[2025-04-10 18:05:20,739] multiqc [DEBUG ] This is MultiQC v1.12 [2025-04-10 18:05:20,740] multiqc [DEBUG ] No MultiQC config found: /modules/uri_apps/software/MultiQC/1.12-foss-2021b/lib/python3.9/site-packages/multiqc_config.yaml [2025-04-10 18:05:20,742] multiqc [DEBUG ] No MultiQC config found: /home/zdellaert_uri_edu/.multiqc_config.yaml [2025-04-10 18:05:20,742] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2025-04-10 18:05:20,742] multiqc [DEBUG ] Command used: /modules/uri_apps/software/MultiQC/1.12-foss-2021b/bin/multiqc trimmed_ACR-140-TP2_S5_R1_001_fastqc.html trimmed_ACR-140-TP2_S5_R1_001_fastqc.zip trimmed_ACR-140-TP2_S5_R2_001_fastqc.html trimmed_ACR-140-TP2_S5_R2_001_fastqc.zip trimmed_ACR-145-TP2_S3_R1_001_fastqc.html trimmed_ACR-145-TP2_S3_R1_001_fastqc.zip trimmed_ACR-145-TP2_S3_R2_001_fastqc.html trimmed_ACR-145-TP2_S3_R2_001_fastqc.zip trimmed_ACR-150-TP2_S2_R1_001_fastqc.html trimmed_ACR-150-TP2_S2_R1_001_fastqc.zip trimmed_ACR-150-TP2_S2_R2_001_fastqc.html trimmed_ACR-150-TP2_S2_R2_001_fastqc.zip trimmed_ACR-173-TP2_S4_R1_001_fastqc.html trimmed_ACR-173-TP2_S4_R1_001_fastqc.zip trimmed_ACR-173-TP2_S4_R2_001_fastqc.html trimmed_ACR-173-TP2_S4_R2_001_fastqc.zip trimmed_ACR-178-TP2_S1_R1_001_fastqc.html trimmed_ACR-178-TP2_S1_R1_001_fastqc.zip trimmed_ACR-178-TP2_S1_R2_001_fastqc.html trimmed_ACR-178-TP2_S1_R2_001_fastqc.zip [2025-04-10 18:05:21,450] multiqc [WARNING] MultiQC Version v1.28 now available! [2025-04-10 18:05:21,450] multiqc [DEBUG ] Command : /modules/uri_apps/software/MultiQC/1.12-foss-2021b/bin/multiqc trimmed_ACR-140-TP2_S5_R1_001_fastqc.html trimmed_ACR-140-TP2_S5_R1_001_fastqc.zip trimmed_ACR-140-TP2_S5_R2_001_fastqc.html trimmed_ACR-140-TP2_S5_R2_001_fastqc.zip trimmed_ACR-145-TP2_S3_R1_001_fastqc.html trimmed_ACR-145-TP2_S3_R1_001_fastqc.zip trimmed_ACR-145-TP2_S3_R2_001_fastqc.html trimmed_ACR-145-TP2_S3_R2_001_fastqc.zip trimmed_ACR-150-TP2_S2_R1_001_fastqc.html trimmed_ACR-150-TP2_S2_R1_001_fastqc.zip trimmed_ACR-150-TP2_S2_R2_001_fastqc.html trimmed_ACR-150-TP2_S2_R2_001_fastqc.zip trimmed_ACR-173-TP2_S4_R1_001_fastqc.html trimmed_ACR-173-TP2_S4_R1_001_fastqc.zip trimmed_ACR-173-TP2_S4_R2_001_fastqc.html trimmed_ACR-173-TP2_S4_R2_001_fastqc.zip trimmed_ACR-178-TP2_S1_R1_001_fastqc.html trimmed_ACR-178-TP2_S1_R1_001_fastqc.zip trimmed_ACR-178-TP2_S1_R2_001_fastqc.html trimmed_ACR-178-TP2_S1_R2_001_fastqc.zip [2025-04-10 18:05:21,450] multiqc [DEBUG ] Working dir : /scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/output/01.00-D-Apul-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_qc [2025-04-10 18:05:21,450] multiqc [DEBUG ] Template : default [2025-04-10 18:05:21,450] multiqc [DEBUG ] Running Python 3.9.6 (default, Nov 15 2024, 16:57:16) [GCC 11.2.0] [2025-04-10 18:05:21,452] multiqc [DEBUG ] Analysing modules: custom_content, ccs, ngsderive, purple, conpair, lima, peddy, somalier, methylQA, mosdepth, phantompeakqualtools, qualimap, preseq, quast, qorts, rna_seqc, rockhopper, rsem, rseqc, busco, bustools, goleft_indexcov, gffcompare, disambiguate, supernova, deeptools, sargasso, verifybamid, mirtrace, happy, mirtop, sambamba, homer, hops, macs2, theta2, snpeff, gatk, htseq, bcftools, featureCounts, fgbio, dragen, dedup, pbmarkdup, damageprofiler, biobambam2, jcvi, mtnucratio, picard, vep, sentieon, prokka, qc3C, nanostat, samblaster, samtools, sexdeterrmine, eigenstratdatabasetools, bamtools, jellyfish, vcftools, longranger, stacks, varscan2, snippy, bbmap, bismark, biscuit, hicexplorer, hicup, hicpro, salmon, kallisto, slamdunk, star, hisat2, tophat, bowtie2, bowtie1, snpsplit, odgi, pangolin, kat, leehom, adapterRemoval, clipandmerge, cutadapt, flexbar, kaiju, kraken, malt, trimmomatic, sickle, skewer, sortmerna, biobloomtools, fastq_screen, afterqc, fastp, fastqc, pychopper, pycoqc, minionqc, multivcfanalyzer, clusterflow, checkqc, bcl2fastq, bclconvert, interop, ivar, flash, seqyclean, optitype, whatshap [2025-04-10 