[2023-05-19 13:49:05,856] multiqc [DEBUG ] No MultiQC config found: /gscratch/srlab/programs/anaconda3/lib/python3.7/site-packages/multiqc_config.yaml [2023-05-19 13:49:05,860] multiqc [DEBUG ] Loading config settings from: /usr/lusers/samwhite/.multiqc_config.yaml [2023-05-19 13:49:05,860] multiqc [DEBUG ] New config 'star': {'fn': '*Log.final.out'} [2023-05-19 13:49:05,861] multiqc [DEBUG ] New config 'star/genecounts': {'fn': '*ReadsPerGene.out.tab'} [2023-05-19 13:49:05,861] multiqc [DEBUG ] Added to filename patterns: {'fastp': {'fn': '*report.json'}} [2023-05-19 13:49:05,861] multiqc [DEBUG ] New config 'hisat2': {'contents': 'HISAT2 summary stats:', 'shared': True} [2023-05-19 13:49:05,861] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-05-19 13:49:05,861] multiqc [DEBUG ] Command used: /gscratch/srlab/programs/anaconda3/bin/multiqc . [2023-05-19 13:49:10,956] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2023-05-19 13:49:10,956] multiqc [INFO ] This is MultiQC v1.8 [2023-05-19 13:49:10,956] multiqc [DEBUG ] Command : /gscratch/srlab/programs/anaconda3/bin/multiqc . [2023-05-19 13:49:10,957] multiqc [DEBUG ] Working dir : /gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_meandrina/raw_fastqc [2023-05-19 13:49:10,957] multiqc [INFO ] Template : default [2023-05-19 13:49:10,957] multiqc [DEBUG ] Running Python 3.7.3 (default, Mar 27 2019, 22:11:17) [GCC 7.3.0] [2023-05-19 13:49:10,957] multiqc [INFO ] Searching : /gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_meandrina/raw_fastqc [2023-05-19 13:49:10,958] 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 13:49:10,958] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmp0jlcfvzy [2023-05-19 13:49:11,232] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POC-47-S1-TP2_R1_001_fastqc.html [2023-05-19 13:49:11,232] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POC-53-S1-TP2_R2_001.fastq.gz [2023-05-19 13:49:11,233] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POC-57-S1-TP2_R1_001_fastqc.html [2023-05-19 13:49:11,233] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POC-48-S1-TP2_R2_001_fastqc.html [2023-05-19 13:49:11,233] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POC-53-S1-TP2_R1_001.fastq.gz [2023-05-19 13:49:11,233] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POC-53-S1-TP2_R1_001_fastqc.html [2023-05-19 13:49:11,234] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POC-48-S1-TP2_R1_001_fastqc.html [2023-05-19 13:49:11,234] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POC-57-S1-TP2_R1_001.fastq.gz [2023-05-19 13:49:11,234] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POC-47-S1-TP2_R2_001.fastq.gz [2023-05-19 13:49:11,234] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POC-50-S1-TP2_R2_001_fastqc.html [2023-05-19 13:49:11,234] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POC-47-S1-TP2_R1_001.fastq.gz [2023-05-19 13:49:11,235] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POC-48-S1-TP2_R2_001.fastq.gz [2023-05-19 13:49:11,235] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POC-53-S1-TP2_R2_001_fastqc.html [2023-05-19 13:49:11,235] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POC-47-S1-TP2_R2_001_fastqc.html [2023-05-19 13:49:11,235] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POC-50-S1-TP2_R2_001.fastq.gz [2023-05-19 13:49:11,235] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POC-48-S1-TP2_R1_001.fastq.gz [2023-05-19 13:49:11,235] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POC-57-S1-TP2_R2_001_fastqc.html [2023-05-19 