[2022-02-24 12:21:21,160] multiqc [DEBUG ] No MultiQC config found: /gscratch/srlab/programs/anaconda3/lib/python3.7/site-packages/multiqc_config.yaml [2022-02-24 12:21:21,163] multiqc [DEBUG ] Loading config settings from: /usr/lusers/samwhite/.multiqc_config.yaml [2022-02-24 12:21:21,163] multiqc [DEBUG ] New config 'star': {'fn': '*Log.final.out'} [2022-02-24 12:21:21,163] multiqc [DEBUG ] New config 'star/genecounts': {'fn': '*ReadsPerGene.out.tab'} [2022-02-24 12:21:21,163] multiqc [DEBUG ] Added to filename patterns: {'fastp': {'fn': '*report.json'}} [2022-02-24 12:21:21,163] multiqc [DEBUG ] New config 'hisat2': {'contents': 'HISAT2 summary stats:', 'shared': True} [2022-02-24 12:21:21,163] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-02-24 12:21:21,163] multiqc [DEBUG ] Command used: /gscratch/srlab/programs/anaconda3/bin/multiqc . [2022-02-24 12:21:26,443] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2022-02-24 12:21:26,444] multiqc [INFO ] This is MultiQC v1.8 [2022-02-24 12:21:26,445] multiqc [DEBUG ] Command : /gscratch/srlab/programs/anaconda3/bin/multiqc . [2022-02-24 12:21:26,445] multiqc [DEBUG ] Working dir : /gscratch/scrubbed/samwhite/outputs/20220224_cvir_gonad_RNAseq_fastp_trimming [2022-02-24 12:21:26,445] multiqc [INFO ] Template : default [2022-02-24 12:21:26,445] multiqc [DEBUG ] Running Python 3.7.3 (default, Mar 27 2019, 22:11:17) [GCC 7.3.0] [2022-02-24 12:21:26,445] multiqc [INFO ] Searching : /gscratch/scrubbed/samwhite/outputs/20220224_cvir_gonad_RNAseq_fastp_trimming [2022-02-24 12:21:26,446] 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 [2022-02-24 12:21:26,446] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpzdf2wl0b [2022-02-24 12:21:26,987] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S36F_R1.fastp-trim.20bp-5prime.20220224.report.html [2022-02-24 12:21:26,988] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S31M_R2.fastp-trim.20bp-5prime.20220224.fq.gz [2022-02-24 12:21:26,998] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S16F_R2.fastp-trim.20bp-5prime.20220224.fq.gz [2022-02-24 12:21:26,998] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S22F_R1.fastp-trim.20bp-5prime.20220224.fq.gz [2022-02-24 12:21:26,998] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S35F_R2.fastp-trim.20bp-5prime.20220224.fq.gz [2022-02-24 12:21:26,999] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S77F_R1.fastp-trim.20bp-5prime.20220224.report.html [2022-02-24 12:21:26,999] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S13M_R1.fastp-trim.20bp-5prime.20220224.report.html [2022-02-24 12:21:27,023] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: slurm-2573198.out [2022-02-24 12:21:27,026] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: slurm-2573198.out [2022-02-24 12:21:27,083] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S59M_R2.fastp-trim.20bp-5prime.20220224.fq.gz [2022-02-24 12:21:27,084] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S22F_R1.fastp-trim.20bp-5prime.20220224.report.html [2022-02-24 12:21:27,084] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S36F_R1.fastp-trim.20bp-5prime.20220224.fq.gz [2022-02-24 12:21:27,084] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S59M_R1.fastp-trim.20bp-5prime.20220224.fq.gz [2022-02-24 