[2023-01-22 11:27:06,292] multiqc [DEBUG ] No MultiQC config found: /gscratch/srlab/programs/anaconda3/lib/python3.7/site-packages/multiqc_config.yaml [2023-01-22 11:27:06,294] multiqc [DEBUG ] Loading config settings from: /usr/lusers/samwhite/.multiqc_config.yaml [2023-01-22 11:27:06,294] multiqc [DEBUG ] New config 'star': {'fn': '*Log.final.out'} [2023-01-22 11:27:06,294] multiqc [DEBUG ] New config 'star/genecounts': {'fn': '*ReadsPerGene.out.tab'} [2023-01-22 11:27:06,294] multiqc [DEBUG ] Added to filename patterns: {'fastp': {'fn': '*report.json'}} [2023-01-22 11:27:06,294] multiqc [DEBUG ] New config 'hisat2': {'contents': 'HISAT2 summary stats:', 'shared': True} [2023-01-22 11:27:06,294] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-01-22 11:27:06,294] multiqc [DEBUG ] Command used: /gscratch/srlab/programs/anaconda3/bin/multiqc . [2023-01-22 11:27:11,446] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2023-01-22 11:27:11,446] multiqc [INFO ] This is MultiQC v1.8 [2023-01-22 11:27:11,448] multiqc [DEBUG ] Command : /gscratch/srlab/programs/anaconda3/bin/multiqc . [2023-01-22 11:27:11,448] multiqc [DEBUG ] Working dir : /gscratch/scrubbed/samwhite/outputs/20230119-coral-fastqc-fastp-multiqc-PRJNA744403/data/P_grandis/RNA-seq/trimmed [2023-01-22 11:27:11,448] multiqc [INFO ] Template : default [2023-01-22 11:27:11,449] multiqc [DEBUG ] Running Python 3.7.3 (default, Mar 27 2019, 22:11:17) [GCC 7.3.0] [2023-01-22 11:27:11,449] multiqc [INFO ] Searching : /gscratch/scrubbed/samwhite/outputs/20230119-coral-fastqc-fastp-multiqc-PRJNA744403/data/P_grandis/RNA-seq/trimmed [2023-01-22 11:27:11,450] 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 [2023-01-22 11:27:11,450] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmps38lwhaw [2023-01-22 11:27:11,621] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRA-SRR15101702_1.P_grandis.fastp-trim.20230122.fq.gz [2023-01-22 11:27:11,621] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRA-SRR15101690_2.P_grandis.fastp-trim.20230122_fastqc.html [2023-01-22 11:27:11,622] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRA-SRR15101720_1.P_grandis.fastp-trim.20230122_fastqc.html [2023-01-22 11:27:11,628] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRA-SRR15101702_2.P_grandis.fastp-trim.20230122.fq.gz [2023-01-22 11:27:11,628] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRA-SRR15101723_2.P_grandis.fastp-trim.20230122.fq.gz [2023-01-22 11:27:11,628] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRA-SRR15101720_2.P_grandis.fastp-trim.20230122_fastqc.html [2023-01-22 11:27:11,628] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRA-SRR15101720_2.P_grandis.fastp-trim.20230122.fq.gz [2023-01-22 11:27:11,629] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRA-SRR15101690_1.P_grandis.fastp-trim.20230122.fq.gz [2023-01-22 11:27:11,629] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRA-SRR15101702_2.P_grandis.fastp-trim.20230122_fastqc.html [2023-01-22 11:27:11,630] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRA-SRR15101723_1.P_grandis.fastp-trim.20230122.fq.gz [2023-01-22 11:27:11,630] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRA-SRR15101715_1.P_grandis.fastp-trim.20230122.fq.gz [2023-01-22 11:27:11,630] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRA-SRR15101723_2.P_grandis.fastp-trim.20230122_fastqc.html [2023-01-22 11:27:11,630] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRA-SRR15101723.P_grandis.fastp-trim.20230122.report.html [2023-01-22 11:27:11,630] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRA-SRR15101715_2.P_grandis.fastp-trim.20230122.fq.gz [2023-01-22 11:27:11,630] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: trimmed_fastq_checksums.md5 [2023-01-22 11:27:11,630] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRA-SRR15101715.P_grandis.fastp-trim.20230122.report.html [2023-01-22 11:27:11,631] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRA-SRR15101715_1.P_grandis.fastp-trim.20230122_fastqc.html [2023-01-22 11:27:11,631] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRA-SRR15101702_1.P_grandis.fastp-trim.20230122_fastqc.html [2023-01-22 11:27:11,631] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRA-SRR15101723_1.P_grandis.fastp-trim.20230122_fastqc.html [2023-01-22 11:27:11,631] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRA-SRR15101715_2.P_grandis.fastp-trim.20230122_fastqc.html [2023-01-22 11:27:11,632] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRA-SRR15101690.P_grandis.fastp-trim.20230122.report.html [2023-01-22 11:27:11,632] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRA-SRR15101702.P_grandis.fastp-trim.20230122.report.html [2023-01-22 11:27:11,632] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRA-SRR15101690_1.P_grandis.fastp-trim.20230122_fastqc.html [2023-01-22 11:27:11,632] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRA-SRR15101720_1.P_grandis.fastp-trim.20230122.fq.gz [2023-01-22 11:27:11,632] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRA-SRR15101720.P_grandis.fastp-trim.20230122.report.html [2023-01-22 11:27:11,632] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRA-SRR15101690_2.P_grandis.fastp-trim.20230122.fq.gz [2023-01-22 11:27:11,928] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 2.2.4 [2023-01-22 11:27:11,929] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 2.2.4 [2023-01-22 11:27:11,930] multiqc [DEBUG ] No samples found: custom_content [2023-01-22 11:27:11,934] multiqc [DEBUG ] No samples found: conpair [2023-01-22 11:27:11,939] multiqc [DEBUG ] No samples found: peddy [2023-01-22 11:27:11,943] multiqc [DEBUG ] No samples found: methylQA [2023-01-22 11:27:11,948] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-01-22 11:27:11,954] multiqc [DEBUG ] No samples found: qualimap [2023-01-22 11:27:11,958] multiqc [DEBUG ] No samples found: preseq [2023-01-22 11:27:11,962] multiqc [DEBUG ] No samples found: quast [2023-01-22 11:27:11,967] multiqc [DEBUG ] No samples found: qorts [2023-01-22 11:27:11,971] multiqc [DEBUG ] No samples found: rna_seqc [2023-01-22 11:27:11,976] multiqc [DEBUG ] No samples found: rsem [2023-01-22 11:27:11,984] multiqc [DEBUG ] No samples found: rseqc [2023-01-22 11:27:11,989] multiqc [DEBUG ] No samples found: busco [2023-01-22 11:27:11,994] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-01-22 11:27:11,998] multiqc [DEBUG ] No samples found: disambiguate [2023-01-22 11:27:12,003] multiqc [DEBUG ] No samples found: supernova [2023-01-22 11:27:12,012] multiqc [DEBUG ] No samples found: deeptools [2023-01-22 11:27:12,018] multiqc [DEBUG ] No samples found: sargasso [2023-01-22 11:27:12,024] multiqc [DEBUG ] No samples found: verifybamid [2023-01-22 11:27:12,030] multiqc [DEBUG ] No samples found: mirtrace [2023-01-22 11:27:12,034] multiqc [DEBUG ] No samples found: happy [2023-01-22 11:27:12,040] multiqc [DEBUG ] No samples found: homer [2023-01-22 11:27:12,044] multiqc [DEBUG ] No samples found: macs2 [2023-01-22 11:27:12,048] multiqc [DEBUG ] No samples found: theta2 [2023-01-22 11:27:12,053] multiqc [DEBUG ] No samples found: snpeff [2023-01-22 11:27:12,072] multiqc [DEBUG ] No samples found: gatk [2023-01-22 11:27:12,076] multiqc [DEBUG ] No samples found: htseq [2023-01-22 11:27:12,080] multiqc [DEBUG ] No samples found: bcftools [2023-01-22 11:27:12,085] multiqc [DEBUG ] No samples found: featureCounts [2023-01-22 11:27:12,090] multiqc [DEBUG ] No samples found: fgbio [2023-01-22 11:27:12,095] multiqc [DEBUG ] No samples found: dedup [2023-01-22 11:27:12,099] multiqc [DEBUG ] No samples found: damageprofiler [2023-01-22 11:27:12,126] multiqc [DEBUG ] No samples found: biobambam2 [2023-01-22 11:27:12,132] multiqc [DEBUG ] No samples found: mtnucratio [2023-01-22 11:27:12,135] multiqc [DEBUG ] No samples found: picard [2023-01-22 11:27:12,140] multiqc [DEBUG ] No samples found: prokka [2023-01-22 11:27:12,144] multiqc [DEBUG ] No samples found: samblaster [2023-01-22 11:27:12,151] multiqc [DEBUG ] No samples found: samtools [2023-01-22 11:27:12,155] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-01-22 11:27:12,159] multiqc [DEBUG ] No samples found: bamtools [2023-01-22 11:27:12,165] multiqc [DEBUG ] No samples found: jellyfish [2023-01-22 11:27:12,173] multiqc [DEBUG ] No samples found: vcftools [2023-01-22 11:27:12,178] multiqc [DEBUG ] No samples found: longranger [2023-01-22 11:27:12,182] multiqc [DEBUG ] No samples found: stacks [2023-01-22 11:27:12,190] multiqc [DEBUG ] No samples found: bbmap [2023-01-22 11:27:12,199] multiqc [DEBUG ] No samples found: bismark [2023-01-22 11:27:12,204] multiqc [DEBUG ] No samples found: biscuit [2023-01-22 11:27:12,208] multiqc [DEBUG ] No samples found: hicexplorer [2023-01-22 11:27:12,212] multiqc [DEBUG ] No samples found: hicup [2023-01-22 11:27:12,216] multiqc [DEBUG ] No samples found: hicpro [2023-01-22 11:27:12,220] multiqc [DEBUG ] No samples found: salmon [2023-01-22 11:27:12,224] multiqc [DEBUG ] No samples found: kallisto [2023-01-22 11:27:12,228] multiqc [DEBUG ] No samples found: slamdunk [2023-01-22 11:27:12,231] multiqc [DEBUG ] No samples found: star [2023-01-22 11:27:12,235] multiqc [DEBUG ] No samples found: hisat2 [2023-01-22 11:27:12,240] multiqc [DEBUG ] No samples found: tophat [2023-01-22 11:27:12,245] multiqc [DEBUG ] No samples found: bowtie2 [2023-01-22 11:27:12,248] multiqc [DEBUG ] No samples found: bowtie1 [2023-01-22 11:27:12,253] multiqc [DEBUG ] No samples found: kat [2023-01-22 11:27:12,257] multiqc [DEBUG ] No samples found: leehom [2023-01-22 11:27:12,261] multiqc [DEBUG ] No samples found: adapterRemoval [2023-01-22 11:27:12,265] multiqc [DEBUG ] No samples found: clipandmerge [2023-01-22 11:27:12,270] multiqc [DEBUG ] No samples found: cutadapt [2023-01-22 11:27:12,274] multiqc [DEBUG ] No samples found: flexbar [2023-01-22 11:27:12,278] multiqc [DEBUG ] No samples found: trimmomatic [2023-01-22 11:27:12,282] multiqc [DEBUG ] No samples found: skewer [2023-01-22 11:27:12,287] multiqc [DEBUG ] No