[2023-05-19 12:28:24,984] multiqc [DEBUG ] No MultiQC config found: /gscratch/srlab/programs/anaconda3/lib/python3.7/site-packages/multiqc_config.yaml [2023-05-19 12:28:24,988] multiqc [DEBUG ] Loading config settings from: /usr/lusers/samwhite/.multiqc_config.yaml [2023-05-19 12:28:24,988] multiqc [DEBUG ] New config 'star': {'fn': '*Log.final.out'} [2023-05-19 12:28:24,988] multiqc [DEBUG ] New config 'star/genecounts': {'fn': '*ReadsPerGene.out.tab'} [2023-05-19 12:28:24,988] multiqc [DEBUG ] Added to filename patterns: {'fastp': {'fn': '*report.json'}} [2023-05-19 12:28:24,988] multiqc [DEBUG ] New config 'hisat2': {'contents': 'HISAT2 summary stats:', 'shared': True} [2023-05-19 12:28:24,989] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-05-19 12:28:24,989] multiqc [DEBUG ] Command used: /gscratch/srlab/programs/anaconda3/bin/multiqc . [2023-05-19 12:28:30,008] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2023-05-19 12:28:30,008] multiqc [INFO ] This is MultiQC v1.8 [2023-05-19 12:28:30,008] multiqc [DEBUG ] Command : /gscratch/srlab/programs/anaconda3/bin/multiqc . [2023-05-19 12:28:30,008] multiqc [DEBUG ] Working dir : /gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/A_pulchra/raw_fastqc [2023-05-19 12:28:30,008] multiqc [INFO ] Template : default [2023-05-19 12:28:30,009] multiqc [DEBUG ] Running Python 3.7.3 (default, Mar 27 2019, 22:11:17) [GCC 7.3.0] [2023-05-19 12:28:30,009] multiqc [INFO ] Searching : /gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/A_pulchra/raw_fastqc [2023-05-19 12:28:30,009] 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 12:28:30,010] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpkbjej9qp [2023-05-19 12:28:30,229] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-ACR-150-S1-TP2_R2_001.fastq.gz [2023-05-19 12:28:30,229] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-ACR-140-S1-TP2_R2_001.fastq.gz [2023-05-19 12:28:30,236] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-ACR-173-S1-TP2_R2_001.fastq.gz [2023-05-19 12:28:30,236] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-ACR-150-S1-TP2_R2_001_fastqc.html [2023-05-19 12:28:30,236] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-ACR-145-S1-TP2_R2_001_fastqc.html [2023-05-19 12:28:30,236] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-ACR-173-S1-TP2_R1_001.fastq.gz [2023-05-19 12:28:30,237] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-ACR-178-S1-TP2_R1_001_fastqc.html [2023-05-19 12:28:30,238] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-ACR-145-S1-TP2_R1_001.fastq.gz [2023-05-19 12:28:30,238] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-ACR-150-S1-TP2_R1_001.fastq.gz [2023-05-19 12:28:30,239] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-ACR-145-S1-TP2_R1_001_fastqc.html [2023-05-19 12:28:30,239] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-ACR-140-S1-TP2_R1_001.fastq.gz [2023-05-19 12:28:30,239] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-ACR-140-S1-TP2_R2_001_fastqc.html [2023-05-19 12:28:30,239] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-ACR-173-S1-TP2_R2_001_fastqc.html [2023-05-19 12:28:30,239] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-ACR-145-S1-TP2_R2_001.fastq.gz [2023-05-19 12:28:30,240] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-ACR-140-S1-TP2_R1_001_fastqc.html [2023-05-19 12:28:30,240] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-ACR-173-S1-TP2_R1_001_fastqc.html [2023-05-19 12:28:30,240] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-ACR-150-S1-TP2_R1_001_fastqc.html [2023-05-19 