[2022-09-08 21:20:27,040] multiqc [DEBUG ] No MultiQC config found: /gscratch/srlab/programs/anaconda3/lib/python3.7/site-packages/multiqc_config.yaml [2022-09-08 21:20:27,052] multiqc [DEBUG ] Loading config settings from: /usr/lusers/samwhite/.multiqc_config.yaml [2022-09-08 21:20:27,052] multiqc [DEBUG ] New config 'star': {'fn': '*Log.final.out'} [2022-09-08 21:20:27,053] multiqc [DEBUG ] New config 'star/genecounts': {'fn': '*ReadsPerGene.out.tab'} [2022-09-08 21:20:27,053] multiqc [DEBUG ] Added to filename patterns: {'fastp': {'fn': '*report.json'}} [2022-09-08 21:20:27,053] multiqc [DEBUG ] New config 'hisat2': {'contents': 'HISAT2 summary stats:', 'shared': True} [2022-09-08 21:20:27,053] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-09-08 21:20:27,053] multiqc [DEBUG ] Command used: /gscratch/srlab/programs/anaconda3/bin/multiqc . [2022-09-08 21:20:32,291] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2022-09-08 21:20:32,291] multiqc [INFO ] This is MultiQC v1.8 [2022-09-08 21:20:32,294] multiqc [DEBUG ] Command : /gscratch/srlab/programs/anaconda3/bin/multiqc . [2022-09-08 21:20:32,294] multiqc [DEBUG ] Working dir : /gscratch/scrubbed/samwhite/outputs/20220909-pgen-fastqc-fastp-mutliqc-rnaseq [2022-09-08 21:20:32,294] multiqc [INFO ] Template : default [2022-09-08 21:20:32,294] multiqc [DEBUG ] Running Python 3.7.3 (default, Mar 27 2019, 22:11:17) [GCC 7.3.0] [2022-09-08 21:20:32,294] multiqc [INFO ] Searching : /gscratch/scrubbed/samwhite/outputs/20220909-pgen-fastqc-fastp-mutliqc-rnaseq [2022-09-08 21:20:32,295] 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 [2022-09-08 21:20:32,295] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpvgz2jcm3 [2022-09-08 21:20:33,098] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-gonad-RNA-5_S33_L005_R2_001_fastqc.html [2022-09-08 21:20:33,111] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-juvenile-ambient-exposure-RNA-EPI-123-1_S6_L001_R2_001.fastp-trim.20220908.fq.gz [2022-09-08 21:20:33,120] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-heart-RNA-3_S18_L003_R2_001.fastp-trim.20220908.fq.gz [2022-09-08 21:20:33,120] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 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[DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-gonad-RNA-1_S1_L001_R1_001.fastp-trim.20220908.report.html [2022-09-08 21:20:33,584] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-juvenile-ambient-exposure-RNA-EPI-123-8_S62_L008_R2_001.fastp-trim.20220908_fastqc.html [2022-09-08 21:20:33,584] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-juvenile-ambient-exposure-RNA-EPI-123-2_S14_L002_R1_001.fastp-trim.20220908.fq.gz [2022-09-08 21:20:33,584] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-juvenile-OA-exposure-RNA-EPI-115-6_S44_L006_R1_001.fastp-trim.20220908.report.html [2022-09-08 21:20:33,584] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-juvenile-ambient-exposure-RNA-EPI-123-7_S54_L007_R1_001.fastp-trim.20220908_fastqc.html [2022-09-08 21:20:33,585] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geo_Pool_M_CTTGTA_L006_R1_001_fastqc.html [2022-09-08 21:20:33,585] 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[2022-09-08 21:20:33,586] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-juvenile-ambient-exposure-RNA-EPI-123-7_S54_L007_R1_001_fastqc.html [2022-09-08 21:20:33,586] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-juvenile-OA-exposure-RNA-EPI-116-3_S21_L003_R1_001.fastp-trim.20220908_fastqc.html [2022-09-08 21:20:33,586] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-juvenile-OA-exposure-RNA-EPI-116-5_S37_L005_R2_001_fastqc.html [2022-09-08 21:20:33,587] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-juvenile-OA-exposure-RNA-EPI-115-5_S36_L005_R2_001_fastqc.html [2022-09-08 21:20:33,587] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-larvae-day5-RNA-EPI-99-8_S64_L008_R2_001_fastqc.html [2022-09-08 21:20:33,587] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-gonad-RNA-2_S9_L002_R2_001.fastp-trim.20220908.fq.gz [2022-09-08 21:20:33,587] multiqc [DEBUG ] 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21:20:33,705] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-juvenile-ambient-exposure-RNA-EPI-124-6_S47_L006_R1_001.fastp-trim.20220908.report.html [2022-09-08 21:20:33,706] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-juvenile-OA-exposure-RNA-EPI-115-1_S4_L001_R2_001.fastp-trim.20220908.fq.gz [2022-09-08 21:20:33,706] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-juvenile-ambient-exposure-RNA-EPI-123-5_S38_L005_R2_001.fastp-trim.20220908_fastqc.html [2022-09-08 21:20:33,706] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-gonad-RNA-2_S9_L002_R1_001.fastp-trim.20220908.report.html [2022-09-08 21:20:33,706] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-juvenile-ambient-exposure-RNA-EPI-124-3_S23_L003_R2_001.fastp-trim.20220908_fastqc.html [2022-09-08 21:20:33,706] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-gonad-RNA-3_S17_L003_R1_001.fastp-trim.20220908.fq.gz [2022-09-08 21:20:33,706] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-juvenile-OA-exposure-RNA-EPI-116-4_S29_L004_R1_001_fastqc.html [2022-09-08 21:20:33,706] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-juvenile-OA-exposure-RNA-EPI-115-6_S44_L006_R1_001.fastp-trim.20220908.fq.gz [2022-09-08 