samples found: sortmerna [2023-01-22 11:27:12,291] multiqc [DEBUG ] No samples found: biobloomtools [2023-01-22 11:27:12,295] multiqc [DEBUG ] No samples found: fastq_screen [2023-01-22 11:27:12,300] multiqc [DEBUG ] No samples found: afterqc [2023-01-22 11:27:12,338] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: SRA-SRR15101723.P_grandis.fastp-trim.20230122.report.json [2023-01-22 11:27:12,344] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: SRA-SRR15101690.P_grandis.fastp-trim.20230122.report.json [2023-01-22 11:27:12,350] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: SRA-SRR15101715.P_grandis.fastp-trim.20230122.report.json [2023-01-22 11:27:12,355] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: SRA-SRR15101720.P_grandis.fastp-trim.20230122.report.json [2023-01-22 11:27:12,360] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: SRA-SRR15101702.P_grandis.fastp-trim.20230122.report.json [2023-01-22 11:27:12,361] multiqc.modules.fastp.fastp [INFO ] Found 5 reports [2023-01-22 11:27:12,462] multiqc.modules.fastqc.fastqc [INFO ] Found 10 reports [2023-01-22 11:27:12,647] multiqc [DEBUG ] No samples found: minionqc [2023-01-22 11:27:12,651] multiqc [DEBUG ] No samples found: mosdepth [2023-01-22 11:27:12,655] multiqc [DEBUG ] No samples found: clusterflow [2023-01-22 11:27:12,659] multiqc [DEBUG ] No samples found: bcl2fastq [2023-01-22 11:27:12,662] multiqc [DEBUG ] No samples found: interop [2023-01-22 11:27:12,666] multiqc [DEBUG ] No samples found: flash [2023-01-22 11:27:12,669] multiqc [DEBUG ] No samples found: seqyclean [2023-01-22 11:27:12,692] multiqc [INFO ] Compressing plot data [2023-01-22 11:27:13,210] multiqc [INFO ] Report : multiqc_report.html [2023-01-22 11:27:13,212] multiqc [INFO ] Data : multiqc_data [2023-01-22 11:27:13,212] multiqc [DEBUG ] Moving data file from '/tmp/tmps38lwhaw/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/gscratch/scrubbed/samwhite/outputs/20230119-coral-fastqc-fastp-multiqc-PRJNA744403/data/P_grandis/RNA-seq/trimmed/multiqc_data' [2023-01-22 11:27:13,213] multiqc [DEBUG ] Moving data file from '/tmp/tmps38lwhaw/multiqc_data/multiqc_fastp.txt' to '/gscratch/scrubbed/samwhite/outputs/20230119-coral-fastqc-fastp-multiqc-PRJNA744403/data/P_grandis/RNA-seq/trimmed/multiqc_data' [2023-01-22 11:27:13,214] multiqc [DEBUG ] Moving data file from '/tmp/tmps38lwhaw/multiqc_data/multiqc_fastqc.txt' to '/gscratch/scrubbed/samwhite/outputs/20230119-coral-fastqc-fastp-multiqc-PRJNA744403/data/P_grandis/RNA-seq/trimmed/multiqc_data' [2023-01-22 11:27:13,215] multiqc [DEBUG ] Moving data file from '/tmp/tmps38lwhaw/multiqc_data/multiqc_general_stats.txt' to '/gscratch/scrubbed/samwhite/outputs/20230119-coral-fastqc-fastp-multiqc-PRJNA744403/data/P_grandis/RNA-seq/trimmed/multiqc_data' [2023-01-22 11:27:13,216] multiqc [DEBUG ] Moving data file from '/tmp/tmps38lwhaw/multiqc_data/multiqc_sources.txt' to '/gscratch/scrubbed/samwhite/outputs/20230119-coral-fastqc-fastp-multiqc-PRJNA744403/data/P_grandis/RNA-seq/trimmed/multiqc_data' [2023-01-22 11:27:13,217] multiqc [DEBUG ] Moving data file from '/tmp/tmps38lwhaw/multiqc_data/multiqc_data.json' to '/gscratch/scrubbed/samwhite/outputs/20230119-coral-fastqc-fastp-multiqc-PRJNA744403/data/P_grandis/RNA-seq/trimmed/multiqc_data' [2023-01-22 11:27:13,405] multiqc [INFO ] MultiQC complete