[2023-01-22 11:11:41,915] multiqc [DEBUG ] No MultiQC config found: /gscratch/srlab/programs/anaconda3/lib/python3.7/site-packages/multiqc_config.yaml [2023-01-22 11:11:41,917] multiqc [DEBUG ] Loading config settings from: /usr/lusers/samwhite/.multiqc_config.yaml [2023-01-22 11:11:41,917] multiqc [DEBUG ] New config 'star': {'fn': '*Log.final.out'} [2023-01-22 11:11:41,917] multiqc [DEBUG ] New config 'star/genecounts': {'fn': '*ReadsPerGene.out.tab'} [2023-01-22 11:11:41,917] multiqc [DEBUG ] Added to filename patterns: {'fastp': {'fn': '*report.json'}} [2023-01-22 11:11:41,917] multiqc [DEBUG ] New config 'hisat2': {'contents': 'HISAT2 summary stats:', 'shared': True} [2023-01-22 11:11:41,917] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-01-22 11:11:41,917] multiqc [DEBUG ] Command used: /gscratch/srlab/programs/anaconda3/bin/multiqc . [2023-01-22 11:11:46,926] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2023-01-22 11:11:46,927] multiqc [INFO ] This is MultiQC v1.8 [2023-01-22 11:11:46,929] multiqc [DEBUG ] Command : /gscratch/srlab/programs/anaconda3/bin/multiqc . [2023-01-22 11:11:46,930] multiqc [DEBUG ] Working dir : /gscratch/scrubbed/samwhite/outputs/20230119-coral-fastqc-fastp-multiqc-PRJNA744403/data/P_grandis/RNA-seq [2023-01-22 11:11:46,930] multiqc [INFO ] Template : default [2023-01-22 11:11:46,930] multiqc [DEBUG ] Running Python 3.7.3 (default, Mar 27 2019, 22:11:17) [GCC 7.3.0] [2023-01-22 11:11:46,930] multiqc [INFO ] Searching : /gscratch/scrubbed/samwhite/outputs/20230119-coral-fastqc-fastp-multiqc-PRJNA744403/data/P_grandis/RNA-seq [2023-01-22 11:11:46,931] 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 [2023-01-22 11:11:46,931] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpoeyv6cs1 [2023-01-22 11:11:47,122] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRR15101702_1.fastq.gz [2023-01-22 11:11:47,128] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRR15101690_2_fastqc.html [2023-01-22 11:11:47,129] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRR15101723_2_fastqc.html [2023-01-22 11:11:47,129] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRR15101720_2.fastq.gz [2023-01-22 11:11:47,129] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRR15101723_2.fastq.gz [2023-01-22 11:11:47,129] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRR15101715_1.fastq.gz [2023-01-22 11:11:47,129] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRR15101723_1.fastq.gz [2023-01-22 11:11:47,129] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRR15101723_1_fastqc.html [2023-01-22 11:11:47,129] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRR15101690_1_fastqc.html [2023-01-22 11:11:47,130] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRR15101720_1_fastqc.html [2023-01-22 11:11:47,130] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRR15101702_1_fastqc.html [2023-01-22 11:11:47,130] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRR15101715_2_fastqc.html [2023-01-22 11:11:47,130] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRR15101720_2_fastqc.html [2023-01-22 11:11:47,130] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRR15101702_2.fastq.gz [2023-01-22 11:11:47,130] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRR15101690_1.fastq.gz [2023-01-22 11:11:47,131] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRR15101720_1.fastq.gz [2023-01-22 11:11:47,131] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRR15101715_1_fastqc.html [2023-01-22 11:11:47,131] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: input_fastq_checksums.md5 [2023-01-22 11:11:47,131] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRR15101715_2.fastq.gz [2023-01-22 11:11:47,132] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRR15101702_2_fastqc.html [2023-01-22 11:11:47,132] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRR15101690_2.fastq.gz [2023-01-22 11:11:47,464] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 2.2.4 [2023-01-22 11:11:47,465] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 2.2.4 [2023-01-22 11:11:47,466] multiqc [DEBUG ] No samples found: custom_content [2023-01-22 11:11:47,470] multiqc [DEBUG ] No samples found: conpair [2023-01-22 11:11:47,475] multiqc [DEBUG ] No samples found: peddy [2023-01-22 11:11:47,479] multiqc [DEBUG ] No samples found: methylQA [2023-01-22 11:11:47,484] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-01-22 11:11:47,489] multiqc [DEBUG ] No samples found: qualimap [2023-01-22 11:11:47,493] multiqc [DEBUG ] No samples found: preseq [2023-01-22 11:11:47,497] multiqc [DEBUG ] No samples found: quast [2023-01-22 11:11:47,502] multiqc [DEBUG ] No samples found: qorts [2023-01-22 11:11:47,506] multiqc [DEBUG ] No samples found: rna_seqc [2023-01-22 11:11:47,510] multiqc [DEBUG ] No samples found: rsem [2023-01-22 11:11:47,516] multiqc [DEBUG ] No samples found: rseqc [2023-01-22 11:11:47,520] multiqc [DEBUG ] No samples found: busco [2023-01-22 11:11:47,525] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-01-22 11:11:47,529] multiqc [DEBUG ] No samples found: disambiguate [2023-01-22 11:11:47,533] multiqc [DEBUG ] No samples found: supernova [2023-01-22 11:11:47,540] multiqc [DEBUG ] No samples found: deeptools [2023-01-22 11:11:47,544] multiqc [DEBUG ] No samples found: sargasso [2023-01-22 11:11:47,548] multiqc [DEBUG ] No samples found: verifybamid [2023-01-22 11:11:47,552] multiqc [DEBUG ] No samples found: mirtrace [2023-01-22 11:11:47,556] multiqc [DEBUG ] No samples found: happy [2023-01-22 11:11:47,561] multiqc [DEBUG ] No samples found: homer [2023-01-22 11:11:47,565] multiqc [DEBUG ] No samples found: macs2 [2023-01-22 11:11:47,569] multiqc [DEBUG ] No samples found: theta2 [2023-01-22 11:11:47,573] multiqc [DEBUG ] No samples found: snpeff [2023-01-22 11:11:47,578] multiqc [DEBUG ] No samples found: gatk [2023-01-22 11:11:47,582] multiqc [DEBUG ] No samples found: htseq [2023-01-22 11:11:47,587] multiqc [DEBUG ] No samples found: bcftools [2023-01-22 11:11:47,591] multiqc [DEBUG ] No samples found: featureCounts [2023-01-22 11:11:47,595] multiqc [DEBUG ] No samples found: fgbio [2023-01-22 11:11:47,599] multiqc [DEBUG ] No samples found: dedup [2023-01-22 11:11:47,603] multiqc [DEBUG ] No samples found: damageprofiler [2023-01-22 11:11:47,611] multiqc [DEBUG ] No samples found: biobambam2 [2023-01-22 11:11:47,616] multiqc [DEBUG ] No samples found: mtnucratio [2023-01-22 11:11:47,619] multiqc [DEBUG ] No samples found: picard [2023-01-22 11:11:47,623] multiqc [DEBUG ] No samples found: prokka [2023-01-22 11:11:47,627] multiqc [DEBUG ] No samples found: samblaster [2023-01-22 11:11:47,633] multiqc [DEBUG ] No samples found: samtools [2023-01-22 11:11:47,637] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-01-22 11:11:47,641] multiqc [DEBUG ] No samples found: bamtools [2023-01-22 11:11:47,645] multiqc [DEBUG ] No samples found: jellyfish [2023-01-22 11:11:47,650] multiqc [DEBUG ] No samples found: vcftools [2023-01-22 11:11:47,654] multiqc [DEBUG ] No samples found: longranger [2023-01-22 11:11:47,659] multiqc [DEBUG ] No samples found: stacks [2023-01-22 11:11:47,665] multiqc [DEBUG ] No samples found: bbmap [2023-01-22 11:11:47,670] multiqc [DEBUG ] No samples found: bismark [2023-01-22 11:11:47,675] multiqc [DEBUG ] No samples found: biscuit [2023-01-22 11:11:47,679] multiqc [DEBUG ] No samples found: hicexplorer [2023-01-22 11:11:47,683] multiqc [DEBUG ] No samples found: hicup [2023-01-22 11:11:47,687] multiqc [DEBUG ] No samples found: hicpro [2023-01-22 11:11:47,691] multiqc [DEBUG ] No samples found: salmon [2023-01-22 11:11:47,695] multiqc [DEBUG ] No samples found: kallisto [2023-01-22 11:11:47,700] multiqc [DEBUG ] No samples found: slamdunk [2023-01-22 11:11:47,704] multiqc [DEBUG ] No samples found: star [2023-01-22 11:11:47,708] multiqc [DEBUG ] No samples found: hisat2 [2023-01-22 11:11:47,712] multiqc [DEBUG ] No samples found: tophat [2023-01-22 11:11:47,719] multiqc [DEBUG ] No samples found: bowtie2 [2023-01-22 11:11:47,723] multiqc [DEBUG ] No samples found: bowtie1 [2023-01-22 11:11:47,727] multiqc [DEBUG ] No samples found: kat [2023-01-22 11:11:47,731] multiqc [DEBUG ] No samples found: leehom [2023-01-22 11:11:47,736] multiqc [DEBUG ] No samples found: adapterRemoval [2023-01-22 11:11:47,740] multiqc [DEBUG ] No samples found: clipandmerge [2023-01-22 11:11:47,744] multiqc [DEBUG ] No samples found: cutadapt [2023-01-22 11:11:47,748] multiqc [DEBUG ] No samples found: flexbar [2023-01-22 11:11:47,752] multiqc [DEBUG ] No samples found: trimmomatic [2023-01-22 11:11:47,756] multiqc [DEBUG ] No samples found: skewer [2023-01-22 11:11:47,760] multiqc [DEBUG ] No samples found: sortmerna [2023-01-22 11:11:47,764] multiqc [DEBUG ] No samples found: biobloomtools [2023-01-22 11:11:47,768] multiqc [DEBUG ] No samples found: fastq_screen [2023-01-22 11:11:47,772] multiqc [DEBUG ] No samples found: afterqc [2023-01-22 11:11:47,777] multiqc [DEBUG ] No samples found: fastp [2023-01-22 11:11:47,827] multiqc.modules.fastqc.fastqc [INFO ] Found 10 reports [2023-01-22 11:11:48,132] multiqc [DEBUG ] No samples found: minionqc [2023-01-22 11:11:48,136] multiqc [DEBUG ] No samples found: mosdepth [2023-01-22 11:11:48,139] multiqc [DEBUG ] No samples found: clusterflow [2023-01-22 11:11:48,143] multiqc [DEBUG ] No samples found: bcl2fastq [2023-01-22 11:11:48,146] multiqc [DEBUG ] No samples found: interop [2023-01-22 11:11:48,149] multiqc [DEBUG ] No samples found: flash [2023-01-22 11:11:48,153] multiqc [DEBUG ] No samples found: seqyclean [2023-01-22 11:11:48,167] multiqc [INFO ] Compressing plot data [2023-01-22 11:11:48,327] multiqc [INFO ] Report : multiqc_report.html [2023-01-22 11:11:48,327] multiqc [INFO ] Data : multiqc_data [2023-01-22 11:11:48,329] multiqc [DEBUG ] Moving data file from '/tmp/tmpoeyv6cs1/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/gscratch/scrubbed/samwhite/outputs/20230119-coral-fastqc-fastp-multiqc-PRJNA744403/data/P_grandis/RNA-seq/multiqc_data' [2023-01-22 11:11:48,330] multiqc [DEBUG ] Moving data file from '/tmp/tmpoeyv6cs1/multiqc_data/multiqc_fastqc.txt' to '/gscratch/scrubbed/samwhite/outputs/20230119-coral-fastqc-fastp-multiqc-PRJNA744403/data/P_grandis/RNA-seq/multiqc_data' [2023-01-22 11:11:48,331] multiqc [DEBUG ] Moving data file from '/tmp/tmpoeyv6cs1/multiqc_data/multiqc_general_stats.txt' to '/gscratch/scrubbed/samwhite/outputs/20230119-coral-fastqc-fastp-multiqc-PRJNA744403/data/P_grandis/RNA-seq/multiqc_data' [2023-01-22 11:11:48,332] multiqc [DEBUG ] Moving data file from '/tmp/tmpoeyv6cs1/multiqc_data/multiqc_sources.txt' to '/gscratch/scrubbed/samwhite/outputs/20230119-coral-fastqc-fastp-multiqc-PRJNA744403/data/P_grandis/RNA-seq/multiqc_data' [2023-01-22 11:11:48,333] multiqc [DEBUG ] Moving data file from '/tmp/tmpoeyv6cs1/multiqc_data/multiqc_data.json' to '/gscratch/scrubbed/samwhite/outputs/20230119-coral-fastqc-fastp-multiqc-PRJNA744403/data/P_grandis/RNA-seq/multiqc_data' [2023-01-22 11:11:48,475] multiqc [INFO ] MultiQC complete