12:21:27,084] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S64M_R1.fastp-trim.20bp-5prime.20220224.report.html [2022-02-24 12:21:27,084] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S9M_R1.fastp-trim.20bp-5prime.20220224.fq.gz [2022-02-24 12:21:27,085] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S13M_R2.fastp-trim.20bp-5prime.20220224.fq.gz [2022-02-24 12:21:27,095] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S3F_R1.fastp-trim.20bp-5prime.20220224.report.html [2022-02-24 12:21:27,096] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S52F_R1.fastp-trim.20bp-5prime.20220224.fq.gz [2022-02-24 12:21:27,096] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S29F_R2.fastp-trim.20bp-5prime.20220224.fq.gz [2022-02-24 12:21:27,096] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S6M_R1.fastp-trim.20bp-5prime.20220224.report.html [2022-02-24 12:21:27,096] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S19F_R2.fastp-trim.20bp-5prime.20220224.fq.gz [2022-02-24 12:21:27,096] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S44F_R1.fastp-trim.20bp-5prime.20220224.fq.gz [2022-02-24 12:21:27,096] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S77F_R2.fastp-trim.20bp-5prime.20220224.fq.gz [2022-02-24 12:21:27,097] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S52F_R2.fastp-trim.20bp-5prime.20220224.fq.gz [2022-02-24 12:21:27,097] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S64M_R2.fastp-trim.20bp-5prime.20220224.fq.gz [2022-02-24 12:21:27,097] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S39F_R1.fastp-trim.20bp-5prime.20220224.fq.gz [2022-02-24 12:21:27,097] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S36F_R2.fastp-trim.20bp-5prime.20220224.fq.gz [2022-02-24 12:21:27,097] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S76F_R1.fastp-trim.20bp-5prime.20220224.report.html [2022-02-24 12:21:27,098] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S39F_R1.fastp-trim.20bp-5prime.20220224.report.html [2022-02-24 12:21:27,098] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S41F_R1.fastp-trim.20bp-5prime.20220224.fq.gz [2022-02-24 12:21:27,098] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S9M_R1.fastp-trim.20bp-5prime.20220224.report.html [2022-02-24 12:21:27,133] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 20220224_cvir_gonad_RNAseq_fastp_trimming.sh [2022-02-24 12:21:27,135] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 20220224_cvir_gonad_RNAseq_fastp_trimming.sh [2022-02-24 12:21:27,144] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S76F_R2.fastp-trim.20bp-5prime.20220224.fq.gz [2022-02-24 12:21:27,145] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S23M_R1.fastp-trim.20bp-5prime.20220224.fq.gz [2022-02-24 12:21:27,145] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S50F_R1.fastp-trim.20bp-5prime.20220224.fq.gz [2022-02-24 12:21:27,145] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S3F_R1.fastp-trim.20bp-5prime.20220224.fq.gz [2022-02-24 12:21:27,145] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S44F_R2.fastp-trim.20bp-5prime.20220224.fq.gz [2022-02-24 12:21:27,145] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S53F_R2.fastp-trim.20bp-5prime.20220224.fq.gz [2022-02-24 12:21:27,145] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S7M_R1.fastp-trim.20bp-5prime.20220224.fq.gz [2022-02-24 