21:20:33,707] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Trueseq-stranded-mRNA-libraries-GeoRNA5-E1-NR005_S3_L001_R1_001.fastp-trim.20220908_fastqc.html [2022-09-08 21:20:33,707] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-juvenile-ambient-exposure-RNA-EPI-124-4_S31_L004_R1_001.fastp-trim.20220908.report.html [2022-09-08 21:20:33,708] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-juvenile-OA-exposure-RNA-EPI-116-4_S29_L004_R1_001.fastp-trim.20220908_fastqc.html [2022-09-08 21:20:33,708] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-juvenile-ambient-exposure-RNA-EPI-124-4_S31_L004_R2_001_fastqc.html [2022-09-08 21:20:33,708] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-ctenidia-RNA-7_S51_L007_R2_001.fastp-trim.20220908.fq.gz [2022-09-08 21:20:33,708] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-juvenile-OA-exposure-RNA-EPI-115-6_S44_L006_R2_001_fastqc.html [2022-09-08 21:20:33,708] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-ctenidia-RNA-1_S3_L001_R2_001_fastqc.html [2022-09-08 21:20:33,709] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-heart-RNA-4_S26_L004_R1_001.fastp-trim.20220908_fastqc.html [2022-09-08 21:20:33,709] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-larvae-day5-RNA-EPI-99-3_S24_L003_R2_001_fastqc.html [2022-09-08 21:20:33,710] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Trueseq-stranded-mRNA-libraries-GeoRNA5-E1-NR005_S3_L002_R1_001.fastp-trim.20220908_fastqc.html [2022-09-08 21:20:33,710] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Geoduck-juvenile-ambient-exposure-RNA-EPI-124-8_S63_L008_R1_001.fastp-trim.20220908.fq.gz [2022-09-08 21:20:33,710] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Trueseq-stranded-mRNA-libraries-GeoRNA3-C1-NR012_S2_L001_R2_001.fastp-trim.20220908.fq.gz [2022-09-08 21:20:37,454] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 2.2.4 [2022-09-08 21:20:37,469] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 2.2.4 [2022-09-08 21:20:37,508] multiqc [DEBUG ] No samples found: custom_content [2022-09-08 21:20:37,544] multiqc [DEBUG ] No samples found: conpair [2022-09-08 21:20:37,571] multiqc [DEBUG ] No samples found: peddy [2022-09-08 21:20:37,617] multiqc [DEBUG ] No samples found: methylQA [2022-09-08 21:20:37,651] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-09-08 21:20:37,740] multiqc [DEBUG ] No samples found: qualimap [2022-09-08 21:20:37,765] multiqc [DEBUG ] No samples found: preseq [2022-09-08 21:20:37,814] multiqc [DEBUG ] No samples found: quast [2022-09-08 21:20:37,878] multiqc [DEBUG ] No samples found: qorts [2022-09-08 21:20:37,902] multiqc [DEBUG ] No samples found: rna_seqc [2022-09-08 21:20:37,954] multiqc [DEBUG ] No samples found: rsem [2022-09-08 21:20:38,057] multiqc [DEBUG ] No samples found: rseqc [2022-09-08 21:20:38,096] multiqc [DEBUG ] No samples found: busco [2022-09-08 21:20:38,151] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-09-08 21:20:38,167] multiqc [DEBUG ] No samples found: disambiguate [2022-09-08 21:20:38,207] multiqc [DEBUG ] No samples found: supernova [2022-09-08 21:20:38,282] multiqc [DEBUG ] No samples found: deeptools [2022-09-08 21:20:38,326] multiqc [DEBUG ] No samples found: sargasso [2022-09-08 21:20:38,357] multiqc [DEBUG ] No samples found: verifybamid [2022-09-08 21:20:38,381] multiqc [DEBUG ] No samples found: mirtrace [2022-09-08 21:20:38,425] multiqc [DEBUG ] No samples found: happy [2022-09-08 21:20:38,455] multiqc [DEBUG ] No samples found: homer [2022-09-08 21:20:38,487] multiqc [DEBUG ] No samples found: macs2 [2022-09-08 21:20:38,500] multiqc [DEBUG ] No samples found: theta2 [2022-09-08 21:20:38,512] multiqc [DEBUG ] No samples found: snpeff [2022-09-08 21:20:38,575] multiqc [DEBUG ] No samples found: gatk [2022-09-08 21:20:38,596] multiqc [DEBUG ] No samples found: htseq [2022-09-08 21:20:38,618] multiqc [DEBUG ] No samples found: bcftools [2022-09-08 21:20:38,628] multiqc [DEBUG ] No samples found: featureCounts [2022-09-08 21:20:38,638] multiqc [DEBUG ] No samples found: fgbio [2022-09-08 21:20:38,646] multiqc [DEBUG ] No samples found: dedup [2022-09-08 21:20:38,665] multiqc [DEBUG ] No samples found: damageprofiler [2022-09-08 21:20:38,810] multiqc [DEBUG ] No samples found: biobambam2 [2022-09-08 21:20:38,822] multiqc [DEBUG ] No samples found: mtnucratio [2022-09-08 21:20:38,829] multiqc [DEBUG ] No samples found: picard [2022-09-08 21:20:38,853] multiqc [DEBUG ] No samples found: prokka [2022-09-08 21:20:38,884] multiqc [DEBUG ] No samples found: samblaster [2022-09-08 21:20:38,946] multiqc [DEBUG ] No samples found: samtools [2022-09-08 21:20:38,962] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-09-08 21:20:38,972] multiqc [DEBUG ] No samples found: bamtools [2022-09-08 21:20:38,980] multiqc [DEBUG ] No samples found: jellyfish [2022-09-08 21:20:38,992] multiqc [DEBUG ] No samples found: vcftools [2022-09-08 21:20:39,033] multiqc [DEBUG ] No samples found: longranger [2022-09-08 21:20:39,085] multiqc [DEBUG ] No samples found: stacks [2022-09-08 21:20:39,128] multiqc [DEBUG ] No samples found: bbmap [2022-09-08 21:20:39,152] multiqc [DEBUG ] No samples found: bismark [2022-09-08 21:20:39,173] multiqc [DEBUG ] No samples found: biscuit [2022-09-08 21:20:39,196] multiqc [DEBUG ] No samples found: hicexplorer [2022-09-08 21:20:39,213] multiqc [DEBUG ] No samples found: hicup [2022-09-08 21:20:39,247] multiqc [DEBUG ] No samples found: hicpro [2022-09-08 