[2023-01-22 11:06:14,424] multiqc [DEBUG ] No MultiQC config found: /gscratch/srlab/programs/anaconda3/lib/python3.7/site-packages/multiqc_config.yaml [2023-01-22 11:06:14,427] multiqc [DEBUG ] Loading config settings from: /usr/lusers/samwhite/.multiqc_config.yaml [2023-01-22 11:06:14,427] multiqc [DEBUG ] New config 'star': {'fn': '*Log.final.out'} [2023-01-22 11:06:14,427] multiqc [DEBUG ] New config 'star/genecounts': {'fn': '*ReadsPerGene.out.tab'} [2023-01-22 11:06:14,428] multiqc [DEBUG ] Added to filename patterns: {'fastp': {'fn': '*report.json'}} [2023-01-22 11:06:14,428] multiqc [DEBUG ] New config 'hisat2': {'contents': 'HISAT2 summary stats:', 'shared': True} [2023-01-22 11:06:14,428] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-01-22 11:06:14,428] multiqc [DEBUG ] Command used: /gscratch/srlab/programs/anaconda3/bin/multiqc . [2023-01-22 11:06:19,745] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2023-01-22 11:06:19,745] multiqc [INFO ] This is MultiQC v1.8 [2023-01-22 11:06:19,747] multiqc [DEBUG ] Command : /gscratch/srlab/programs/anaconda3/bin/multiqc . [2023-01-22 11:06:19,747] multiqc [DEBUG ] Working dir : /gscratch/scrubbed/samwhite/outputs/20230119-coral-fastqc-fastp-multiqc-PRJNA744403/data/P_grandis/BS-seq/trimmed [2023-01-22 11:06:19,747] multiqc [INFO ] Template : default [2023-01-22 11:06:19,747] multiqc [DEBUG ] Running Python 3.7.3 (default, Mar 27 2019, 22:11:17) [GCC 7.3.0] [2023-01-22 11:06:19,747] multiqc [INFO ] Searching : /gscratch/scrubbed/samwhite/outputs/20230119-coral-fastqc-fastp-multiqc-PRJNA744403/data/P_grandis/BS-seq/trimmed [2023-01-22 11:06:19,748] 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 11:06:19,748] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpecua9pz8 [2023-01-22 11:06:20,213] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRA-SRR15101728_2.P_grandis.fastp-trim.20230122_fastqc.html [2023-01-22 11:06:20,220] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRA-SRR15101728_1.P_grandis.fastp-trim.20230122.fq.gz [2023-01-22 11:06:20,221] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRA-SRR15101727.P_grandis.fastp-trim.20230122.report.html [2023-01-22 11:06:20,221] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRA-SRR15101744_1.P_grandis.fastp-trim.20230122.fq.gz [2023-01-22 11:06:20,221] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRA-SRR15101744_2.P_grandis.fastp-trim.20230122.fq.gz [2023-01-22 11:06:20,221] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRA-SRR15101749_1.P_grandis.fastp-trim.20230122.fq.gz [2023-01-22 11:06:20,221] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRA-SRR15101749.P_grandis.fastp-trim.20230122.report.html [2023-01-22 11:06:20,221] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRA-SRR15101728.P_grandis.fastp-trim.20230122.report.html [2023-01-22 11:06:20,221] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRA-SRR15101749_2.P_grandis.fastp-trim.20230122.fq.gz [2023-01-22 11:06:20,221] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRA-SRR15101749_2.P_grandis.fastp-trim.20230122_fastqc.html [2023-01-22 11:06:20,222] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRA-SRR15101732_1.P_grandis.fastp-trim.20230122_fastqc.html [2023-01-22 11:06:20,222] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRA-SRR15101732.P_grandis.fastp-trim.20230122.report.html [2023-01-22 11:06:20,223] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRA-SRR15101727_1.P_grandis.fastp-trim.20230122_fastqc.html [2023-01-22 11:06:20,223] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRA-SRR15101727_2.P_grandis.fastp-trim.20230122.fq.gz [2023-01-22 11:06:20,223] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRA-SRR15101727_1.P_grandis.fastp-trim.20230122.fq.gz [2023-01-22 11:06:20,223] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: trimmed_fastq_checksums.md5 [2023-01-22 11:06:20,224] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRA-SRR15101744_1.P_grandis.fastp-trim.20230122_fastqc.html [2023-01-22 11:06:20,224] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRA-SRR15101727_2.P_grandis.fastp-trim.20230122_fastqc.html [2023-01-22 11:06:20,225] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRA-SRR15101744.P_grandis.fastp-trim.20230122.report.html [2023-01-22 11:06:20,225] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRA-SRR15101749_1.P_grandis.fastp-trim.20230122_fastqc.html [2023-01-22 11:06:20,225] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRA-SRR15101728_2.P_grandis.fastp-trim.20230122.fq.gz [2023-01-22 11:06:20,225] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRA-SRR15101744_2.P_grandis.fastp-trim.20230122_fastqc.html [2023-01-22 11:06:20,225] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRA-SRR15101732_2.P_grandis.fastp-trim.20230122_fastqc.html [2023-01-22 11:06:20,225] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRA-SRR15101732_1.P_grandis.fastp-trim.20230122.fq.gz [2023-01-22 11:06:20,225] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRA-SRR15101732_2.P_grandis.fastp-trim.20230122.fq.gz [2023-01-22 11:06:20,226] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: SRA-SRR15101728_1.P_grandis.fastp-trim.20230122_fastqc.html [2023-01-22 11:06:23,136] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 2.2.4 [2023-01-22 11:06:23,158] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 2.2.4 [2023-01-22 11:06:23,171] multiqc [DEBUG ] No samples found: custom_content [2023-01-22 11:06:23,198] multiqc [DEBUG ] No samples found: conpair [2023-01-22 11:06:23,240] multiqc [DEBUG ] No samples found: peddy [2023-01-22 11:06:23,303] multiqc [DEBUG ] No samples found: methylQA [2023-01-22 11:06:23,340] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-01-22 11:06:23,391] multiqc [DEBUG ] No samples found: qualimap [2023-01-22 11:06:23,442] multiqc [DEBUG ] No samples found: preseq [2023-01-22 11:06:23,460] multiqc [DEBUG ] No samples found: quast [2023-01-22 11:06:23,467] multiqc [DEBUG ] No samples found: qorts [2023-01-22 11:06:23,519] multiqc [DEBUG ] No samples found: rna_seqc [2023-01-22 11:06:23,542] multiqc [DEBUG ] No samples found: rsem [2023-01-22 11:06:23,595] multiqc [DEBUG ] No samples found: rseqc [2023-01-22 11:06:23,638] multiqc [DEBUG ] No samples found: busco [2023-01-22 11:06:23,679] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-01-22 11:06:23,693] multiqc [DEBUG ] No samples found: disambiguate [2023-01-22 11:06:23,721] multiqc [DEBUG ] No samples found: supernova [2023-01-22 11:06:23,820] multiqc [DEBUG ] No samples found: deeptools [2023-01-22 11:06:23,830] multiqc [DEBUG ] No samples found: sargasso [2023-01-22 11:06:23,913] multiqc [DEBUG ] No samples found: verifybamid [2023-01-22 11:06:23,922] multiqc [DEBUG ] No samples found: mirtrace [2023-01-22 11:06:23,946] multiqc [DEBUG ] No samples found: happy [2023-01-22 11:06:23,958] multiqc [DEBUG ] No samples found: homer [2023-01-22 11:06:23,995] multiqc [DEBUG ] No samples found: macs2 [2023-01-22 11:06:24,047] multiqc [DEBUG ] No samples found: theta2 [2023-01-22 11:06:24,074] multiqc [DEBUG ] No samples found: snpeff [2023-01-22 11:06:24,087] multiqc [DEBUG ] No samples found: gatk [2023-01-22 11:06:24,096] multiqc [DEBUG ] No samples found: htseq [2023-01-22 11:06:24,106] multiqc [DEBUG ] No samples found: bcftools [2023-01-22 11:06:24,113] multiqc [DEBUG ] No samples found: featureCounts [2023-01-22 11:06:24,145] multiqc [DEBUG ] No samples found: fgbio [2023-01-22 11:06:24,171] multiqc [DEBUG ] No samples found: dedup [2023-01-22 11:06:24,179] multiqc [DEBUG ] No samples found: damageprofiler [2023-01-22 11:06:24,208] multiqc [DEBUG ] No samples found: biobambam2 [2023-01-22 11:06:24,215] multiqc [DEBUG ] No samples found: mtnucratio [2023-01-22 11:06:24,219] multiqc [DEBUG ] No samples found: picard [2023-01-22 11:06:24,225] multiqc [DEBUG ] No samples found: prokka [2023-01-22 11:06:24,232] multiqc [DEBUG ] No samples found: samblaster [2023-01-22 11:06:24,265] multiqc [DEBUG ] No samples found: samtools [2023-01-22 11:06:24,294] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-01-22 11:06:24,327] multiqc [DEBUG ] No samples found: bamtools [2023-01-22 11:06:24,336] multiqc [DEBUG ] No samples found: jellyfish [2023-01-22 11:06:24,348] multiqc [DEBUG ] No samples found: vcftools [2023-01-22 11:06:24,356] multiqc [DEBUG ] No samples found: longranger [2023-01-22 11:06:24,364] multiqc [DEBUG ] No samples found: stacks [2023-01-22 11:06:24,382] multiqc [DEBUG ] No samples found: bbmap [2023-01-22 11:06:24,411] multiqc [DEBUG ] No samples found: bismark [2023-01-22 11:06:24,437] multiqc [DEBUG ] No samples found: biscuit [2023-01-22 11:06:24,444] multiqc [DEBUG ] No samples found: hicexplorer [2023-01-22 11:06:24,450] multiqc [DEBUG ] No samples found: hicup [2023-01-22 11:06:24,455] multiqc [DEBUG ] No samples found: hicpro [2023-01-22 11:06:24,461] multiqc [DEBUG ] No samples found: salmon [2023-01-22 11:06:24,466] multiqc [DEBUG ] No samples found: kallisto [2023-01-22 11:06:24,490] multiqc [DEBUG ] No samples found: slamdunk [2023-01-22 11:06:24,495] multiqc [DEBUG ] No samples found: star [2023-01-22 11:06:24,500] multiqc [DEBUG ] No samples found: hisat2 [2023-01-22 11:06:24,519] multiqc [DEBUG ] No samples found: tophat [2023-01-22 11:06:24,525] multiqc [DEBUG ] No samples found: bowtie2 [2023-01-22 11:06:24,549] multiqc [DEBUG ] No samples found: bowtie1 [2023-01-22 11:06:24,568] multiqc [DEBUG ] No samples found: kat [2023-01-22 11:06:24,574] multiqc [DEBUG ] No samples found: leehom [2023-01-22 11:06:24,591] multiqc [DEBUG ] No samples found: adapterRemoval [2023-01-22 11:06:24,596] multiqc [DEBUG ] No samples found: clipandmerge [2023-01-22 11:06:24,602] multiqc [DEBUG ] No samples found: cutadapt [2023-01-22 11:06:24,608] multiqc [DEBUG ] No samples found: flexbar [2023-01-22 11:06:24,613] multiqc [DEBUG ] No samples found: trimmomatic [2023-01-22 11:06:24,638] multiqc [DEBUG ] No samples found: skewer [2023-01-22 11:06:24,643] multiqc [DEBUG ] No