[2022-07-18 08:50:24,002] multiqc [DEBUG ] This is MultiQC v1.12 (a3a6d4f) [2022-07-18 08:50:24,002] multiqc [DEBUG ] No MultiQC config found: /home/nolson/projects_ndo/sars-cov2-rtgm-seq/.snakemake/conda/3a434bf294cb8eba84e5ec414f7d8877/lib/python3.10/site-packages/multiqc_config.yaml [2022-07-18 08:50:24,002] multiqc [DEBUG ] No MultiQC config found: /home/nolson/.multiqc_config.yaml [2022-07-18 08:50:24,003] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-07-18 08:50:24,003] multiqc [DEBUG ] Command used: /home/nolson/projects_ndo/sars-cov2-rtgm-seq/.snakemake/conda/3a434bf294cb8eba84e5ec414f7d8877/bin/multiqc --force -o results/qc -n multiqc.html results/qc/fq results/qc/bam [2022-07-18 08:50:24,618] multiqc [DEBUG ] Latest MultiQC version is v1.12 [2022-07-18 08:50:24,618] multiqc [DEBUG ] Command : /home/nolson/projects_ndo/sars-cov2-rtgm-seq/.snakemake/conda/3a434bf294cb8eba84e5ec414f7d8877/bin/multiqc --force -o results/qc -n multiqc.html results/qc/fq results/qc/bam [2022-07-18 08:50:24,619] multiqc [DEBUG ] Working dir : /home/nolson/projects_ndo/sars-cov2-rtgm-seq [2022-07-18 08:50:24,619] multiqc [DEBUG ] Template : default [2022-07-18 08:50:24,619] multiqc [DEBUG ] Running Python 3.10.5 | packaged by conda-forge | (main, Jun 14 2022, 07:06:46) [GCC 10.3.0] [2022-07-18 08:50:24,620] 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 [2022-07-18 08:50:24,620] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmp2u35e6k4 [2022-07-18 08:50:24,794] multiqc [INFO ] Search path : /home/nolson/projects_ndo/sars-cov2-rtgm-seq/results/qc/fq [2022-07-18 08:50:24,794] multiqc [INFO ] Search path : /home/nolson/projects_ndo/sars-cov2-rtgm-seq/results/qc/bam [2022-07-18 08:50:24,815] multiqc [DEBUG ] File ignored by ccs/v4 because it exceeded search pattern filesize limit: ill_c2_R1_fastqc.html [2022-07-18 08:50:24,816] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: ill_c2_R1_fastqc.html [2022-07-18 08:50:24,816] multiqc [DEBUG ] File ignored by lima/summary because it exceeded search pattern filesize limit: ill_c2_R1_fastqc.html [2022-07-18 08:50:24,818] multiqc [DEBUG ] File ignored by vep/vep_txt because it exceeded search pattern filesize limit: ill_c2_R1_fastqc.html [2022-07-18 08:50:24,818] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: ill_c2_R1_fastqc.html [2022-07-18 08:50:24,818] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: ill_c2_R1_fastqc.html [2022-07-18 08:50:24,818] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: ill_c2_R1_fastqc.html [2022-07-18 08:50:24,818] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: 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pattern filesize limit: ill_c2_R2_fastqc.html [2022-07-18 08:50:24,881] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: ill_c2_R2_fastqc.html [2022-07-18 08:50:24,881] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: ill_c2_R2_fastqc.html [2022-07-18 08:50:24,881] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: ill_c2_R2_fastqc.html [2022-07-18 08:50:24,881] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: ill_c2_R2_fastqc.html [2022-07-18 08:50:24,881] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: ill_c2_R2_fastqc.html [2022-07-18 08:50:24,881] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: ill_c2_R2_fastqc.html [2022-07-18 08:50:24,934] multiqc [DEBUG ] File ignored by nanostat because it exceeded search pattern filesize limit: ill_c2_R2_fastqc.html [2022-07-18 08:50:24,941] multiqc [DEBUG ] File ignored by ccs/v4 because it exceeded search pattern filesize limit: ill_c1_R2_fastqc.html [2022-07-18 08:50:24,942] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: ill_c1_R2_fastqc.html [2022-07-18 08:50:24,942] multiqc [DEBUG ] File ignored by lima/summary because it exceeded search pattern filesize limit: ill_c1_R2_fastqc.html [2022-07-18 08:50:24,943] multiqc [DEBUG ] File ignored by vep/vep_txt because it exceeded search pattern filesize limit: ill_c1_R2_fastqc.html [2022-07-18 08:50:24,943] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: ill_c1_R2_fastqc.html [2022-07-18 08:50:24,943] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: ill_c1_R2_fastqc.html [2022-07-18 08:50:24,943] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: ill_c1_R2_fastqc.html [2022-07-18 08:50:24,943] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: ill_c1_R2_fastqc.html [2022-07-18 08:50:24,943] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: ill_c1_R2_fastqc.html [2022-07-18 08:50:24,943] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: ill_c1_R2_fastqc.html [2022-07-18 08:50:24,996] multiqc [DEBUG ] File ignored by nanostat because it exceeded search pattern filesize limit: ill_c1_R2_fastqc.html [2022-07-18 08:50:25,003] multiqc [DEBUG ] File ignored by ccs/v4 because it exceeded search pattern filesize limit: ill_c1_R1_fastqc.html [2022-07-18 08:50:25,004] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: ill_c1_R1_fastqc.html [2022-07-18 08:50:25,004] multiqc [DEBUG ] File ignored by lima/summary because it exceeded search pattern filesize limit: ill_c1_R1_fastqc.html [2022-07-18 08:50:25,005] multiqc [DEBUG ] File ignored by vep/vep_txt because it exceeded search pattern filesize limit: ill_c1_R1_fastqc.html [2022-07-18 08:50:25,006] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: ill_c1_R1_fastqc.html [2022-07-18 08:50:25,006] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: ill_c1_R1_fastqc.html [2022-07-18 08:50:25,006] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: ill_c1_R1_fastqc.html [2022-07-18 08:50:25,006] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: ill_c1_R1_fastqc.html [2022-07-18 08:50:25,006] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: ill_c1_R1_fastqc.html [2022-07-18 08:50:25,006] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: ill_c1_R1_fastqc.html [2022-07-18 08:50:25,058] multiqc [DEBUG ] File ignored by nanostat because it exceeded search pattern filesize limit: ill_c1_R1_fastqc.html [2022-07-18 08:50:25,063] multiqc [DEBUG ] File ignored by ccs/v4 because it exceeded search pattern filesize limit: ont.txt [2022-07-18 08:50:25,064] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: ont.txt [2022-07-18 08:50:25,064] multiqc [DEBUG ] File ignored by lima/summary because it exceeded search pattern filesize limit: ont.txt [2022-07-18 08:50:25,065] multiqc [DEBUG ] File ignored by vep/vep_html because it exceeded search pattern filesize limit: ont.txt [2022-07-18 08:50:25,065] multiqc [DEBUG ] File ignored by vep/vep_txt because it exceeded search pattern filesize limit: ont.txt [2022-07-18 08:50:25,065] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: ont.txt [2022-07-18 08:50:25,065] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: ont.txt [2022-07-18 08:50:25,065] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: ont.txt [2022-07-18 08:50:25,065] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: ont.txt [2022-07-18 08:50:25,065] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: ont.txt [2022-07-18 08:50:25,065] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: ont.txt [2022-07-18 08:50:25,065] multiqc [DEBUG ] File ignored by snpeff because it exceeded search pattern filesize limit: ont.txt [2022-07-18 08:50:25,065] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: ont.txt [2022-07-18 08:50:25,565] multiqc [DEBUG ] File ignored by nanostat because it exceeded search pattern filesize limit: ont.txt [2022-07-18 08:50:25,611] multiqc [DEBUG ] File ignored by ccs/v4 because it exceeded search pattern filesize limit: ill_c2.txt [2022-07-18 08:50:25,612] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: ill_c2.txt [2022-07-18 08:50:25,612] multiqc [DEBUG ] File ignored by lima/summary because it exceeded search pattern filesize limit: ill_c2.txt [2022-07-18 08:50:25,615] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: ill_c2.txt [2022-07-18 08:50:25,653] multiqc [DEBUG ] File ignored by nanostat because it exceeded search pattern filesize limit: ill_c2.txt [2022-07-18 08:50:25,656] multiqc [DEBUG ] File ignored by ccs/v4 because it exceeded search pattern filesize limit: ill_c1.txt [2022-07-18 08:50:25,656] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: ill_c1.txt [2022-07-18 08:50:25,656] multiqc [DEBUG ] File ignored by lima/summary because it exceeded search pattern filesize limit: ill_c1.txt [2022-07-18 08:50:25,657] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: ill_c1.txt [2022-07-18 08:50:25,684] multiqc [DEBUG ] File ignored by nanostat because it exceeded search pattern filesize limit: ill_c1.txt [2022-07-18 08:50:26,910] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.5.2 [2022-07-18 08:50:26,911] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.5.2 [2022-07-18 08:50:26,934] multiqc.modules.samtools.samtools [INFO ] Found 3 stats reports [2022-07-18 08:50:27,022] multiqc.modules.fastqc.fastqc [INFO ] Found 4 reports [2022-07-18 08:50:27,096] multiqc [INFO ] Compressing plot data [2022-07-18 08:50:27,139] multiqc [WARNING] Deleting : results/qc/multiqc_data (-f was specified) [2022-07-18 08:50:27,139] multiqc [INFO ] Report : results/qc/multiqc.html [2022-07-18 08:50:27,139] multiqc [INFO ] Data : results/qc/multiqc_data [2022-07-18 08:50:27,140] multiqc [DEBUG ] Moving data file from '/tmp/tmp2u35e6k4/multiqc_data' to 'results/qc/multiqc_data' [2022-07-18 08:50:27,201] multiqc [INFO ] MultiQC complete