21:20:39,259] multiqc [DEBUG ] No samples found: salmon [2022-09-08 21:20:39,272] multiqc [DEBUG ] No samples found: kallisto [2022-09-08 21:20:39,296] multiqc [DEBUG ] No samples found: slamdunk [2022-09-08 21:20:39,324] multiqc [DEBUG ] No samples found: star [2022-09-08 21:20:39,341] multiqc [DEBUG ] No samples found: hisat2 [2022-09-08 21:20:39,367] multiqc [DEBUG ] No samples found: tophat [2022-09-08 21:20:39,375] multiqc [DEBUG ] No samples found: bowtie2 [2022-09-08 21:20:39,383] multiqc [DEBUG ] No samples found: bowtie1 [2022-09-08 21:20:39,403] multiqc [DEBUG ] No samples found: kat [2022-09-08 21:20:39,410] multiqc [DEBUG ] No samples found: leehom [2022-09-08 21:20:39,435] multiqc [DEBUG ] No samples found: adapterRemoval [2022-09-08 21:20:39,442] multiqc [DEBUG ] No samples found: clipandmerge [2022-09-08 21:20:39,474] multiqc [DEBUG ] No samples found: cutadapt [2022-09-08 21:20:39,481] multiqc [DEBUG ] No samples found: flexbar [2022-09-08 21:20:39,514] multiqc [DEBUG ] No samples found: trimmomatic [2022-09-08 21:20:39,535] multiqc [DEBUG ] No samples found: skewer [2022-09-08 21:20:39,542] multiqc [DEBUG ] No samples found: sortmerna [2022-09-08 21:20:39,549] multiqc [DEBUG ] No samples found: biobloomtools [2022-09-08 21:20:39,570] multiqc [DEBUG ] No samples found: fastq_screen [2022-09-08 21:20:39,592] multiqc [DEBUG ] No samples found: afterqc [2022-09-08 21:20:39,751] multiqc.modules.fastp.fastp [DEBUG ] No insert size plot data: Geoduck-heart-RNA-1_S2_L001_R1_001.fastp-trim.20220908.report.json [2022-09-08 21:20:39,802] multiqc.modules.fastp.fastp [DEBUG ] No insert size plot data: Geoduck-juvenile-OA-exposure-RNA-EPI-116-7_S53_L007_R1_001.fastp-trim.20220908.report.json [2022-09-08 21:20:39,851] multiqc.modules.fastp.fastp [DEBUG ] No insert size plot data: Geoduck-larvae-day5-RNA-EPI-99-8_S64_L008_R1_001.fastp-trim.20220908.report.json [2022-09-08 21:20:39,915] multiqc.modules.fastp.fastp [DEBUG ] No insert size plot data: Geoduck-juvenile-ambient-exposure-RNA-EPI-123-5_S38_L005_R1_001.fastp-trim.20220908.report.json [2022-09-08 21:20:40,132] multiqc.modules.fastp.fastp [DEBUG ] No insert size plot data: Geoduck-gonad-RNA-7_S49_L007_R1_001.fastp-trim.20220908.report.json [2022-09-08 21:20:40,158] multiqc.modules.fastp.fastp [DEBUG ] No insert size plot data: Geoduck-gonad-RNA-6_S41_L006_R1_001.fastp-trim.20220908.report.json [2022-09-08 21:20:40,204] multiqc.modules.fastp.fastp [DEBUG ] No insert size plot data: Geoduck-heart-RNA-6_S42_L006_R1_001.fastp-trim.20220908.report.json [2022-09-08 21:20:40,268] multiqc.modules.fastp.fastp [DEBUG ] No insert size plot data: Geoduck-ctenidia-RNA-8_S59_L008_R1_001.fastp-trim.20220908.report.json [2022-09-08 21:20:40,372] multiqc.modules.fastp.fastp [DEBUG ] No insert size plot data: Geoduck-juvenile-OA-exposure-RNA-EPI-115-1_S4_L001_R1_001.fastp-trim.20220908.report.json [2022-09-08 21:20:40,390] multiqc.modules.fastp.fastp [DEBUG ] No insert size plot data: Geoduck-juvenile-OA-exposure-RNA-EPI-115-6_S44_L006_R1_001.fastp-trim.20220908.report.json [2022-09-08 21:20:40,429] multiqc.modules.fastp.fastp [DEBUG ] No insert size plot data: Geoduck-juvenile-OA-exposure-RNA-EPI-116-5_S37_L005_R1_001.fastp-trim.20220908.report.json [2022-09-08 21:20:40,508] multiqc.modules.fastp.fastp [DEBUG ] No insert size plot data: Geoduck-juvenile-ambient-exposure-RNA-EPI-123-4_S30_L004_R1_001.fastp-trim.20220908.report.json [2022-09-08 21:20:40,564] multiqc.modules.fastp.fastp [DEBUG ] No insert size plot data: Geoduck-larvae-day5-RNA-EPI-99-3_S24_L003_R1_001.fastp-trim.20220908.report.json [2022-09-08 21:20:40,587] multiqc.modules.fastp.fastp [DEBUG ] No insert size plot data: Geoduck-ctenidia-RNA-2_S11_L002_R1_001.fastp-trim.20220908.report.json [2022-09-08 21:20:40,645] multiqc.modules.fastp.fastp [DEBUG ] No insert size plot data: Geoduck-juvenile-OA-exposure-RNA-EPI-116-6_S45_L006_R1_001.fastp-trim.20220908.report.json [2022-09-08 21:20:40,744] multiqc.modules.fastp.fastp [DEBUG ] No insert size plot data: Geoduck-juvenile-ambient-exposure-RNA-EPI-123-6_S46_L006_R1_001.fastp-trim.20220908.report.json [2022-09-08 21:20:40,859] multiqc.modules.fastp.fastp [DEBUG ] No insert size plot data: Geoduck-juvenile-ambient-exposure-RNA-EPI-124-7_S55_L007_R1_001.fastp-trim.20220908.report.json [2022-09-08 21:20:40,869] multiqc.modules.fastp.fastp [DEBUG ] No insert size plot data: Geoduck-juvenile-ambient-exposure-RNA-EPI-124-3_S23_L003_R1_001.fastp-trim.20220908.report.json [2022-09-08 21:20:40,895] multiqc.modules.fastp.fastp [DEBUG ] No insert size plot data: Geoduck-gonad-RNA-5_S33_L005_R1_001.fastp-trim.20220908.report.json [2022-09-08 21:20:40,986] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: Trueseq-stranded-mRNA-libraries-GeoRNA8-H1-NR021_S5_L001_R1_001.fastp-trim.20220908.report.json [2022-09-08 21:20:41,186] multiqc.modules.fastp.fastp [DEBUG ] No insert size plot data: Geoduck-ctenidia-RNA-3_S19_L003_R1_001.fastp-trim.20220908.report.json [2022-09-08 21:20:41,265] multiqc.modules.fastp.fastp [INFO ] Found 76 reports [2022-09-08 21:20:43,270] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-heart-RNA-5_S34_L005_R2_001 [2022-09-08 21:20:43,695] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-juvenile-OA-exposure-RNA-EPI-116-1_S5_L001_R1_001 [2022-09-08 21:20:43,761] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-juvenile-OA-exposure-RNA-EPI-116-2_S13_L002_R2_001_fastqc.zip' as