12:28:30,240] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-ACR-178-S1-TP2_R1_001.fastq.gz [2023-05-19 12:28:30,240] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-ACR-178-S1-TP2_R2_001.fastq.gz [2023-05-19 12:28:30,240] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-ACR-178-S1-TP2_R2_001_fastqc.html [2023-05-19 12:28:30,835] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 2.2.4 [2023-05-19 12:28:30,836] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 2.2.4 [2023-05-19 12:28:30,837] multiqc [DEBUG ] No samples found: custom_content [2023-05-19 12:28:30,844] multiqc [DEBUG ] No samples found: conpair [2023-05-19 12:28:30,848] multiqc [DEBUG ] No samples found: peddy [2023-05-19 12:28:30,853] multiqc [DEBUG ] No samples found: methylQA [2023-05-19 12:28:30,858] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-05-19 12:28:30,864] multiqc [DEBUG ] No samples found: qualimap [2023-05-19 12:28:30,869] multiqc [DEBUG ] No samples found: preseq [2023-05-19 12:28:30,873] multiqc [DEBUG ] No samples found: quast [2023-05-19 12:28:30,877] multiqc [DEBUG ] No samples found: qorts [2023-05-19 12:28:30,882] multiqc [DEBUG ] No samples found: rna_seqc [2023-05-19 12:28:30,887] multiqc [DEBUG ] No samples found: rsem [2023-05-19 12:28:30,894] multiqc [DEBUG ] No samples found: rseqc [2023-05-19 12:28:30,898] multiqc [DEBUG ] No samples found: busco [2023-05-19 12:28:30,902] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-05-19 12:28:30,906] multiqc [DEBUG ] No samples found: disambiguate [2023-05-19 12:28:30,911] multiqc [DEBUG ] No samples found: supernova [2023-05-19 12:28:30,918] multiqc [DEBUG ] No samples found: deeptools [2023-05-19 12:28:30,922] multiqc [DEBUG ] No samples found: sargasso [2023-05-19 12:28:30,926] multiqc [DEBUG ] No samples found: verifybamid [2023-05-19 12:28:30,930] multiqc [DEBUG ] No samples found: mirtrace [2023-05-19 12:28:30,935] multiqc [DEBUG ] No samples found: happy [2023-05-19 12:28:30,940] multiqc [DEBUG ] No samples found: homer [2023-05-19 12:28:30,944] multiqc [DEBUG ] No samples found: macs2 [2023-05-19 12:28:30,949] multiqc [DEBUG ] No samples found: theta2 [2023-05-19 12:28:31,020] multiqc [DEBUG ] No samples found: snpeff [2023-05-19 12:28:31,025] multiqc [DEBUG ] No samples found: gatk [2023-05-19 12:28:31,028] multiqc [DEBUG ] No samples found: htseq [2023-05-19 12:28:31,032] multiqc [DEBUG ] No samples found: bcftools [2023-05-19 12:28:31,035] multiqc [DEBUG ] No samples found: featureCounts [2023-05-19 12:28:31,039] multiqc [DEBUG ] No samples found: fgbio [2023-05-19 12:28:31,043] multiqc [DEBUG ] No samples found: dedup [2023-05-19 12:28:31,046] multiqc [DEBUG ] No samples found: damageprofiler [2023-05-19 12:28:31,053] multiqc [DEBUG ] No samples found: biobambam2 [2023-05-19 12:28:31,057] multiqc [DEBUG ] No samples found: mtnucratio [2023-05-19 12:28:31,060] multiqc [DEBUG ] No samples found: picard [2023-05-19 12:28:31,064] multiqc [DEBUG ] No samples found: prokka [2023-05-19 12:28:31,067] multiqc [DEBUG ] No samples found: samblaster [2023-05-19 12:28:31,072] multiqc [DEBUG ] No samples found: samtools [2023-05-19 12:28:31,075] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-05-19 12:28:31,079] multiqc [DEBUG ] No samples found: bamtools [2023-05-19 12:28:31,082] multiqc [DEBUG ] No samples found: jellyfish [2023-05-19 12:28:31,103] multiqc [DEBUG ] No samples found: vcftools [2023-05-19 12:28:31,106] multiqc [DEBUG ] No samples found: longranger [2023-05-19 12:28:31,110] multiqc [DEBUG ] No samples found: stacks [2023-05-19 12:28:31,116] multiqc [DEBUG ] No samples found: bbmap [2023-05-19 