12:21:27,145] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 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[DEBUG ] Ignoring file as matched an ignore pattern: S12M_R2.fastp-trim.20bp-5prime.20220224.fq.gz [2022-02-24 12:21:27,146] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S54F_R1.fastp-trim.20bp-5prime.20220224.fq.gz [2022-02-24 12:21:27,147] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S16F_R1.fastp-trim.20bp-5prime.20220224.report.html [2022-02-24 12:21:27,147] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S29F_R1.fastp-trim.20bp-5prime.20220224.fq.gz [2022-02-24 12:21:27,147] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S59M_R1.fastp-trim.20bp-5prime.20220224.report.html [2022-02-24 12:21:27,147] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S29F_R1.fastp-trim.20bp-5prime.20220224.report.html [2022-02-24 12:21:27,147] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S7M_R1.fastp-trim.20bp-5prime.20220224.report.html [2022-02-24 12:21:27,147] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S54F_R1.fastp-trim.20bp-5prime.20220224.report.html [2022-02-24 12:21:27,147] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S77F_R1.fastp-trim.20bp-5prime.20220224.fq.gz [2022-02-24 12:21:27,148] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S7M_R2.fastp-trim.20bp-5prime.20220224.fq.gz [2022-02-24 12:21:27,148] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S35F_R1.fastp-trim.20bp-5prime.20220224.report.html [2022-02-24 12:21:27,148] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S53F_R1.fastp-trim.20bp-5prime.20220224.report.html [2022-02-24 12:21:27,148] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S19F_R1.fastp-trim.20bp-5prime.20220224.report.html [2022-02-24 12:21:27,148] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S23M_R1.fastp-trim.20bp-5prime.20220224.report.html [2022-02-24 12:21:27,148] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S48M_R1.fastp-trim.20bp-5prime.20220224.report.html [2022-02-24 12:21:27,148] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S41F_R2.fastp-trim.20bp-5prime.20220224.fq.gz [2022-02-24 12:21:27,148] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S13M_R1.fastp-trim.20bp-5prime.20220224.fq.gz [2022-02-24 12:21:27,149] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S35F_R1.fastp-trim.20bp-5prime.20220224.fq.gz [2022-02-24 12:21:27,149] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S52F_R1.fastp-trim.20bp-5prime.20220224.report.html [2022-02-24 12:21:27,149] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: input_fastq_checksums.md5 [2022-02-24 12:21:27,150] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S48M_R2.fastp-trim.20bp-5prime.20220224.fq.gz [2022-02-24 12:21:27,150] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S50F_R1.fastp-trim.20bp-5prime.20220224.report.html [2022-02-24 12:21:27,150] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S48M_R1.fastp-trim.20bp-5prime.20220224.fq.gz [2022-02-24 12:21:27,150] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S3F_R2.fastp-trim.20bp-5prime.20220224.fq.gz [2022-02-24 12:21:27,151] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S31M_R1.fastp-trim.20bp-5prime.20220224.report.html [2022-02-24 12:21:27,151] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S53F_R1.fastp-trim.20bp-5prime.20220224.fq.gz [2022-02-24 12:21:27,151] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S44F_R1.fastp-trim.20bp-5prime.20220224.report.html [2022-02-24 12:21:27,151] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S64M_R1.fastp-trim.20bp-5prime.20220224.fq.gz [2022-02-24 12:21:27,151] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S41F_R1.fastp-trim.20bp-5prime.20220224.report.html [2022-02-24 12:21:27,151] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S19F_R1.fastp-trim.20bp-5prime.20220224.fq.gz [2022-02-24 12:21:27,151] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S9M_R2.fastp-trim.20bp-5prime.20220224.fq.gz [2022-02-24 12:21:27,151] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S76F_R1.fastp-trim.20bp-5prime.20220224.fq.gz [2022-02-24 12:21:27,151] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S6M_R2.fastp-trim.20bp-5prime.20220224.fq.gz [2022-02-24 12:21:27,151] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S23M_R2.fastp-trim.20bp-5prime.20220224.fq.gz [2022-02-24 12:21:27,152] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S50F_R2.fastp-trim.20bp-5prime.20220224.fq.gz [2022-02-24 12:21:27,152] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: S16F_R1.fastp-trim.20bp-5prime.20220224.fq.gz [2022-02-24 12:21:29,940] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 2.2.4 [2022-02-24 12:21:29,941] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 2.2.4 [2022-02-24 12:21:29,985] multiqc [DEBUG ] No samples found: custom_content [2022-02-24 12:21:30,030] multiqc [DEBUG ] No samples found: conpair [2022-02-24 12:21:30,050] multiqc [DEBUG ] No samples found: peddy [2022-02-24 12:21:30,106] multiqc [DEBUG ] No samples found: methylQA [2022-02-24 12:21:30,128] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-02-24 12:21:30,187] multiqc [DEBUG ] No samples found: qualimap [2022-02-24 12:21:30,208] multiqc [DEBUG ] No samples found: preseq [2022-02-24 12:21:30,214] multiqc [DEBUG ] No samples found: quast [2022-02-24 12:21:30,222] multiqc [DEBUG ] No samples found: qorts [2022-02-24 12:21:30,237] multiqc [DEBUG ] No samples found: rna_seqc [2022-02-24 12:21:30,249] multiqc [DEBUG ] No samples found: rsem [2022-02-24 12:21:30,259] multiqc [DEBUG ] No samples found: rseqc [2022-02-24 12:21:30,271] multiqc [DEBUG ] No samples found: busco [2022-02-24 12:21:30,313] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-02-24 12:21:30,345] multiqc [DEBUG ] No samples found: disambiguate [2022-02-24 12:21:30,352] multiqc [DEBUG ] No samples found: supernova [2022-02-24 12:21:30,402] multiqc [DEBUG ] No samples found: deeptools [2022-02-24 12:21:30,423] multiqc [DEBUG ] No samples found: sargasso [2022-02-24 12:21:30,433] multiqc [DEBUG ] No samples found: verifybamid [2022-02-24 12:21:30,442] multiqc [DEBUG ] No samples found: mirtrace [2022-02-24 12:21:30,464] multiqc [DEBUG ] No samples found: happy [2022-02-24 12:21:30,494] multiqc [DEBUG ] No samples found: homer [2022-02-24 12:21:30,503] multiqc [DEBUG ] No samples found: macs2 [2022-02-24 12:21:30,510] multiqc [DEBUG ] No samples found: theta2 [2022-02-24 12:21:30,529] multiqc [DEBUG ] No samples found: snpeff [2022-02-24 12:21:30,557] multiqc [DEBUG ] No samples found: gatk [2022-02-24 12:21:30,566] multiqc [DEBUG ] No samples found: htseq [2022-02-24 12:21:30,572] multiqc [DEBUG ] No samples