already parsed 'Geoduck-juvenile-OA-exposure-RNA-EPI-116-2_S13_L002_R2_001' [2022-09-08 21:20:44,136] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-gonad-RNA-8_S57_L008_R2_001 [2022-09-08 21:20:44,235] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-juvenile-OA-exposure-RNA-EPI-116-7_S53_L007_R1_001 [2022-09-08 21:20:44,393] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-heart-RNA-2_S10_L002_R2_001 [2022-09-08 21:20:44,411] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-gonad-RNA-2_S9_L002_R2_001 [2022-09-08 21:20:44,424] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Trueseq-stranded-mRNA-libraries-GeoRNA1-A1-NR006_S1_L001_R2_001_fastqc.zip' as already parsed 'Trueseq-stranded-mRNA-libraries-GeoRNA1-A1-NR006_S1_L001_R2_001' [2022-09-08 21:20:44,642] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Trueseq-stranded-mRNA-libraries-GeoRNA3-C1-NR012_S2_L002_R2_001_fastqc.zip' as already parsed 'Trueseq-stranded-mRNA-libraries-GeoRNA3-C1-NR012_S2_L002_R2_001' [2022-09-08 21:20:45,008] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-juvenile-OA-exposure-RNA-EPI-116-3_S21_L003_R2_001 [2022-09-08 21:20:45,028] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-juvenile-ambient-exposure-RNA-EPI-124-4_S31_L004_R1_001 [2022-09-08 21:20:45,038] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-heart-RNA-8_S58_L008_R1_001 [2022-09-08 21:20:45,061] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Trueseq-stranded-mRNA-libraries-GeoRNA8-H1-NR021_S5_L002_R1_001 [2022-09-08 21:20:45,418] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-ctenidia-RNA-2_S11_L002_R2_001 [2022-09-08 21:20:45,489] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-juvenile-OA-exposure-RNA-EPI-116-6_S45_L006_R1_001_fastqc.zip' as already parsed 'Geoduck-juvenile-OA-exposure-RNA-EPI-116-6_S45_L006_R1_001' [2022-09-08 21:20:45,970] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-larvae-day5-RNA-EPI-99-2_S16_L002_R1_001 [2022-09-08 21:20:46,053] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-gonad-RNA-8_S57_L008_R1_001 [2022-09-08 21:20:46,075] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Trueseq-stranded-mRNA-libraries-GeoRNA3-C1-NR012_S2_L001_R2_001 [2022-09-08 21:20:46,214] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-juvenile-ambient-exposure-RNA-EPI-124-3_S23_L003_R1_001_fastqc.zip' as already parsed 'Geoduck-juvenile-ambient-exposure-RNA-EPI-124-3_S23_L003_R1_001' [2022-09-08 21:20:46,360] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-gonad-RNA-3_S17_L003_R2_001_fastqc.zip' as already parsed 'Geoduck-gonad-RNA-3_S17_L003_R2_001' [2022-09-08 21:20:46,362] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-juvenile-OA-exposure-RNA-EPI-116-6_S45_L006_R2_001 [2022-09-08 21:20:46,790] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-gonad-RNA-2_S9_L002_R1_001_fastqc.zip' as already parsed 'Geoduck-gonad-RNA-2_S9_L002_R1_001' [2022-09-08 21:20:46,888] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Trueseq-stranded-mRNA-libraries-GeoRNA5-E1-NR005_S3_L002_R2_001_fastqc.zip' as already parsed 'Trueseq-stranded-mRNA-libraries-GeoRNA5-E1-NR005_S3_L002_R2_001' [2022-09-08 21:20:46,891] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-juvenile-OA-exposure-RNA-EPI-115-6_S44_L006_R2_001 [2022-09-08 21:20:46,910] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-ctenidia-RNA-3_S19_L003_R1_001 [2022-09-08 21:20:47,073] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-juvenile-ambient-exposure-RNA-EPI-124-7_S55_L007_R2_001_fastqc.zip' as already parsed 'Geoduck-juvenile-ambient-exposure-RNA-EPI-124-7_S55_L007_R2_001' [2022-09-08 21:20:47,097] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-larvae-day5-RNA-EPI-99-5_S40_L005_R2_001_fastqc.zip' as already parsed 'Geoduck-larvae-day5-RNA-EPI-99-5_S40_L005_R2_001' [2022-09-08 21:20:47,117] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-juvenile-OA-exposure-RNA-EPI-115-8_S60_L008_R2_001 [2022-09-08 21:20:47,224] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-juvenile-ambient-exposure-RNA-EPI-123-6_S46_L006_R2_001_fastqc.zip' as already parsed 'Geoduck-juvenile-ambient-exposure-RNA-EPI-123-6_S46_L006_R2_001' [2022-09-08 21:20:47,228] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-ctenidia-RNA-4_S27_L004_R2_001 [2022-09-08 21:20:47,429] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-juvenile-OA-exposure-RNA-EPI-115-5_S36_L005_R1_001_fastqc.zip' as already parsed 'Geoduck-juvenile-OA-exposure-RNA-EPI-115-5_S36_L005_R1_001' [2022-09-08 21:20:47,431] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-ctenidia-RNA-5_S35_L005_R2_001 [2022-09-08 21:20:47,518] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-juvenile-ambient-exposure-RNA-EPI-124-7_S55_L007_R1_001_fastqc.zip' as already parsed 'Geoduck-juvenile-ambient-exposure-RNA-EPI-124-7_S55_L007_R1_001' [2022-09-08 21:20:47,626] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-heart-RNA-2_S10_L002_R1_001 [2022-09-08 21:20:47,935] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-gonad-RNA-6_S41_L006_R1_001 [2022-09-08 21:20:47,943] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-juvenile-ambient-exposure-RNA-EPI-123-4_S30_L004_R1_001 [2022-09-08 21:20:48,040] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-juvenile-OA-exposure-RNA-EPI-116-4_S29_L004_R2_001 [2022-09-08 21:20:48,247] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-juvenile-ambient-exposure-RNA-EPI-124-8_S63_L008_R1_001_fastqc.zip' as