12:28:31,119] multiqc [DEBUG ] No samples found: bismark [2023-05-19 12:28:31,124] multiqc [DEBUG ] No samples found: biscuit [2023-05-19 12:28:31,127] multiqc [DEBUG ] No samples found: hicexplorer [2023-05-19 12:28:31,131] multiqc [DEBUG ] No samples found: hicup [2023-05-19 12:28:31,134] multiqc [DEBUG ] No samples found: hicpro [2023-05-19 12:28:31,138] multiqc [DEBUG ] No samples found: salmon [2023-05-19 12:28:31,141] multiqc [DEBUG ] No samples found: kallisto [2023-05-19 12:28:31,145] multiqc [DEBUG ] No samples found: slamdunk [2023-05-19 12:28:31,149] multiqc [DEBUG ] No samples found: star [2023-05-19 12:28:31,152] multiqc [DEBUG ] No samples found: hisat2 [2023-05-19 12:28:31,156] multiqc [DEBUG ] No samples found: tophat [2023-05-19 12:28:31,159] multiqc [DEBUG ] No samples found: bowtie2 [2023-05-19 12:28:31,163] multiqc [DEBUG ] No samples found: bowtie1 [2023-05-19 12:28:31,166] multiqc [DEBUG ] No samples found: kat [2023-05-19 12:28:31,170] multiqc [DEBUG ] No samples found: leehom [2023-05-19 12:28:31,173] multiqc [DEBUG ] No samples found: adapterRemoval [2023-05-19 12:28:31,177] multiqc [DEBUG ] No samples found: clipandmerge [2023-05-19 12:28:31,180] multiqc [DEBUG ] No samples found: cutadapt [2023-05-19 12:28:31,184] multiqc [DEBUG ] No samples found: flexbar [2023-05-19 12:28:31,188] multiqc [DEBUG ] No samples found: trimmomatic [2023-05-19 12:28:31,191] multiqc [DEBUG ] No samples found: skewer [2023-05-19 12:28:31,195] multiqc [DEBUG ] No samples found: sortmerna [2023-05-19 12:28:31,199] multiqc [DEBUG ] No samples found: biobloomtools [2023-05-19 12:28:31,202] multiqc [DEBUG ] No samples found: fastq_screen [2023-05-19 12:28:31,206] multiqc [DEBUG ] No samples found: afterqc [2023-05-19 12:28:31,210] multiqc [DEBUG ] No samples found: fastp [2023-05-19 12:28:32,463] multiqc.modules.fastqc.fastqc [INFO ] Found 10 reports [2023-05-19 12:28:32,710] multiqc [DEBUG ] No samples found: minionqc [2023-05-19 12:28:32,713] multiqc [DEBUG ] No samples found: mosdepth [2023-05-19 12:28:32,717] multiqc [DEBUG ] No samples found: clusterflow [2023-05-19 12:28:32,720] multiqc [DEBUG ] No samples found: bcl2fastq [2023-05-19 12:28:32,724] multiqc [DEBUG ] No samples found: interop [2023-05-19 12:28:32,727] multiqc [DEBUG ] No samples found: flash [2023-05-19 12:28:32,731] multiqc [DEBUG ] No samples found: seqyclean [2023-05-19 12:28:32,748] multiqc [INFO ] Compressing plot data [2023-05-19 12:28:32,905] multiqc [INFO ] Report : multiqc_report.html [2023-05-19 12:28:32,905] multiqc [INFO ] Data : multiqc_data [2023-05-19 12:28:32,906] multiqc [DEBUG ] Moving data file from '/tmp/tmpkbjej9qp/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/A_pulchra/raw_fastqc/multiqc_data' [2023-05-19 12:28:32,908] multiqc [DEBUG ] Moving data file from '/tmp/tmpkbjej9qp/multiqc_data/multiqc_fastqc.txt' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/A_pulchra/raw_fastqc/multiqc_data' [2023-05-19 12:28:32,909] multiqc [DEBUG ] Moving data file from '/tmp/tmpkbjej9qp/multiqc_data/multiqc_general_stats.txt' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/A_pulchra/raw_fastqc/multiqc_data' [2023-05-19 12:28:32,911] multiqc [DEBUG ] Moving data file from '/tmp/tmpkbjej9qp/multiqc_data/multiqc_sources.txt' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/A_pulchra/raw_fastqc/multiqc_data' [2023-05-19 12:28:32,912] multiqc [DEBUG ] Moving data file from '/tmp/tmpkbjej9qp/multiqc_data/multiqc_data.json' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/A_pulchra/raw_fastqc/multiqc_data' [2023-05-19 12:28:33,118] multiqc [INFO ] MultiQC complete