samples found: sortmerna [2023-01-22 11:06:24,649] multiqc [DEBUG ] No samples found: biobloomtools [2023-01-22 11:06:24,655] multiqc [DEBUG ] No samples found: fastq_screen [2023-01-22 11:06:24,660] multiqc [DEBUG ] No samples found: afterqc [2023-01-22 11:06:24,670] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: SRA-SRR15101744.P_grandis.fastp-trim.20230122.report.json [2023-01-22 11:06:24,674] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: SRA-SRR15101732.P_grandis.fastp-trim.20230122.report.json [2023-01-22 11:06:24,679] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: SRA-SRR15101727.P_grandis.fastp-trim.20230122.report.json [2023-01-22 11:06:24,683] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: SRA-SRR15101749.P_grandis.fastp-trim.20230122.report.json [2023-01-22 11:06:24,687] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: SRA-SRR15101728.P_grandis.fastp-trim.20230122.report.json [2023-01-22 11:06:24,688] multiqc.modules.fastp.fastp [INFO ] Found 5 reports [2023-01-22 11:06:24,822] multiqc.modules.fastqc.fastqc [INFO ] Found 10 reports [2023-01-22 11:06:25,070] multiqc [DEBUG ] No samples found: minionqc [2023-01-22 11:06:25,075] multiqc [DEBUG ] No samples found: mosdepth [2023-01-22 11:06:25,081] multiqc [DEBUG ] No samples found: clusterflow [2023-01-22 11:06:25,145] multiqc [DEBUG ] No samples found: bcl2fastq [2023-01-22 11:06:25,154] multiqc [DEBUG ] No samples found: interop [2023-01-22 11:06:25,175] multiqc [DEBUG ] No samples found: flash [2023-01-22 11:06:25,202] multiqc [DEBUG ] No samples found: seqyclean [2023-01-22 11:06:25,240] multiqc [INFO ] Compressing plot data [2023-01-22 11:06:25,858] multiqc [INFO ] Report : multiqc_report.html [2023-01-22 11:06:25,859] multiqc [INFO ] Data : multiqc_data [2023-01-22 11:06:25,860] multiqc [DEBUG ] Moving data file from '/tmp/tmpecua9pz8/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/gscratch/scrubbed/samwhite/outputs/20230119-coral-fastqc-fastp-multiqc-PRJNA744403/data/P_grandis/BS-seq/trimmed/multiqc_data' [2023-01-22 11:06:25,861] multiqc [DEBUG ] Moving data file from '/tmp/tmpecua9pz8/multiqc_data/multiqc_fastp.txt' to '/gscratch/scrubbed/samwhite/outputs/20230119-coral-fastqc-fastp-multiqc-PRJNA744403/data/P_grandis/BS-seq/trimmed/multiqc_data' [2023-01-22 11:06:25,862] multiqc [DEBUG ] Moving data file from '/tmp/tmpecua9pz8/multiqc_data/multiqc_fastqc.txt' to '/gscratch/scrubbed/samwhite/outputs/20230119-coral-fastqc-fastp-multiqc-PRJNA744403/data/P_grandis/BS-seq/trimmed/multiqc_data' [2023-01-22 11:06:25,863] multiqc [DEBUG ] Moving data file from '/tmp/tmpecua9pz8/multiqc_data/multiqc_general_stats.txt' to '/gscratch/scrubbed/samwhite/outputs/20230119-coral-fastqc-fastp-multiqc-PRJNA744403/data/P_grandis/BS-seq/trimmed/multiqc_data' [2023-01-22 11:06:25,863] multiqc [DEBUG ] Moving data file from '/tmp/tmpecua9pz8/multiqc_data/multiqc_sources.txt' to '/gscratch/scrubbed/samwhite/outputs/20230119-coral-fastqc-fastp-multiqc-PRJNA744403/data/P_grandis/BS-seq/trimmed/multiqc_data' [2023-01-22 11:06:25,864] multiqc [DEBUG ] Moving data file from '/tmp/tmpecua9pz8/multiqc_data/multiqc_data.json' to '/gscratch/scrubbed/samwhite/outputs/20230119-coral-fastqc-fastp-multiqc-PRJNA744403/data/P_grandis/BS-seq/trimmed/multiqc_data' [2023-01-22 11:06:26,248] multiqc [INFO ] MultiQC complete