already parsed 'Geoduck-juvenile-ambient-exposure-RNA-EPI-124-8_S63_L008_R1_001' [2022-09-08 21:20:48,249] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geo_Pool_M_CTTGTA_L006_R1_001 [2022-09-08 21:20:48,418] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Trueseq-stranded-mRNA-libraries-GeoRNA3-C1-NR012_S2_L001_R1_001 [2022-09-08 21:20:48,608] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-ctenidia-RNA-5_S35_L005_R1_001 [2022-09-08 21:20:48,782] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geo_Pool_F_GGCTAC_L006_R1_001_fastqc.zip' as already parsed 'Geo_Pool_F_GGCTAC_L006_R1_001' [2022-09-08 21:20:48,782] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-gonad-RNA-5_S33_L005_R2_001_fastqc.zip' as already parsed 'Geoduck-gonad-RNA-5_S33_L005_R2_001' [2022-09-08 21:20:48,783] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-gonad-RNA-4_S25_L004_R1_001 [2022-09-08 21:20:48,870] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-ctenidia-RNA-2_S11_L002_R1_001_fastqc.zip' as already parsed 'Geoduck-ctenidia-RNA-2_S11_L002_R1_001' [2022-09-08 21:20:48,871] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-gonad-RNA-4_S25_L004_R2_001 [2022-09-08 21:20:48,881] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-juvenile-ambient-exposure-RNA-EPI-123-1_S6_L001_R1_001 [2022-09-08 21:20:48,996] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-larvae-day5-RNA-EPI-99-2_S16_L002_R2_001_fastqc.zip' as already parsed 'Geoduck-larvae-day5-RNA-EPI-99-2_S16_L002_R2_001' [2022-09-08 21:20:48,997] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-juvenile-ambient-exposure-RNA-EPI-124-2_S15_L002_R1_001_fastqc.zip' as already parsed 'Geoduck-juvenile-ambient-exposure-RNA-EPI-124-2_S15_L002_R1_001' [2022-09-08 21:20:48,997] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-juvenile-ambient-exposure-RNA-EPI-123-5_S38_L005_R2_001_fastqc.zip' as already parsed 'Geoduck-juvenile-ambient-exposure-RNA-EPI-123-5_S38_L005_R2_001' [2022-09-08 21:20:48,997] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-larvae-day5-RNA-EPI-99-5_S40_L005_R1_001_fastqc.zip' as already parsed 'Geoduck-larvae-day5-RNA-EPI-99-5_S40_L005_R1_001' [2022-09-08 21:20:48,997] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-heart-RNA-7_S50_L007_R1_001_fastqc.zip' as already parsed 'Geoduck-heart-RNA-7_S50_L007_R1_001' [2022-09-08 21:20:48,997] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-juvenile-OA-exposure-RNA-EPI-115-1_S4_L001_R2_001_fastqc.zip' as already parsed 'Geoduck-juvenile-OA-exposure-RNA-EPI-115-1_S4_L001_R2_001' [2022-09-08 21:20:49,056] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-heart-RNA-8_S58_L008_R2_001_fastqc.zip' as already parsed 'Geoduck-heart-RNA-8_S58_L008_R2_001' [2022-09-08 21:20:49,056] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-juvenile-ambient-exposure-RNA-EPI-124-5_S39_L005_R2_001_fastqc.zip' as already parsed 'Geoduck-juvenile-ambient-exposure-RNA-EPI-124-5_S39_L005_R2_001' [2022-09-08 21:20:49,316] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-ctenidia-RNA-1_S3_L001_R1_001 [2022-09-08 21:20:49,483] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-juvenile-ambient-exposure-RNA-EPI-123-6_S46_L006_R1_001 [2022-09-08 21:20:49,507] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-juvenile-OA-exposure-RNA-EPI-115-8_S60_L008_R1_001_fastqc.zip' as already parsed 'Geoduck-juvenile-OA-exposure-RNA-EPI-115-8_S60_L008_R1_001' [2022-09-08 21:20:49,769] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-heart-RNA-1_S2_L001_R1_001_fastqc.zip' as already parsed 'Geoduck-heart-RNA-1_S2_L001_R1_001' [2022-09-08 21:20:49,872] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-larvae-day5-RNA-EPI-99-6_S48_L006_R1_001_fastqc.zip' as already parsed 'Geoduck-larvae-day5-RNA-EPI-99-6_S48_L006_R1_001' [2022-09-08 21:20:49,952] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-heart-RNA-1_S2_L001_R2_001 [2022-09-08 21:20:49,980] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-gonad-RNA-5_S33_L005_R1_001 [2022-09-08 21:20:50,360] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-larvae-day5-RNA-EPI-99-3_S24_L003_R1_001 [2022-09-08 21:20:50,381] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-juvenile-OA-exposure-RNA-EPI-115-5_S36_L005_R2_001_fastqc.zip' as already parsed 'Geoduck-juvenile-OA-exposure-RNA-EPI-115-5_S36_L005_R2_001' [2022-09-08 21:20:50,409] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-juvenile-ambient-exposure-RNA-EPI-124-8_S63_L008_R2_001_fastqc.zip' as already parsed 'Geoduck-juvenile-ambient-exposure-RNA-EPI-124-8_S63_L008_R2_001' [2022-09-08 21:20:50,458] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-ctenidia-RNA-7_S51_L007_R1_001_fastqc.zip' as already parsed 'Geoduck-ctenidia-RNA-7_S51_L007_R1_001' [2022-09-08 21:20:50,459] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-juvenile-OA-exposure-RNA-EPI-115-7_S52_L007_R2_001 [2022-09-08 21:20:50,481] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-juvenile-OA-exposure-RNA-EPI-115-2_S12_L002_R1_001 [2022-09-08 21:20:50,721] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-juvenile-OA-exposure-RNA-EPI-115-7_S52_L007_R1_001 [2022-09-08 21:20:50,738] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-juvenile-ambient-exposure-RNA-EPI-124-3_S23_L003_R2_001_fastqc.zip' as already parsed 'Geoduck-juvenile-ambient-exposure-RNA-EPI-124-3_S23_L003_R2_001' [2022-09-08 