18:05:21,452] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmp9gwq3rqm [2025-04-10 18:05:22,087] multiqc [INFO ] Search path : /scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/output/01.00-D-Apul-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_qc/trimmed_ACR-140-TP2_S5_R1_001_fastqc.html [2025-04-10 18:05:22,087] multiqc [INFO ] Search path : 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ignored by ccs/v4 because it exceeded search pattern filesize limit: trimmed_ACR-150-TP2_S2_R2_001_fastqc.html [2025-04-10 18:05:22,314] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: trimmed_ACR-150-TP2_S2_R2_001_fastqc.html [2025-04-10 18:05:22,314] multiqc [DEBUG ] File ignored by lima/summary because it exceeded search pattern filesize limit: trimmed_ACR-150-TP2_S2_R2_001_fastqc.html [2025-04-10 18:05:22,316] multiqc [DEBUG ] File ignored by vep/vep_txt because it exceeded search pattern filesize limit: trimmed_ACR-150-TP2_S2_R2_001_fastqc.html [2025-04-10 18:05:22,316] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: trimmed_ACR-150-TP2_S2_R2_001_fastqc.html [2025-04-10 18:05:22,316] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: trimmed_ACR-150-TP2_S2_R2_001_fastqc.html [2025-04-10 18:05:22,316] multiqc [DEBUG ] File ignored by 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File ignored by hicexplorer because it exceeded search pattern filesize limit: trimmed_ACR-173-TP2_S4_R1_001_fastqc.html [2025-04-10 18:05:22,348] multiqc [DEBUG ] File ignored by lima/summary because it exceeded search pattern filesize limit: trimmed_ACR-173-TP2_S4_R1_001_fastqc.html [2025-04-10 18:05:22,350] multiqc [DEBUG ] File ignored by vep/vep_txt because it exceeded search pattern filesize limit: trimmed_ACR-173-TP2_S4_R1_001_fastqc.html [2025-04-10 18:05:22,350] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: trimmed_ACR-173-TP2_S4_R1_001_fastqc.html [2025-04-10 18:05:22,350] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: trimmed_ACR-173-TP2_S4_R1_001_fastqc.html [2025-04-10 18:05:22,350] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: trimmed_ACR-173-TP2_S4_R1_001_fastqc.html [2025-04-10 18:05:22,350] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: trimmed_ACR-173-TP2_S4_R1_001_fastqc.html [2025-04-10 18:05:22,350] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: trimmed_ACR-173-TP2_S4_R1_001_fastqc.html [2025-04-10 18:05:22,350] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: trimmed_ACR-173-TP2_S4_R1_001_fastqc.html [2025-04-10 18:05:22,376] multiqc [DEBUG ] File ignored by nanostat because it exceeded search pattern filesize limit: trimmed_ACR-173-TP2_S4_R1_001_fastqc.html [2025-04-10 18:05:22,381] multiqc [DEBUG ] File ignored by ccs/v4 because it exceeded search pattern filesize limit: trimmed_ACR-173-TP2_S4_R2_001_fastqc.html [2025-04-10 18:05:22,382] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: trimmed_ACR-173-TP2_S4_R2_001_fastqc.html [2025-04-10 18:05:22,382] multiqc [DEBUG ] File ignored by lima/summary because it exceeded search pattern filesize limit: trimmed_ACR-173-TP2_S4_R2_001_fastqc.html [2025-04-10 18:05:22,384] multiqc [DEBUG ] File ignored by vep/vep_txt because it exceeded search pattern filesize limit: trimmed_ACR-173-TP2_S4_R2_001_fastqc.html [2025-04-10 18:05:22,384] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: trimmed_ACR-173-TP2_S4_R2_001_fastqc.html [2025-04-10 18:05:22,384] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: trimmed_ACR-173-TP2_S4_R2_001_fastqc.html [2025-04-10 18:05:22,384] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: trimmed_ACR-173-TP2_S4_R2_001_fastqc.html [2025-04-10 18:05:22,384] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: trimmed_ACR-173-TP2_S4_R2_001_fastqc.html [2025-04-10 18:05:22,384] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: trimmed_ACR-173-TP2_S4_R2_001_fastqc.html [2025-04-10 18:05:22,384] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: trimmed_ACR-173-TP2_S4_R2_001_fastqc.html [2025-04-10 18:05:22,411] multiqc [DEBUG ] File ignored by nanostat because it exceeded search pattern filesize limit: trimmed_ACR-173-TP2_S4_R2_001_fastqc.html [2025-04-10 18:05:22,416] multiqc [DEBUG ] File ignored by ccs/v4 because it exceeded search pattern filesize limit: trimmed_ACR-178-TP2_S1_R1_001_fastqc.html [2025-04-10 18:05:22,417] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: trimmed_ACR-178-TP2_S1_R1_001_fastqc.html [2025-04-10 18:05:22,417] multiqc [DEBUG ] File ignored by lima/summary because it exceeded search pattern filesize limit: trimmed_ACR-178-TP2_S1_R1_001_fastqc.html [2025-04-10 18:05:22,418] multiqc [DEBUG ] File ignored by vep/vep_txt because it exceeded search pattern filesize limit: trimmed_ACR-178-TP2_S1_R1_001_fastqc.html [2025-04-10 18:05:22,419] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: trimmed_ACR-178-TP2_S1_R1_001_fastqc.html [2025-04-10 18:05:22,419] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: trimmed_ACR-178-TP2_S1_R1_001_fastqc.html [2025-04-10 18:05:22,419] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: trimmed_ACR-178-TP2_S1_R1_001_fastqc.html [2025-04-10 18:05:22,419] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: trimmed_ACR-178-TP2_S1_R1_001_fastqc.html [2025-04-10 18:05:22,419] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: trimmed_ACR-178-TP2_S1_R1_001_fastqc.html [2025-04-10 18:05:22,419] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: trimmed_ACR-178-TP2_S1_R1_001_fastqc.html [2025-04-10 18:05:22,444] multiqc [DEBUG ] File ignored by nanostat because it exceeded search pattern filesize limit: trimmed_ACR-178-TP2_S1_R1_001_fastqc.html [2025-04-10 18:05:22,450] multiqc [DEBUG ] File ignored by ccs/v4 because it exceeded search pattern filesize limit: trimmed_ACR-178-TP2_S1_R2_001_fastqc.html [2025-04-10 18:05:22,451] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: trimmed_ACR-178-TP2_S1_R2_001_fastqc.html [2025-04-10 18:05:22,451] multiqc [DEBUG ] File ignored by lima/summary because it exceeded search pattern filesize limit: trimmed_ACR-178-TP2_S1_R2_001_fastqc.html [2025-04-10 18:05:22,452] multiqc [DEBUG ] File ignored by vep/vep_txt because it exceeded search pattern filesize limit: trimmed_ACR-178-TP2_S1_R2_001_fastqc.html [2025-04-10 18:05:22,452] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: trimmed_ACR-178-TP2_S1_R2_001_fastqc.html [2025-04-10 18:05:22,453] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: trimmed_ACR-178-TP2_S1_R2_001_fastqc.html [2025-04-10 18:05:22,453] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: trimmed_ACR-178-TP2_S1_R2_001_fastqc.html [2025-04-10 18:05:22,453] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: trimmed_ACR-178-TP2_S1_R2_001_fastqc.html [2025-04-10 18:05:22,453] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: trimmed_ACR-178-TP2_S1_R2_001_fastqc.html [2025-04-10 18:05:22,453] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: trimmed_ACR-178-TP2_S1_R2_001_fastqc.html [2025-04-10 18:05:22,479] multiqc [DEBUG ] File ignored by nanostat because it exceeded search pattern filesize limit: trimmed_ACR-178-TP2_S1_R2_001_fastqc.html [2025-04-10 18:05:25,132] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.4.3 [2025-04-10 18:05:25,139] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.4.3 [2025-04-10 18:05:26,340] multiqc.modules.fastqc.fastqc [INFO ] Found 10 reports [2025-04-10 18:05:26,472] multiqc [INFO ] Compressing plot data [2025-04-10 18:05:26,639] multiqc [INFO ] Report : multiqc_report.html [2025-04-10 18:05:26,639] multiqc [INFO ] Data : multiqc_data [2025-04-10 18:05:26,639] multiqc [DEBUG ] Moving data file from '/tmp/tmp9gwq3rqm/multiqc_data' to '/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/output/01.00-D-Apul-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_qc/multiqc_data' [2025-04-10 18:05:27,086] multiqc [INFO ] MultiQC complete