found: bcftools [2022-02-24 12:21:30,581] multiqc [DEBUG ] No samples found: featureCounts [2022-02-24 12:21:30,598] multiqc [DEBUG ] No samples found: fgbio [2022-02-24 12:21:30,607] multiqc [DEBUG ] No samples found: dedup [2022-02-24 12:21:30,629] multiqc [DEBUG ] No samples found: damageprofiler [2022-02-24 12:21:30,716] multiqc [DEBUG ] No samples found: biobambam2 [2022-02-24 12:21:30,722] multiqc [DEBUG ] No samples found: mtnucratio [2022-02-24 12:21:30,726] multiqc [DEBUG ] No samples found: picard [2022-02-24 12:21:30,745] multiqc [DEBUG ] No samples found: prokka [2022-02-24 12:21:30,772] multiqc [DEBUG ] No samples found: samblaster [2022-02-24 12:21:30,780] multiqc [DEBUG ] No samples found: samtools [2022-02-24 12:21:30,786] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-02-24 12:21:30,791] multiqc [DEBUG ] No samples found: bamtools [2022-02-24 12:21:30,798] multiqc [DEBUG ] No samples found: jellyfish [2022-02-24 12:21:30,819] multiqc [DEBUG ] No samples found: vcftools [2022-02-24 12:21:30,823] multiqc [DEBUG ] No samples found: longranger [2022-02-24 12:21:30,845] multiqc [DEBUG ] No samples found: stacks [2022-02-24 12:21:30,856] multiqc [DEBUG ] No samples found: bbmap [2022-02-24 12:21:30,861] multiqc [DEBUG ] No samples found: bismark [2022-02-24 12:21:30,884] multiqc [DEBUG ] No samples found: biscuit [2022-02-24 12:21:30,889] multiqc [DEBUG ] No samples found: hicexplorer [2022-02-24 12:21:30,894] multiqc [DEBUG ] No samples found: hicup [2022-02-24 12:21:30,899] multiqc [DEBUG ] No samples found: hicpro [2022-02-24 12:21:30,904] multiqc [DEBUG ] No samples found: salmon [2022-02-24 12:21:30,923] multiqc [DEBUG ] No samples found: kallisto [2022-02-24 12:21:30,938] multiqc [DEBUG ] No samples found: slamdunk [2022-02-24 12:21:30,957] multiqc [DEBUG ] No samples found: star [2022-02-24 12:21:30,981] multiqc [DEBUG ] No samples found: hisat2 [2022-02-24 12:21:31,017] multiqc [DEBUG ] No samples found: tophat [2022-02-24 12:21:31,023] multiqc [DEBUG ] No samples found: bowtie2 [2022-02-24 12:21:31,028] multiqc [DEBUG ] No samples found: bowtie1 [2022-02-24 12:21:31,034] multiqc [DEBUG ] No samples found: kat [2022-02-24 12:21:31,051] multiqc [DEBUG ] No samples found: leehom [2022-02-24 12:21:31,083] multiqc [DEBUG ] No samples found: adapterRemoval [2022-02-24 12:21:31,089] multiqc [DEBUG ] No samples found: clipandmerge [2022-02-24 12:21:31,095] multiqc [DEBUG ] No samples found: cutadapt [2022-02-24 12:21:31,101] multiqc [DEBUG ] No samples found: flexbar [2022-02-24 12:21:31,106] multiqc [DEBUG ] No samples found: trimmomatic [2022-02-24 12:21:31,138] multiqc [DEBUG ] No samples found: skewer [2022-02-24 12:21:31,147] multiqc [DEBUG ] No samples found: sortmerna [2022-02-24 12:21:31,168] multiqc [DEBUG ] No samples found: biobloomtools [2022-02-24 12:21:31,175] multiqc [DEBUG ] No samples found: fastq_screen [2022-02-24 12:21:31,236] multiqc [DEBUG ] No samples found: afterqc [2022-02-24 12:21:31,263] multiqc.modules.fastp.fastp [DEBUG ] fastp JSON did not have a 'adapter_cutting' key, skipping: 'S3F_R1.fastp-trim.20bp-5prime.20220224.report.json' [2022-02-24 12:21:31,263] multiqc.modules.fastp.fastp [DEBUG ] Could not calculate 'pct_adapter': S3F_R1.fastp-trim.20bp-5prime.20220224.report.json [2022-02-24 12:21:31,287] multiqc.modules.fastp.fastp [DEBUG ] fastp