21:20:50,741] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-juvenile-ambient-exposure-RNA-EPI-123-7_S54_L007_R1_001 [2022-09-08 21:20:50,818] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-larvae-day5-RNA-EPI-99-6_S48_L006_R2_001 [2022-09-08 21:20:50,823] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-gonad-RNA-1_S1_L001_R1_001 [2022-09-08 21:20:50,850] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-juvenile-OA-exposure-RNA-EPI-116-5_S37_L005_R1_001_fastqc.zip' as already parsed 'Geoduck-juvenile-OA-exposure-RNA-EPI-116-5_S37_L005_R1_001' [2022-09-08 21:20:50,850] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-juvenile-ambient-exposure-RNA-EPI-123-5_S38_L005_R1_001_fastqc.zip' as already parsed 'Geoduck-juvenile-ambient-exposure-RNA-EPI-123-5_S38_L005_R1_001' [2022-09-08 21:20:51,032] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-ctenidia-RNA-4_S27_L004_R1_001 [2022-09-08 21:20:51,062] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-juvenile-OA-exposure-RNA-EPI-115-4_S28_L004_R2_001_fastqc.zip' as already parsed 'Geoduck-juvenile-OA-exposure-RNA-EPI-115-4_S28_L004_R2_001' [2022-09-08 21:20:51,065] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geo_Pool_F_GGCTAC_L006_R2_001 [2022-09-08 21:20:51,187] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-heart-RNA-4_S26_L004_R1_001 [2022-09-08 21:20:51,213] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-gonad-RNA-1_S1_L001_R2_001_fastqc.zip' as already parsed 'Geoduck-gonad-RNA-1_S1_L001_R2_001' [2022-09-08 21:20:51,213] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-juvenile-ambient-exposure-RNA-EPI-124-5_S39_L005_R1_001_fastqc.zip' as already parsed 'Geoduck-juvenile-ambient-exposure-RNA-EPI-124-5_S39_L005_R1_001' [2022-09-08 21:20:51,215] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-juvenile-ambient-exposure-RNA-EPI-124-1_S7_L001_R2_001 [2022-09-08 21:20:51,239] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-gonad-RNA-6_S41_L006_R2_001 [2022-09-08 21:20:51,646] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Trueseq-stranded-mRNA-libraries-GeoRNA8-H1-NR021_S5_L001_R2_001 [2022-09-08 21:20:51,652] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geo_Pool_M_CTTGTA_L006_R2_001 [2022-09-08 21:20:51,688] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Trueseq-stranded-mRNA-libraries-GeoRNA7-G1-NR019_S4_L001_R1_001_fastqc.zip' as already parsed 'Trueseq-stranded-mRNA-libraries-GeoRNA7-G1-NR019_S4_L001_R1_001' [2022-09-08 21:20:51,878] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-juvenile-OA-exposure-RNA-EPI-115-4_S28_L004_R1_001 [2022-09-08 21:20:51,908] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-juvenile-ambient-exposure-RNA-EPI-123-2_S14_L002_R2_001_fastqc.zip' as already parsed 'Geoduck-juvenile-ambient-exposure-RNA-EPI-123-2_S14_L002_R2_001' [2022-09-08 21:20:51,912] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-juvenile-OA-exposure-RNA-EPI-115-1_S4_L001_R1_001 [2022-09-08 21:20:51,938] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-juvenile-ambient-exposure-RNA-EPI-124-1_S7_L001_R1_001_fastqc.zip' as already parsed 'Geoduck-juvenile-ambient-exposure-RNA-EPI-124-1_S7_L001_R1_001' [2022-09-08 21:20:51,961] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-heart-RNA-3_S18_L003_R1_001_fastqc.zip' as already parsed 'Geoduck-heart-RNA-3_S18_L003_R1_001' [2022-09-08 21:20:52,060] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Trueseq-stranded-mRNA-libraries-GeoRNA5-E1-NR005_S3_L002_R1_001 [2022-09-08 21:20:52,210] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-larvae-day5-RNA-EPI-99-4_S32_L004_R1_001 [2022-09-08 21:20:52,228] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-heart-RNA-4_S26_L004_R2_001 [2022-09-08 21:20:52,372] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-juvenile-OA-exposure-RNA-EPI-115-2_S12_L002_R2_001 [2022-09-08 21:20:52,391] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-ctenidia-RNA-6_S43_L006_R2_001_fastqc.zip' as already parsed 'Geoduck-ctenidia-RNA-6_S43_L006_R2_001' [2022-09-08 21:20:52,391] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Trueseq-stranded-mRNA-libraries-GeoRNA8-H1-NR021_S5_L002_R2_001_fastqc.zip' as already parsed 'Trueseq-stranded-mRNA-libraries-GeoRNA8-H1-NR021_S5_L002_R2_001' [2022-09-08 21:20:52,395] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-ctenidia-RNA-8_S59_L008_R1_001 [2022-09-08 21:20:52,419] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-juvenile-ambient-exposure-RNA-EPI-124-4_S31_L004_R2_001 [2022-09-08 21:20:52,533] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-juvenile-OA-exposure-RNA-EPI-116-2_S13_L002_R1_001 [2022-09-08 21:20:52,556] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-juvenile-OA-exposure-RNA-EPI-116-5_S37_L005_R2_001 [2022-09-08 21:20:52,583] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-juvenile-ambient-exposure-RNA-EPI-123-3_S22_L003_R1_001 [2022-09-08 21:20:52,605] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-juvenile-OA-exposure-RNA-EPI-115-3_S20_L003_R1_001_fastqc.zip' as already parsed 'Geoduck-juvenile-OA-exposure-RNA-EPI-115-3_S20_L003_R1_001' [2022-09-08 21:20:52,607] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-gonad-RNA-7_S49_L007_R2_001 [2022-09-08 21:20:52,625] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-ctenidia-RNA-1_S3_L001_R2_001_fastqc.zip' as already parsed 