[2023-05-22 16:52:53,345] multiqc [DEBUG ] No MultiQC config found: /gscratch/srlab/programs/anaconda3/lib/python3.7/site-packages/multiqc_config.yaml [2023-05-22 16:52:53,347] multiqc [DEBUG ] Loading config settings from: /usr/lusers/samwhite/.multiqc_config.yaml [2023-05-22 16:52:53,347] multiqc [DEBUG ] New config 'star': {'fn': '*Log.final.out'} [2023-05-22 16:52:53,347] multiqc [DEBUG ] New config 'star/genecounts': {'fn': '*ReadsPerGene.out.tab'} [2023-05-22 16:52:53,347] multiqc [DEBUG ] Added to filename patterns: {'fastp': {'fn': '*report.json'}} [2023-05-22 16:52:53,347] multiqc [DEBUG ] New config 'hisat2': {'contents': 'HISAT2 summary stats:', 'shared': True} [2023-05-22 16:52:53,348] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-05-22 16:52:53,348] multiqc [DEBUG ] Command used: /gscratch/srlab/programs/anaconda3/bin/multiqc . [2023-05-22 16:52:58,357] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2023-05-22 16:52:58,357] multiqc [INFO ] This is MultiQC v1.8 [2023-05-22 16:52:58,359] multiqc [DEBUG ] Command : /gscratch/srlab/programs/anaconda3/bin/multiqc . [2023-05-22 16:52:58,359] multiqc [DEBUG ] Working dir : /gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-sRNAseq/P_meandrina/raw_fastqc [2023-05-22 16:52:58,359] multiqc [INFO ] Template : default [2023-05-22 16:52:58,359] multiqc [DEBUG ] Running Python 3.7.3 (default, Mar 27 2019, 22:11:17) [GCC 7.3.0] [2023-05-22 16:52:58,360] multiqc [INFO ] Searching : /gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-sRNAseq/P_meandrina/raw_fastqc [2023-05-22 16:52:58,360] 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 16:52:58,361] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpnyeezwa6 [2023-05-22 16:52:58,538] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-47-S1-TP2_R1_001.fastq.gz [2023-05-22 16:52:58,544] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-53-S1-TP2_R2_001_fastqc.html [2023-05-22 16:52:58,544] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-53-S1-TP2_R1_001.fastq.gz [2023-05-22 16:52:58,544] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-57-S1-TP2_R1_001_fastqc.html [2023-05-22 16:52:58,544] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-47-S1-TP2_R2_001_fastqc.html [2023-05-22 16:52:58,545] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-48-S1-TP2_R2_001.fastq.gz [2023-05-22 16:52:58,546] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-47-S1-TP2_R2_001.fastq.gz [2023-05-22 16:52:58,546] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-48-S1-TP2_R1_001_fastqc.html [2023-05-22 16:52:58,546] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-57-S1-TP2_R2_001_fastqc.html [2023-05-22 16:52:58,546] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-48-S1-TP2_R2_001_fastqc.html [2023-05-22 16:52:58,546] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-50-S1-TP2_R2_001.fastq.gz [2023-05-22 16:52:58,546] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-48-S1-TP2_R1_001.fastq.gz [2023-05-22 16:52:58,546] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-53-S1-TP2_R1_001_fastqc.html [2023-05-22 16:52:58,546] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-47-S1-TP2_R1_001_fastqc.html [2023-05-22 16:52:58,547] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-57-S1-TP2_R1_001.fastq.gz [2023-05-22 16:52:58,547] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-53-S1-TP2_R2_001.fastq.gz [2023-05-22 16:52:58,547] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-50-S1-TP2_R1_001_fastqc.html [2023-05-22 16:52:58,547] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-57-S1-TP2_R2_001.fastq.gz [2023-05-22 16:52:58,547] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-50-S1-TP2_R2_001_fastqc.html [2023-05-22 16:52:58,547] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-POC-50-S1-TP2_R1_001.fastq.gz [2023-05-22 16:52:59,085] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 2.2.4 [2023-05-22 16:52:59,086] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 2.2.4 [2023-05-22 16:52:59,087] multiqc [DEBUG ] No samples found: custom_content [2023-05-22 16:52:59,094] multiqc [DEBUG ] No samples found: conpair [2023-05-22 16:52:59,101] multiqc [DEBUG ] No samples found: peddy [2023-05-22 16:52:59,107] multiqc [DEBUG ] No samples found: methylQA [2023-05-22 16:52:59,113] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-05-22 16:52:59,121] multiqc [DEBUG ] No samples found: qualimap [2023-05-22 16:52:59,127] multiqc [DEBUG ] No samples found: preseq [2023-05-22 16:52:59,132] multiqc [DEBUG ] No samples found: quast [2023-05-22 16:52:59,141] multiqc [DEBUG ] No samples found: qorts [2023-05-22 16:52:59,146] multiqc [DEBUG ] No samples found: rna_seqc [2023-05-22 16:52:59,151] multiqc [DEBUG ] No samples found: rsem [2023-05-22 16:52:59,161] multiqc [DEBUG ] No samples found: rseqc [2023-05-22 16:52:59,166] multiqc [DEBUG ] No samples found: busco [2023-05-22 16:52:59,172] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-05-22 16:52:59,177] multiqc [DEBUG ] No samples found: disambiguate [2023-05-22 16:52:59,183] multiqc [DEBUG ] No samples found: supernova [2023-05-22 16:52:59,194] multiqc [DEBUG ] No samples found: deeptools [2023-05-22 16:52:59,199] multiqc [DEBUG ] No samples found: sargasso [2023-05-22 16:52:59,205] multiqc [DEBUG ] No samples found: verifybamid [2023-05-22 16:52:59,210] multiqc [DEBUG ] No samples found: mirtrace [2023-05-22 16:52:59,216] multiqc [DEBUG ] No samples found: happy [2023-05-22 16:52:59,223] multiqc [DEBUG ] No samples found: homer [2023-05-22 16:52:59,228] multiqc [DEBUG ] No samples found: macs2 [2023-05-22 16:52:59,233] multiqc [DEBUG ] No samples found: theta2 [2023-05-22 16:52:59,255] multiqc [DEBUG ] No samples found: snpeff [2023-05-22 16:52:59,261] multiqc [DEBUG ] No samples found: gatk [2023-05-22 16:52:59,267] multiqc [DEBUG ] No samples found: htseq [2023-05-22 16:52:59,273] multiqc [DEBUG ] No samples found: bcftools [2023-05-22 16:52:59,278] multiqc [DEBUG ] No samples found: featureCounts [2023-05-22 16:52:59,284] multiqc [DEBUG ] No samples found: fgbio [2023-05-22 16:52:59,289] multiqc [DEBUG ] No samples found: dedup [2023-05-22 16:52:59,294] multiqc [DEBUG ] No samples found: damageprofiler [2023-05-22 16:52:59,310] multiqc [DEBUG ] No samples found: biobambam2 [2023-05-22 16:52:59,315] multiqc [DEBUG ] No samples found: mtnucratio [2023-05-22 16:52:59,319] multiqc [DEBUG ] No samples found: picard [2023-05-22 16:52:59,324] multiqc [DEBUG ] No samples found: prokka [2023-05-22 16:52:59,329] multiqc [DEBUG ] No samples found: samblaster [2023-05-22 16:52:59,339] multiqc [DEBUG ] No samples found: samtools [2023-05-22 16:52:59,345] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-05-22 16:52:59,352] multiqc [DEBUG ] No samples found: bamtools [2023-05-22 16:52:59,357] multiqc [DEBUG ] No samples found: jellyfish [2023-05-22 16:52:59,365] multiqc [DEBUG ] No samples found: vcftools [2023-05-22 16:52:59,370] multiqc [DEBUG ] No samples found: longranger [2023-05-22 16:52:59,376] multiqc [DEBUG ] No samples found: stacks [2023-05-22 16:52:59,389] multiqc [DEBUG ] No samples found: bbmap [2023-05-22 16:52:59,394] multiqc [DEBUG ] No samples found: bismark [2023-05-22 16:52:59,400] multiqc [DEBUG ] No samples found: biscuit [2023-05-22 16:52:59,406] multiqc [DEBUG ] No samples found: hicexplorer [2023-05-22 16:52:59,412] multiqc [DEBUG ] No samples found: hicup [2023-05-22 16:52:59,417] multiqc [DEBUG ] No samples found: hicpro [2023-05-22 16:52:59,423] multiqc [DEBUG ] No samples found: salmon [2023-05-22 16:52:59,429] multiqc [DEBUG ] No samples found: kallisto [2023-05-22 16:52:59,435] multiqc [DEBUG ] No samples found: slamdunk [2023-05-22 16:52:59,440] multiqc [DEBUG ] No samples found: star [2023-05-22 16:52:59,445] multiqc [DEBUG ] No samples found: hisat2 [2023-05-22 16:52:59,450] multiqc [DEBUG ] No samples found: tophat [2023-05-22 16:52:59,457] multiqc [DEBUG ] No samples found: bowtie2 [2023-05-22 16:52:59,463] multiqc [DEBUG ] No samples found: bowtie1 [2023-05-22 16:52:59,477] multiqc [DEBUG ] No samples found: kat [2023-05-22 16:52:59,482] multiqc [DEBUG ] No samples found: leehom [2023-05-22 16:52:59,488] multiqc [DEBUG ] No samples found: adapterRemoval [2023-05-22 16:52:59,493] multiqc [DEBUG ] No samples found: clipandmerge [2023-05-22 16:52:59,498] multiqc [DEBUG ] No samples found: cutadapt [2023-05-22 16:52:59,504] multiqc [DEBUG ] No samples found: flexbar [2023-05-22 16:52:59,509] multiqc [DEBUG ] No samples found: trimmomatic [2023-05-22 16:52:59,516] multiqc [DEBUG ] No samples found: skewer [2023-05-22 16:52:59,521] multiqc [DEBUG ] No samples found: sortmerna [2023-05-22 16:52:59,527] multiqc [DEBUG ] No samples found: biobloomtools [2023-05-22 16:52:59,532] multiqc [DEBUG ] No samples found: fastq_screen [2023-05-22 16:52:59,537] multiqc [DEBUG ] No samples found: afterqc [2023-05-22 16:52:59,542] multiqc [DEBUG ] No samples found: fastp [2023-05-22 16:53:00,769] multiqc.modules.fastqc.fastqc [INFO ] Found 10 reports [2023-05-22 16:53:01,016] multiqc [DEBUG ] No samples found: minionqc [2023-05-22 16:53:01,022] multiqc [DEBUG ] No samples found: mosdepth [2023-05-22 16:53:01,027] multiqc [DEBUG ] No samples found: clusterflow [2023-05-22 16:53:01,032] multiqc [DEBUG ] No samples found: bcl2fastq [2023-05-22 16:53:01,036] multiqc [DEBUG ] No samples found: interop [2023-05-22 16:53:01,042] multiqc [DEBUG ] No samples found: flash [2023-05-22 16:53:01,048] multiqc [DEBUG ] No samples found: seqyclean [2023-05-22 16:53:01,062] multiqc [INFO ] Compressing plot data [2023-05-22 16:53:01,223] multiqc [INFO ] Report : multiqc_report.html [2023-05-22 16:53:01,223] multiqc [INFO ] Data : multiqc_data [2023-05-22 16:53:01,225] multiqc [DEBUG ] Moving data file from '/tmp/tmpnyeezwa6/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-sRNAseq/P_meandrina/raw_fastqc/multiqc_data' [2023-05-22 16:53:01,226] multiqc [DEBUG ] Moving data file from '/tmp/tmpnyeezwa6/multiqc_data/multiqc_fastqc.txt' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-sRNAseq/P_meandrina/raw_fastqc/multiqc_data' [2023-05-22 16:53:01,227] multiqc [DEBUG ] Moving data file from '/tmp/tmpnyeezwa6/multiqc_data/multiqc_general_stats.txt' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-sRNAseq/P_meandrina/raw_fastqc/multiqc_data' [2023-05-22 16:53:01,227] multiqc [DEBUG ] Moving data file from '/tmp/tmpnyeezwa6/multiqc_data/multiqc_sources.txt' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-sRNAseq/P_meandrina/raw_fastqc/multiqc_data' [2023-05-22 16:53:01,228] multiqc [DEBUG ] Moving data file from '/tmp/tmpnyeezwa6/multiqc_data/multiqc_data.json' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-sRNAseq/P_meandrina/raw_fastqc/multiqc_data' [2023-05-22 16:53:01,480] multiqc [INFO ] MultiQC complete