JSON did not have a 'adapter_cutting' key, skipping: 'S36F_R1.fastp-trim.20bp-5prime.20220224.report.json' [2022-02-24 12:21:31,287] multiqc.modules.fastp.fastp [DEBUG ] Could not calculate 'pct_adapter': S36F_R1.fastp-trim.20bp-5prime.20220224.report.json [2022-02-24 12:21:31,313] multiqc.modules.fastp.fastp [DEBUG ] fastp JSON did not have a 'adapter_cutting' key, skipping: 'S50F_R1.fastp-trim.20bp-5prime.20220224.report.json' [2022-02-24 12:21:31,313] multiqc.modules.fastp.fastp [DEBUG ] Could not calculate 'pct_adapter': S50F_R1.fastp-trim.20bp-5prime.20220224.report.json [2022-02-24 12:21:31,327] multiqc.modules.fastp.fastp [DEBUG ] fastp JSON did not have a 'adapter_cutting' key, skipping: 'S52F_R1.fastp-trim.20bp-5prime.20220224.report.json' [2022-02-24 12:21:31,327] multiqc.modules.fastp.fastp [DEBUG ] Could not calculate 'pct_adapter': S52F_R1.fastp-trim.20bp-5prime.20220224.report.json [2022-02-24 12:21:31,340] multiqc.modules.fastp.fastp [DEBUG ] fastp JSON did not have a 'adapter_cutting' key, skipping: 'S31M_R1.fastp-trim.20bp-5prime.20220224.report.json' [2022-02-24 12:21:31,340] multiqc.modules.fastp.fastp [DEBUG ] Could not calculate 'pct_adapter': S31M_R1.fastp-trim.20bp-5prime.20220224.report.json [2022-02-24 12:21:31,357] multiqc.modules.fastp.fastp [DEBUG ] fastp JSON did not have a 'adapter_cutting' key, skipping: 'S64M_R1.fastp-trim.20bp-5prime.20220224.report.json' [2022-02-24 12:21:31,357] multiqc.modules.fastp.fastp [DEBUG ] Could not calculate 'pct_adapter': S64M_R1.fastp-trim.20bp-5prime.20220224.report.json [2022-02-24 12:21:31,379] multiqc.modules.fastp.fastp [DEBUG ] fastp JSON did not have a 'adapter_cutting' key, skipping: 'S76F_R1.fastp-trim.20bp-5prime.20220224.report.json' [2022-02-24 12:21:31,379] multiqc.modules.fastp.fastp [DEBUG ] Could not calculate 'pct_adapter': S76F_R1.fastp-trim.20bp-5prime.20220224.report.json [2022-02-24 12:21:31,384] multiqc.modules.fastp.fastp [DEBUG ] fastp JSON did not have a 'adapter_cutting' key, skipping: 'S7M_R1.fastp-trim.20bp-5prime.20220224.report.json' [2022-02-24 12:21:31,384] multiqc.modules.fastp.fastp [DEBUG ] Could not calculate 'pct_adapter': S7M_R1.fastp-trim.20bp-5prime.20220224.report.json [2022-02-24 12:21:31,402] multiqc.modules.fastp.fastp [DEBUG ] fastp JSON did not have a 'adapter_cutting' key, skipping: 'S29F_R1.fastp-trim.20bp-5prime.20220224.report.json' [2022-02-24 12:21:31,402] multiqc.modules.fastp.fastp [DEBUG ] Could not calculate 'pct_adapter': S29F_R1.fastp-trim.20bp-5prime.20220224.report.json [2022-02-24 12:21:31,421] multiqc.modules.fastp.fastp [DEBUG ] fastp JSON did not have a 'adapter_cutting' key, skipping: 'S59M_R1.fastp-trim.20bp-5prime.20220224.report.json' [2022-02-24 12:21:31,421] multiqc.modules.fastp.fastp [DEBUG ] Could not calculate 'pct_adapter': S59M_R1.fastp-trim.20bp-5prime.20220224.report.json [2022-02-24 12:21:31,449] multiqc.modules.fastp.fastp [DEBUG ] fastp JSON did not have a 'adapter_cutting' key, skipping: 'S39F_R1.fastp-trim.20bp-5prime.20220224.report.json' [2022-02-24 12:21:31,449] multiqc.modules.fastp.fastp [DEBUG ] Could not calculate 'pct_adapter': S39F_R1.fastp-trim.20bp-5prime.20220224.report.json [2022-02-24 12:21:31,454] multiqc.modules.fastp.fastp [DEBUG ] fastp JSON did not have a 'adapter_cutting' key, skipping: 'S9M_R1.fastp-trim.20bp-5prime.20220224.report.json' [2022-02-24 