqc [2023-05-19 13:08:22,489] 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 [2023-05-19 13:08:22,490] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpn6l2nny3 [2023-05-19 13:08:22,752] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POR-79-S1-TP2_R1_001.fastq.gz [2023-05-19 13:08:22,752] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POR-76-S1-TP2_R1_001_fastqc.html [2023-05-19 13:08:22,752] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POR-82-S1-TP2_R2_001_fastqc.html [2023-05-19 13:08:22,760] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POR-82-S1-TP2_R1_001.fastq.gz [2023-05-19 13:08:22,760] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POR-71-S1-TP2_R2_001.fastq.gz [2023-05-19 13:08:22,760] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POR-71-S1-TP2_R1_001_fastqc.html [2023-05-19 13:08:22,760] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POR-76-S1-TP2_R2_001_fastqc.html [2023-05-19 13:08:22,761] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POR-76-S1-TP2_R2_001.fastq.gz [2023-05-19 13:08:22,761] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POR-71-S1-TP2_R2_001_fastqc.html [2023-05-19 13:08:22,761] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POR-71-S1-TP2_R1_001.fastq.gz [2023-05-19 13:08:22,761] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POR-73-S1-TP2_R1_001_fastqc.html [2023-05-19 13:08:22,761] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POR-79-S1-TP2_R2_001.fastq.gz [2023-05-19 13:08:22,761] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POR-82-S1-TP2_R2_001.fastq.gz [2023-05-19 13:08:22,761] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POR-76-S1-TP2_R1_001.fastq.gz [2023-05-19 13:08:22,762] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POR-79-S1-TP2_R2_001_fastqc.html [2023-05-19 13:08:22,762] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POR-82-S1-TP2_R1_001_fastqc.html [2023-05-19 13:08:22,762] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POR-73-S1-TP2_R2_001.fastq.gz [2023-05-19 13:08:22,762] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POR-79-S1-TP2_R1_001_fastqc.html [2023-05-19 13:08:22,763] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POR-73-S1-TP2_R2_001_fastqc.html [2023-05-19 13:08:22,763] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POR-73-S1-TP2_R1_001.fastq.gz [2023-05-19 13:08:24,822] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 2.2.4 [2023-05-19 13:08:24,823] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 2.2.4 [2023-05-19 13:08:24,825] multiqc [DEBUG ] No samples found: custom_content [2023-05-19 13:08:24,834] multiqc [DEBUG ] No samples found: conpair [2023-05-19 13:08:24,842] multiqc [DEBUG ] No samples found: peddy [2023-05-19 13:08:24,850] multiqc [DEBUG ] No samples found: methylQA [2023-05-19 13:08:24,860] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-05-19 13:08:24,884] multiqc [DEBUG ] No samples found: qualimap [2023-05-19 13:08:24,892] multiqc [DEBUG ] No samples found: preseq [2023-05-19 13:08:24,901] multiqc [DEBUG ] No samples found: quast [2023-05-19 13:08:24,909] multiqc [DEBUG ] No samples found: qorts [2023-05-19 13:08:24,917] multiqc [DEBUG ] No samples found: rna_seqc [2023-05-19 13:08:24,925] multiqc [DEBUG ] No samples found: rsem [2023-05-19 13:08:24,938] multiqc [DEBUG ] No samples found: rseqc [2023-05-19 13:08:24,946] multiqc [DEBUG ] No samples found: busco [2023-05-19 13:08:24,954] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-05-19 13:08:24,961] multiqc [DEBUG ] No samples found: disambiguate [2023-05-19 13:08:24,966] multiqc [DEBUG ] No samples found: supernova [2023-05-19 13:08:24,974] multiqc [DEBUG ] No samples found: deeptools [2023-05-19 13:08:24,979] multiqc [DEBUG ] No samples found: sargasso [2023-05-19 13:08:24,983] multiqc [DEBUG ] No samples found: verifybamid [2023-05-19 13:08:24,988] multiqc [DEBUG ] No samples found: mirtrace [2023-05-19 13:08:24,992] multiqc [DEBUG ] No samples found: happy [2023-05-19 13:08:24,998] multiqc [DEBUG ] No samples found: homer [2023-05-19 13:08:25,002] multiqc [DEBUG ] No samples found: macs2 [2023-05-19 13:08:25,006] multiqc [DEBUG ] No samples found: theta2 [2023-05-19 13:08:25,011] multiqc [DEBUG ] No samples found: snpeff [2023-05-19 13:08:25,016] multiqc [DEBUG ] No samples found: gatk [2023-05-19 13:08:25,020] multiqc [DEBUG ] No samples found: htseq [2023-05-19 13:08:25,025] multiqc [DEBUG ] No samples found: bcftools [2023-05-19 13:08:25,029] multiqc [DEBUG ] No samples found: featureCounts [2023-05-19 13:08:25,033] multiqc [DEBUG ] No samples found: fgbio [2023-05-19 13:08:25,038] multiqc [DEBUG ] No samples found: dedup [2023-05-19 13:08:25,042] multiqc [DEBUG ] No samples found: damageprofiler [2023-05-19 13:08:25,050] multiqc [DEBUG ] No samples found: biobambam2 [2023-05-19 13:08:25,054] multiqc [DEBUG ] No samples found: mtnucratio [2023-05-19 13:08:25,058] multiqc [DEBUG ] No samples found: picard [2023-05-19 13:08:25,062] multiqc [DEBUG ] No samples found: prokka [2023-05-19 13:08:25,066] multiqc [DEBUG ] No samples found: samblaster [2023-05-19 13:08:25,071] multiqc [DEBUG ] No samples found: samtools [2023-05-19 13:08:25,076] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-05-19 13:08:25,080] multiqc [DEBUG ] No samples found: bamtools [2023-05-19 13:08:25,084] multiqc [DEBUG ] No samples found: jellyfish [2023-05-19 13:08:25,089] multiqc [DEBUG ] No samples found: vcftools [2023-05-19 13:08:25,094] multiqc [DEBUG ] No samples found: longranger [2023-05-19 13:08:25,098] multiqc [DEBUG ] No samples found: stacks [2023-05-19 13:08:25,105] multiqc [DEBUG ] No samples found: bbmap [2023-05-19 13:08:25,109] multiqc [DEBUG ] No samples found: bismark [2023-05-19 13:08:25,129] multiqc [DEBUG ] No samples found: biscuit [2023-05-19 13:08:25,133] multiqc [DEBUG ] No samples found: hicexplorer [2023-05-19 13:08:25,137] multiqc [DEBUG ] No samples found: hicup [2023-05-19 13:08:25,141] multiqc [DEBUG ] No samples found: hicpro [2023-05-19 13:08:25,145] multiqc [DEBUG ] No samples found: salmon [2023-05-19 13:08:25,150] multiqc [DEBUG ] No samples found: kallisto [2023-05-19 13:08:25,169] multiqc [DEBUG ] No samples found: slamdunk [2023-05-19 13:08:25,173] multiqc [DEBUG ] No samples found: star [2023-05-19 13:08:25,178] multiqc [DEBUG ] No samples found: hisat2 [2023-05-19 13:08:25,182] multiqc [DEBUG ] No samples found: tophat [2023-05-19 13:08:25,186] multiqc [DEBUG ] No samples found: bowtie2 [2023-05-19 13:08:25,190] multiqc [DEBUG ] No samples found: bowtie1 [2023-05-19 13:08:25,194] multiqc [DEBUG ] No samples found: kat [2023-05-19 13:08:25,198] multiqc [DEBUG ] No samples found: leehom [2023-05-19 13:08:25,202] multiqc [DEBUG ] No samples found: adapterRemoval [2023-05-19 13:08:25,207] multiqc [DEBUG ] No samples found: clipandmerge [2023-05-19 13:08:25,211] multiqc [DEBUG ] No samples found: cutadapt [2023-05-19 13:08:25,215] multiqc [DEBUG ] No samples found: flexbar [2023-05-19 13:08:25,219] multiqc [DEBUG ] No samples found: trimmomatic [2023-05-19 13:08:25,223] multiqc [DEBUG ] No samples found: skewer [2023-05-19 13:08:25,227] multiqc [DEBUG ] No samples found: sortmerna [2023-05-19 13:08:25,231] multiqc [DEBUG ] No samples found: biobloomtools [2023-05-19 13:08:25,235] multiqc [DEBUG ] No samples found: fastq_screen [2023-05-19 13:08:25,240] multiqc [DEBUG ] No samples found: afterqc [2023-05-19 13:08:25,244] multiqc [DEBUG ] No samples found: fastp [2023-05-19 13:08:26,464] multiqc.modules.fastqc.fastqc [INFO ] Found 10 reports [2023-05-19 13:08:26,740] multiqc [DEBUG ] No samples found: minionqc [2023-05-19 13:08:26,744] multiqc [DEBUG ] No samples found: mosdepth [2023-05-19 13:08:26,747] multiqc [DEBUG ] No samples found: clusterflow [2023-05-19 13:08:26,751] multiqc [DEBUG ] No samples found: bcl2fastq [2023-05-19 13:08:26,754] multiqc [DEBUG ] No samples found: interop [2023-05-19 13:08:26,758] multiqc [DEBUG ] No samples found: flash [2023-05-19 13:08:26,761] multiqc [DEBUG ] No samples found: seqyclean [2023-05-19 13:08:26,775] multiqc [INFO ] Compressing plot data [2023-05-19 13:08:26,929] multiqc [INFO ] Report : multiqc_report.html [2023-05-19 13:08:26,929] multiqc [INFO ] Data : multiqc_data [2023-05-19 13:08:26,930] multiqc [DEBUG ] Moving data file from '/tmp/tmpn6l2nny3/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_evermanni/raw_fastqc/multiqc_data' [2023-05-19 13:08:26,931] multiqc [DEBUG ] Moving data file from '/tmp/tmpn6l2nny3/multiqc_data/multiqc_fastqc.txt' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_evermanni/raw_fastqc/multiqc_data' [2023-05-19 13:08:26,932] multiqc [DEBUG ] Moving data file from '/tmp/tmpn6l2nny3/multiqc_data/multiqc_general_stats.txt' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_evermanni/raw_fastqc/multiqc_data' [2023-05-19 13:08:26,933] multiqc [DEBUG ] Moving data file from '/tmp/tmpn6l2nny3/multiqc_data/multiqc_sources.txt' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_evermanni/raw_fastqc/multiqc_data' [2023-05-19 13:08:26,934] multiqc [DEBUG ] Moving data file from '/tmp/tmpn6l2nny3/multiqc_data/multiqc_data.json' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_evermanni/raw_fastqc/multiqc_data' [2023-05-19 13:08:27,205] multiqc [INFO ] MultiQC complete