'Geoduck-ctenidia-RNA-1_S3_L001_R2_001' [2022-09-08 21:20:52,625] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-gonad-RNA-3_S17_L003_R1_001_fastqc.zip' as already parsed 'Geoduck-gonad-RNA-3_S17_L003_R1_001' [2022-09-08 21:20:52,628] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-heart-RNA-6_S42_L006_R1_001 [2022-09-08 21:20:52,647] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-ctenidia-RNA-3_S19_L003_R2_001_fastqc.zip' as already parsed 'Geoduck-ctenidia-RNA-3_S19_L003_R2_001' [2022-09-08 21:20:52,649] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-juvenile-ambient-exposure-RNA-EPI-123-7_S54_L007_R2_001 [2022-09-08 21:20:52,665] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-juvenile-OA-exposure-RNA-EPI-116-3_S21_L003_R1_001_fastqc.zip' as already parsed 'Geoduck-juvenile-OA-exposure-RNA-EPI-116-3_S21_L003_R1_001' [2022-09-08 21:20:52,667] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-juvenile-ambient-exposure-RNA-EPI-123-2_S14_L002_R1_001 [2022-09-08 21:20:52,787] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-juvenile-ambient-exposure-RNA-EPI-124-6_S47_L006_R1_001 [2022-09-08 21:20:52,798] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-heart-RNA-7_S50_L007_R2_001_fastqc.zip' as already parsed 'Geoduck-heart-RNA-7_S50_L007_R2_001' [2022-09-08 21:20:52,864] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-larvae-day5-RNA-EPI-99-7_S56_L007_R1_001 [2022-09-08 21:20:52,873] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Trueseq-stranded-mRNA-libraries-GeoRNA7-G1-NR019_S4_L001_R2_001_fastqc.zip' as already parsed 'Trueseq-stranded-mRNA-libraries-GeoRNA7-G1-NR019_S4_L001_R2_001' [2022-09-08 21:20:52,881] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Trueseq-stranded-mRNA-libraries-GeoRNA7-G1-NR019_S4_L002_R1_001 [2022-09-08 21:20:52,997] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-larvae-day5-RNA-EPI-99-8_S64_L008_R2_001_fastqc.zip' as already parsed 'Geoduck-larvae-day5-RNA-EPI-99-8_S64_L008_R2_001' [2022-09-08 21:20:52,997] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-juvenile-OA-exposure-RNA-EPI-115-3_S20_L003_R2_001_fastqc.zip' as already parsed 'Geoduck-juvenile-OA-exposure-RNA-EPI-115-3_S20_L003_R2_001' [2022-09-08 21:20:52,999] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-juvenile-OA-exposure-RNA-EPI-115-6_S44_L006_R1_001 [2022-09-08 21:20:53,334] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-juvenile-OA-exposure-RNA-EPI-116-1_S5_L001_R2_001_fastqc.zip' as already parsed 'Geoduck-juvenile-OA-exposure-RNA-EPI-116-1_S5_L001_R2_001' [2022-09-08 21:20:53,335] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-juvenile-OA-exposure-RNA-EPI-116-7_S53_L007_R2_001 [2022-09-08 21:20:53,353] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-juvenile-ambient-exposure-RNA-EPI-123-1_S6_L001_R2_001 [2022-09-08 21:20:53,366] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Trueseq-stranded-mRNA-libraries-GeoRNA3-C1-NR012_S2_L002_R1_001_fastqc.zip' as already parsed 'Trueseq-stranded-mRNA-libraries-GeoRNA3-C1-NR012_S2_L002_R1_001' [2022-09-08 21:20:53,371] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Trueseq-stranded-mRNA-libraries-GeoRNA1-A1-NR006_S1_L001_R1_001 [2022-09-08 21:20:53,475] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Trueseq-stranded-mRNA-libraries-GeoRNA1-A1-NR006_S1_L002_R2_001_fastqc.zip' as already parsed 'Trueseq-stranded-mRNA-libraries-GeoRNA1-A1-NR006_S1_L002_R2_001' [2022-09-08 21:20:53,477] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-heart-RNA-3_S18_L003_R2_001 [2022-09-08 21:20:53,494] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-larvae-day5-RNA-EPI-99-3_S24_L003_R2_001 [2022-09-08 21:20:53,506] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-ctenidia-RNA-6_S43_L006_R1_001_fastqc.zip' as already parsed 'Geoduck-ctenidia-RNA-6_S43_L006_R1_001' [2022-09-08 21:20:53,506] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-larvae-day5-RNA-EPI-99-1_S8_L001_R1_001_fastqc.zip' as already parsed 'Geoduck-larvae-day5-RNA-EPI-99-1_S8_L001_R1_001' [2022-09-08 21:20:53,506] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-larvae-day5-RNA-EPI-99-1_S8_L001_R2_001_fastqc.zip' as already parsed 'Geoduck-larvae-day5-RNA-EPI-99-1_S8_L001_R2_001' [2022-09-08 21:20:53,510] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-juvenile-OA-exposure-RNA-EPI-116-4_S29_L004_R1_001 [2022-09-08 21:20:53,527] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-gonad-RNA-7_S49_L007_R1_001_fastqc.zip' as already parsed 'Geoduck-gonad-RNA-7_S49_L007_R1_001' [2022-09-08 21:20:53,528] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-juvenile-ambient-exposure-RNA-EPI-123-8_S62_L008_R2_001_fastqc.zip' as already parsed 'Geoduck-juvenile-ambient-exposure-RNA-EPI-123-8_S62_L008_R2_001' [2022-09-08 21:20:53,528] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-larvae-day5-RNA-EPI-99-7_S56_L007_R2_001_fastqc.zip' as already parsed 'Geoduck-larvae-day5-RNA-EPI-99-7_S56_L007_R2_001' [2022-09-08 21:20:53,529] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-juvenile-OA-exposure-RNA-EPI-116-8_S61_L008_R2_001 [2022-09-08 21:20:53,550] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-juvenile-ambient-exposure-RNA-EPI-123-3_S22_L003_R2_001 [2022-09-08 21:20:53,570] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-juvenile-ambient-exposure-RNA-EPI-123-4_S30_L004_R2_001 [2022-09-08 21:20:53,586] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-larvae-day5-RNA-EPI-99-8_S64_L008_R1_001 [2022-09-08 21:20:53,598] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-ctenidia-RNA-8_S59_L008_R2_001 [2022-09-08 21:20:53,615] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-ctenidia-RNA-7_S51_L007_R2_001_fastqc.zip' as already parsed 'Geoduck-ctenidia-RNA-7_S51_L007_R2_001' [2022-09-08 21:20:53,620] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Trueseq-stranded-mRNA-libraries-GeoRNA5-E1-NR005_S3_L001_R2_001 [2022-09-08 21:20:53,726] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Trueseq-stranded-mRNA-libraries-GeoRNA7-G1-NR019_S4_L002_R2_001 [2022-09-08 21:20:53,827] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Trueseq-stranded-mRNA-libraries-GeoRNA5-E1-NR005_S3_L001_R1_001_fastqc.zip' as already parsed 'Trueseq-stranded-mRNA-libraries-GeoRNA5-E1-NR005_S3_L001_R1_001' [2022-09-08 21:20:53,830] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-juvenile-ambient-exposure-RNA-EPI-123-8_S62_L008_R1_001 [2022-09-08 21:20:53,844] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Trueseq-stranded-mRNA-libraries-GeoRNA1-A1-NR006_S1_L002_R1_001 [2022-09-08 21:20:53,945] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-juvenile-ambient-exposure-RNA-EPI-124-6_S47_L006_R2_001 [2022-09-08 21:20:53,973] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-heart-RNA-6_S42_L006_R2_001 [2022-09-08 21:20:53,992] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-heart-RNA-5_S34_L005_R1_001 [2022-09-08 21:20:54,010] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Trueseq-stranded-mRNA-libraries-GeoRNA8-H1-NR021_S5_L001_R1_001_fastqc.zip' as already parsed 'Trueseq-stranded-mRNA-libraries-GeoRNA8-H1-NR021_S5_L001_R1_001' [2022-09-08 21:20:54,014] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: Geoduck-juvenile-OA-exposure-RNA-EPI-116-8_S61_L008_R1_001 [2022-09-08 21:20:54,032] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-juvenile-ambient-exposure-RNA-EPI-124-2_S15_L002_R2_001_fastqc.zip' as already parsed 'Geoduck-juvenile-ambient-exposure-RNA-EPI-124-2_S15_L002_R2_001' [2022-09-08 21:20:54,033] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'Geoduck-larvae-day5-RNA-EPI-99-4_S32_L004_R2_001_fastqc.zip' as already parsed 'Geoduck-larvae-day5-RNA-EPI-99-4_S32_L004_R2_001' [2022-09-08 21:20:54,033] multiqc.modules.fastqc.fastqc [INFO ] Found 152 reports [2022-09-08 21:20:54,056] multiqc [ERROR ] Oops! The 'fastqc' MultiQC module broke... Please copy the following traceback and report it at https://github.com/ewels/MultiQC/issues If possible, please include a log file that triggers the error - the last file found was: ./Geoduck-larvae-day5-RNA-EPI-99-4_S32_L004_R2_001_fastqc.zip ============================================================ Module fastqc raised an exception: Traceback (most recent call last): File "/gscratch/srlab/programs/anaconda3/lib/python3.7/site-packages/multiqc/multiqc.py", line 546, in run output = mod() File "/gscratch/srlab/programs/anaconda3/lib/python3.7/site-packages/multiqc/modules/fastqc/fastqc.py", line 94, in __init__ self.fastqc_general_stats() File "/gscratch/srlab/programs/anaconda3/lib/python3.7/site-packages/multiqc/modules/fastqc/fastqc.py", line 204, in fastqc_general_stats 'avg_sequence_length': bs['avg_sequence_length'], KeyError: 'avg_sequence_length' ============================================================ [2022-09-08 21:20:54,220] multiqc [DEBUG ] No samples found: minionqc [2022-09-08 21:20:54,237] multiqc [DEBUG ] No samples found: mosdepth [2022-09-08 21:20:54,252] multiqc [DEBUG ] No samples found: clusterflow [2022-09-08 21:20:54,273] multiqc [DEBUG ] No samples found: bcl2fastq [2022-09-08 21:20:54,296] multiqc [DEBUG ] No samples found: interop [2022-09-08 21:20:54,314] multiqc [DEBUG ] No samples found: flash [2022-09-08 21:20:54,351] multiqc [DEBUG ] No samples found: seqyclean [2022-09-08 21:20:54,470] multiqc [INFO ] Compressing plot data [2022-09-08 21:20:59,179] multiqc [INFO ] Report : multiqc_report.html [2022-09-08 21:20:59,180] multiqc [INFO ] Data : multiqc_data [2022-09-08 21:20:59,182] multiqc [DEBUG ] Moving data file from '/tmp/tmpvgz2jcm3/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/gscratch/scrubbed/samwhite/outputs/20220909-pgen-fastqc-fastp-mutliqc-rnaseq/multiqc_data' [2022-09-08 21:20:59,183] multiqc [DEBUG ] Moving data file from '/tmp/tmpvgz2jcm3/multiqc_data/multiqc_fastp.txt' to '/gscratch/scrubbed/samwhite/outputs/20220909-pgen-fastqc-fastp-mutliqc-rnaseq/multiqc_data' [2022-09-08 21:20:59,184] multiqc [DEBUG ] Moving data file from '/tmp/tmpvgz2jcm3/multiqc_data/multiqc_fastqc.txt' to '/gscratch/scrubbed/samwhite/outputs/20220909-pgen-fastqc-fastp-mutliqc-rnaseq/multiqc_data' [2022-09-08 21:20:59,185] multiqc [DEBUG ] Moving data file from '/tmp/tmpvgz2jcm3/multiqc_data/multiqc_general_stats.txt' to '/gscratch/scrubbed/samwhite/outputs/20220909-pgen-fastqc-fastp-mutliqc-rnaseq/multiqc_data' [2022-09-08 21:20:59,186] multiqc [DEBUG ] Moving data file from '/tmp/tmpvgz2jcm3/multiqc_data/multiqc_sources.txt' to '/gscratch/scrubbed/samwhite/outputs/20220909-pgen-fastqc-fastp-mutliqc-rnaseq/multiqc_data' [2022-09-08 21:20:59,186] multiqc [DEBUG ] Moving data file from '/tmp/tmpvgz2jcm3/multiqc_data/multiqc_data.json' to '/gscratch/scrubbed/samwhite/outputs/20220909-pgen-fastqc-fastp-mutliqc-rnaseq/multiqc_data' [2022-09-08 21:20:59,878] multiqc [INFO ] MultiQC complete