12:21:31,454] multiqc.modules.fastp.fastp [DEBUG ] Could not calculate 'pct_adapter': S9M_R1.fastp-trim.20bp-5prime.20220224.report.json [2022-02-24 12:21:31,467] multiqc.modules.fastp.fastp [DEBUG ] fastp JSON did not have a 'adapter_cutting' key, skipping: 'S23M_R1.fastp-trim.20bp-5prime.20220224.report.json' [2022-02-24 12:21:31,467] multiqc.modules.fastp.fastp [DEBUG ] Could not calculate 'pct_adapter': S23M_R1.fastp-trim.20bp-5prime.20220224.report.json [2022-02-24 12:21:31,482] multiqc.modules.fastp.fastp [DEBUG ] fastp JSON did not have a 'adapter_cutting' key, skipping: 'S48M_R1.fastp-trim.20bp-5prime.20220224.report.json' [2022-02-24 12:21:31,482] multiqc.modules.fastp.fastp [DEBUG ] Could not calculate 'pct_adapter': S48M_R1.fastp-trim.20bp-5prime.20220224.report.json [2022-02-24 12:21:31,507] multiqc.modules.fastp.fastp [DEBUG ] fastp JSON did not have a 'adapter_cutting' key, skipping: 'S12M_R1.fastp-trim.20bp-5prime.20220224.report.json' [2022-02-24 12:21:31,507] multiqc.modules.fastp.fastp [DEBUG ] Could not calculate 'pct_adapter': S12M_R1.fastp-trim.20bp-5prime.20220224.report.json [2022-02-24 12:21:31,527] multiqc.modules.fastp.fastp [DEBUG ] fastp JSON did not have a 'adapter_cutting' key, skipping: 'S19F_R1.fastp-trim.20bp-5prime.20220224.report.json' [2022-02-24 12:21:31,527] multiqc.modules.fastp.fastp [DEBUG ] Could not calculate 'pct_adapter': S19F_R1.fastp-trim.20bp-5prime.20220224.report.json [2022-02-24 12:21:31,542] multiqc.modules.fastp.fastp [DEBUG ] fastp JSON did not have a 'adapter_cutting' key, skipping: 'S22F_R1.fastp-trim.20bp-5prime.20220224.report.json' [2022-02-24 12:21:31,542] multiqc.modules.fastp.fastp [DEBUG ] Could not calculate 'pct_adapter': S22F_R1.fastp-trim.20bp-5prime.20220224.report.json [2022-02-24 12:21:31,565] multiqc.modules.fastp.fastp [DEBUG ] fastp JSON did not have a 'adapter_cutting' key, skipping: 'S16F_R1.fastp-trim.20bp-5prime.20220224.report.json' [2022-02-24 12:21:31,565] multiqc.modules.fastp.fastp [DEBUG ] Could not calculate 'pct_adapter': S16F_R1.fastp-trim.20bp-5prime.20220224.report.json [2022-02-24 12:21:31,587] multiqc.modules.fastp.fastp [DEBUG ] fastp JSON did not have a 'adapter_cutting' key, skipping: 'S13M_R1.fastp-trim.20bp-5prime.20220224.report.json' [2022-02-24 12:21:31,587] multiqc.modules.fastp.fastp [DEBUG ] Could not calculate 'pct_adapter': S13M_R1.fastp-trim.20bp-5prime.20220224.report.json [2022-02-24 12:21:31,606] multiqc.modules.fastp.fastp [DEBUG ] fastp JSON did not have a 'adapter_cutting' key, skipping: 'S54F_R1.fastp-trim.20bp-5prime.20220224.report.json' [2022-02-24 12:21:31,606] multiqc.modules.fastp.fastp [DEBUG ] Could not calculate 'pct_adapter': S54F_R1.fastp-trim.20bp-5prime.20220224.report.json [2022-02-24 12:21:31,626] multiqc.modules.fastp.fastp [DEBUG ] fastp JSON did not have a 'adapter_cutting' key, skipping: 'S44F_R1.fastp-trim.20bp-5prime.20220224.report.json' [2022-02-24 12:21:31,626] multiqc.modules.fastp.fastp [DEBUG ] Could not calculate 'pct_adapter': S44F_R1.fastp-trim.20bp-5prime.20220224.report.json [2022-02-24 12:21:31,631] multiqc.modules.fastp.fastp [DEBUG ] fastp JSON did not have a 'adapter_cutting' key, skipping: 'S41F_R1.fastp-trim.20bp-5prime.20220224.report.json' [2022-02-24 12:21:31,631] multiqc.modules.fastp.fastp [DEBUG ] Could not