13:49:11,235] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POC-50-S1-TP2_R1_001_fastqc.html [2023-05-19 13:49:11,236] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POC-57-S1-TP2_R2_001.fastq.gz [2023-05-19 13:49:11,236] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POC-50-S1-TP2_R1_001.fastq.gz [2023-05-19 13:49:13,350] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 2.2.4 [2023-05-19 13:49:13,351] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 2.2.4 [2023-05-19 13:49:13,353] multiqc [DEBUG ] No samples found: custom_content [2023-05-19 13:49:13,361] multiqc [DEBUG ] No samples found: conpair [2023-05-19 13:49:13,370] multiqc [DEBUG ] No samples found: peddy [2023-05-19 13:49:13,378] multiqc [DEBUG ] No samples found: methylQA [2023-05-19 13:49:13,388] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-05-19 13:49:13,433] multiqc [DEBUG ] No samples found: qualimap [2023-05-19 13:49:13,442] multiqc [DEBUG ] No samples found: preseq [2023-05-19 13:49:13,465] multiqc [DEBUG ] No samples found: quast [2023-05-19 13:49:13,474] multiqc [DEBUG ] No samples found: qorts [2023-05-19 13:49:13,483] multiqc [DEBUG ] No samples found: rna_seqc [2023-05-19 13:49:13,491] multiqc [DEBUG ] No samples found: rsem [2023-05-19 13:49:13,601] multiqc [DEBUG ] No samples found: rseqc [2023-05-19 13:49:13,610] multiqc [DEBUG ] No samples found: busco [2023-05-19 13:49:13,618] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-05-19 13:49:13,627] multiqc [DEBUG ] No samples found: disambiguate [2023-05-19 13:49:13,668] multiqc [DEBUG ] No samples found: supernova [2023-05-19 13:49:13,682] multiqc [DEBUG ] No samples found: deeptools [2023-05-19 13:49:13,732] multiqc [DEBUG ] No samples found: sargasso [2023-05-19 13:49:13,741] multiqc [DEBUG ] No samples found: verifybamid [2023-05-19 13:49:13,749] multiqc [DEBUG ] No samples found: mirtrace [2023-05-19 13:49:13,758] multiqc [DEBUG ] No samples found: happy [2023-05-19 13:49:13,768] multiqc [DEBUG ] No samples found: homer [2023-05-19 13:49:13,776] multiqc [DEBUG ] No samples found: macs2 [2023-05-19 13:49:13,785] multiqc [DEBUG ] No samples found: theta2 [2023-05-19 13:49:13,793] multiqc [DEBUG ] No samples found: snpeff [2023-05-19 13:49:13,804] multiqc [DEBUG ] No samples found: gatk [2023-05-19 13:49:13,811] multiqc [DEBUG ] No samples found: htseq [2023-05-19 13:49:13,818] multiqc [DEBUG ] No samples found: bcftools [2023-05-19 13:49:13,824] multiqc [DEBUG ] No samples found: featureCounts [2023-05-19 13:49:13,830] multiqc [DEBUG ] No samples found: fgbio [2023-05-19 13:49:13,835] multiqc [DEBUG ] No samples found: dedup [2023-05-19 13:49:13,840] multiqc [DEBUG ] No samples found: damageprofiler [2023-05-19 13:49:13,850] multiqc [DEBUG ] No samples found: biobambam2 [2023-05-19 13:49:13,854] multiqc [DEBUG ] No samples found: mtnucratio [2023-05-19 13:49:13,858] multiqc [DEBUG ] No samples found: picard [2023-05-19 13:49:13,862] multiqc [DEBUG ] No samples found: prokka [2023-05-19 13:49:13,867] multiqc [DEBUG ] No samples found: samblaster [2023-05-19 13:49:13,873] multiqc [DEBUG ] No samples found: samtools [2023-05-19 13:49:13,878] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-05-19 13:49:13,882] multiqc [DEBUG ] No samples found: bamtools [2023-05-19 13:49:13,887] multiqc [DEBUG ] No samples found: jellyfish [2023-05-19 13:49:13,901] multiqc [DEBUG ] No samples found: vcftools [2023-05-19 13:49:13,905] multiqc [DEBUG ] No samples found: longranger [2023-05-19 13:49:13,941] multiqc [DEBUG ] No samples found: stacks [2023-05-19 13:49:13,966] multiqc [DEBUG ] No samples found: bbmap [2023-05-19 13:49:13,971] multiqc [DEBUG ] No samples found: bismark [2023-05-19 13:49:14,001] multiqc [DEBUG ] No samples found: biscuit [2023-05-19 13:49:14,006] multiqc [DEBUG ] No samples found: hicexplorer [2023-05-19 13:49:14,010] multiqc [DEBUG ] No samples found: hicup [2023-05-19 13:49:14,015] multiqc [DEBUG ] No samples found: hicpro [2023-05-19 13:49:14,019] multiqc [DEBUG ] No samples found: salmon [2023-05-19 13:49:14,024] multiqc [DEBUG ] No samples found: kallisto [2023-05-19 13:49:14,046] multiqc [DEBUG ] No samples found: slamdunk [2023-05-19 13:49:14,050] multiqc [DEBUG ] No samples found: star [2023-05-19 13:49:14,055] multiqc [DEBUG ] No samples found: hisat2 [2023-05-19 13:49:14,059] multiqc [DEBUG ] No samples found: tophat [2023-05-19 13:49:14,064] multiqc [DEBUG ] No samples found: bowtie2 [2023-05-19 13:49:14,069] multiqc [DEBUG ] No samples found: bowtie1 [2023-05-19 13:49:14,074] multiqc [DEBUG ] No samples found: kat [2023-05-19 13:49:14,113] multiqc [DEBUG ] No samples found: leehom [2023-05-19 13:49:14,118] multiqc [DEBUG ] No samples found: adapterRemoval [2023-05-19 13:49:14,122] multiqc [DEBUG ] No samples found: clipandmerge [2023-05-19 13:49:14,127] multiqc [DEBUG ] No samples found: cutadapt [2023-05-19 13:49:14,132] multiqc [DEBUG ] No samples found: flexbar [2023-05-19 13:49:14,136] multiqc [DEBUG ] No samples found: trimmomatic [2023-05-19 13:49:14,141] multiqc [DEBUG ] No samples found: skewer [2023-05-19 13:49:14,145] multiqc [DEBUG ] No samples found: sortmerna [2023-05-19 13:49:14,150] multiqc [DEBUG ] No samples found: biobloomtools [2023-05-19 13:49:14,154] multiqc [DEBUG ] No samples found: fastq_screen [2023-05-19 13:49:14,159] multiqc [DEBUG ] No samples found: afterqc [2023-05-19 13:49:14,163] multiqc [DEBUG ] No samples found: fastp [2023-05-19 13:49:15,397] multiqc.modules.fastqc.fastqc [INFO ] Found 10 reports [2023-05-19 13:49:15,673] multiqc [DEBUG ] No samples found: minionqc [2023-05-19 13:49:15,677] multiqc [DEBUG ] No samples found: mosdepth [2023-05-19 13:49:15,680] multiqc [DEBUG ] No samples found: clusterflow [2023-05-19 13:49:15,684] multiqc [DEBUG ] No samples found: bcl2fastq [2023-05-19 13:49:15,688] multiqc [DEBUG ] No samples found: interop [2023-05-19 13:49:15,691] multiqc [DEBUG ] No samples found: flash [2023-05-19 13:49:15,717] multiqc [DEBUG ] No samples found: seqyclean [2023-05-19 13:49:15,731] multiqc [INFO ] Compressing plot data [2023-05-19 13:49:15,887] multiqc [INFO ] Report : multiqc_report.html [2023-05-19 13:49:15,887] multiqc [INFO ] Data : multiqc_data [2023-05-19 13:49:15,887] multiqc [DEBUG ] Moving data file from '/tmp/tmp0jlcfvzy/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_meandrina/raw_fastqc/multiqc_data' [2023-05-19 13:49:15,888] multiqc [DEBUG ] Moving data file from '/tmp/tmp0jlcfvzy/multiqc_data/multiqc_fastqc.txt' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_meandrina/raw_fastqc/multiqc_data' [2023-05-19 13:49:15,889] multiqc [DEBUG ] Moving data file from '/tmp/tmp0jlcfvzy/multiqc_data/multiqc_general_stats.txt' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_meandrina/raw_fastqc/multiqc_data' [2023-05-19 13:49:15,890] multiqc [DEBUG ] Moving data file from '/tmp/tmp0jlcfvzy/multiqc_data/multiqc_sources.txt' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_meandrina/raw_fastqc/multiqc_data' [2023-05-19 13:49:15,891] multiqc [DEBUG ] Moving data file from '/tmp/tmp0jlcfvzy/multiqc_data/multiqc_data.json' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_meandrina/raw_fastqc/multiqc_data' [2023-05-19 13:49:16,269] multiqc [INFO ] MultiQC complete