calculate 'pct_adapter': S41F_R1.fastp-trim.20bp-5prime.20220224.report.json [2022-02-24 12:21:31,636] multiqc.modules.fastp.fastp [DEBUG ] fastp JSON did not have a 'adapter_cutting' key, skipping: 'S77F_R1.fastp-trim.20bp-5prime.20220224.report.json' [2022-02-24 12:21:31,636] multiqc.modules.fastp.fastp [DEBUG ] Could not calculate 'pct_adapter': S77F_R1.fastp-trim.20bp-5prime.20220224.report.json [2022-02-24 12:21:31,654] multiqc.modules.fastp.fastp [DEBUG ] fastp JSON did not have a 'adapter_cutting' key, skipping: 'S53F_R1.fastp-trim.20bp-5prime.20220224.report.json' [2022-02-24 12:21:31,655] multiqc.modules.fastp.fastp [DEBUG ] Could not calculate 'pct_adapter': S53F_R1.fastp-trim.20bp-5prime.20220224.report.json [2022-02-24 12:21:31,675] multiqc.modules.fastp.fastp [DEBUG ] fastp JSON did not have a 'adapter_cutting' key, skipping: 'S35F_R1.fastp-trim.20bp-5prime.20220224.report.json' [2022-02-24 12:21:31,675] multiqc.modules.fastp.fastp [DEBUG ] Could not calculate 'pct_adapter': S35F_R1.fastp-trim.20bp-5prime.20220224.report.json [2022-02-24 12:21:31,694] multiqc.modules.fastp.fastp [DEBUG ] fastp JSON did not have a 'adapter_cutting' key, skipping: 'S6M_R1.fastp-trim.20bp-5prime.20220224.report.json' [2022-02-24 12:21:31,695] multiqc.modules.fastp.fastp [DEBUG ] Could not calculate 'pct_adapter': S6M_R1.fastp-trim.20bp-5prime.20220224.report.json [2022-02-24 12:21:31,696] multiqc.modules.fastp.fastp [INFO ] Found 26 reports [2022-02-24 12:21:31,822] multiqc [DEBUG ] No samples found: fastqc [2022-02-24 12:21:31,851] multiqc [DEBUG ] No samples found: minionqc [2022-02-24 12:21:31,869] multiqc [DEBUG ] No samples found: mosdepth [2022-02-24 12:21:31,893] multiqc [DEBUG ] No samples found: clusterflow [2022-02-24 12:21:31,899] multiqc [DEBUG ] No samples found: bcl2fastq [2022-02-24 12:21:31,906] multiqc [DEBUG ] No samples found: interop [2022-02-24 12:21:31,914] multiqc [DEBUG ] No samples found: flash [2022-02-24 12:21:31,941] multiqc [DEBUG ] No samples found: seqyclean [2022-02-24 12:21:31,993] multiqc [INFO ] Compressing plot data [2022-02-24 12:21:33,761] multiqc [INFO ] Report : multiqc_report.html [2022-02-24 12:21:33,761] multiqc [INFO ] Data : multiqc_data [2022-02-24 12:21:33,762] multiqc [DEBUG ] Moving data file from '/tmp/tmpzdf2wl0b/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/gscratch/scrubbed/samwhite/outputs/20220224_cvir_gonad_RNAseq_fastp_trimming/multiqc_data' [2022-02-24 12:21:33,763] multiqc [DEBUG ] Moving data file from '/tmp/tmpzdf2wl0b/multiqc_data/multiqc_fastp.txt' to '/gscratch/scrubbed/samwhite/outputs/20220224_cvir_gonad_RNAseq_fastp_trimming/multiqc_data' [2022-02-24 12:21:33,764] multiqc [DEBUG ] Moving data file from '/tmp/tmpzdf2wl0b/multiqc_data/multiqc_general_stats.txt' to '/gscratch/scrubbed/samwhite/outputs/20220224_cvir_gonad_RNAseq_fastp_trimming/multiqc_data' [2022-02-24 12:21:33,788] multiqc [DEBUG ] Moving data file from '/tmp/tmpzdf2wl0b/multiqc_data/multiqc_sources.txt' to '/gscratch/scrubbed/samwhite/outputs/20220224_cvir_gonad_RNAseq_fastp_trimming/multiqc_data' [2022-02-24 12:21:33,789] multiqc [DEBUG ] Moving data file from '/tmp/tmpzdf2wl0b/multiqc_data/multiqc_data.json' to '/gscratch/scrubbed/samwhite/outputs/20220224_cvir_gonad_RNAseq_fastp_trimming/multiqc_data' [2022-02-24 12:21:34,323] multiqc [INFO ] MultiQC complete