[2019-09-24 09:22:17,799] multiqc [DEBUG ] No MultiQC config found: /home/sam/.local/lib/python3.5/site-packages/multiqc-1.6-py3.5.egg/multiqc_config.yaml [2019-09-24 09:22:17,799] multiqc [DEBUG ] No MultiQC config found: /home/sam/.multiqc_config.yaml [2019-09-24 09:22:17,799] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2019-09-24 09:22:17,800] multiqc [DEBUG ] Command used: /usr/local/bin/multiqc . [2019-09-24 09:22:18,993] multiqc [WARNING] MultiQC Version v1.7 now available! [2019-09-24 09:22:18,993] multiqc [INFO ] This is MultiQC v1.6 [2019-09-24 09:22:18,993] multiqc [DEBUG ] Command : /usr/local/bin/multiqc . [2019-09-24 09:22:18,993] multiqc [DEBUG ] Working dir : /home/sam/analyses/20190923_pgen_fastp_EPI_trimming [2019-09-24 09:22:18,993] multiqc [INFO ] Template : default [2019-09-24 09:22:18,993] multiqc [INFO ] Searching '.' [2019-09-24 09:22:18,995] multiqc [DEBUG ] Analysing modules: custom_content, conpair, peddy, methylQA, 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, dedup, picard, prokka, samblaster, samtools, bamtools, jellyfish, vcftools, longranger, bbmap, bismark, 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, clusterflow, bcl2fastq, interop [2019-09-24 09:22:18,995] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmp1_wibq6w [2019-09-24 09:22:19,013] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-182_S17_L003_R2_001_val_2.20bp-trim_fastqc.html [2019-09-24 09:22:19,013] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-169_S12_L002_R2_001_val_2.20bp-trim_fastqc.html [2019-09-24 09:22:19,013] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-153_S4_L002_R1_001_val_1.20bp-trim_fastqc.html [2019-09-24 09:22:19,013] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-128_S34_L005_R2_001_val_2.20bp-trim.fq.gz [2019-09-24 09:22:19,013] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-136_S36_L005_R1_001_val_1.20bp-trim_fastqc.html [2019-09-24 09:22:19,013] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-194_S23_L003_R2_001_val_2.20bp-trim_fastqc.html [2019-09-24 09:22:19,014] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-42_S39_L005_R2_001_val_2.20bp-trim_fastqc.html [2019-09-24 09:22:19,014] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-182_S17_L003_R1_001_val_1.20bp-trim.fq.gz [2019-09-24 09:22:19,014] multiqc [DEBUG ] Ignoring file as matched an ignore 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09:22:19,039] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-103_S27_L005_R1_001_val_1.20bp-trim_fastqc.html [2019-09-24 09:22:19,039] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-221_S33_L004_R2_001_val_2.20bp-trim_fastqc.html [2019-09-24 09:22:19,040] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-176_S15_L003_R1_001_val_1.20bp-trim_fastqc.html [2019-09-24 09:22:19,040] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-43_S40_L005_R1_001_val_1.20bp-trim_fastqc.html [2019-09-24 09:22:19,040] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-135_S35_L005_R2_001_val_2.20bp-trim_fastqc.html [2019-09-24 09:22:19,040] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-209_S29_L004_R2_001_val_2.20bp-trim_fastqc.html [2019-09-24 09:22:19,041] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-111_S29_L005_R1_001_val_1.20bp-trim_fastqc.html [2019-09-24 09:22:19,041] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-193_S22_L003_R1_001_val_1.20bp-trim_fastqc.html [2019-09-24 09:22:19,041] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-184_S18_L003_R2_001_val_2.20bp-trim_fastqc.html [2019-09-24 09:22:19,041] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-153_S4_L002_R1_001_val_1.20bp-trim.fq.gz [2019-09-24 09:22:19,041] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-182_S17_L003_R1_001_val_1.20bp-trim_fastqc.html [2019-09-24 09:22:19,077] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-206_S27_L004_R1_001_val_1.20bp-trim_fastqc.html [2019-09-24 09:22:19,078] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-182_S17_L003_R2_001_val_2.20bp-trim.fq.gz [2019-09-24 09:22:19,078] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-194_S23_L003_R2_001_val_2.20bp-trim.fq.gz [2019-09-24 09:22:19,078] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-42_S39_L005_R1_001_val_1.20bp-trim_fastqc.html [2019-09-24 09:22:19,078] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-176_S15_L003_R1_001_val_1.20bp-trim.fq.gz [2019-09-24 09:22:19,078] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-199_S24_L003_R1_001_val_1.20bp-trim.fq.gz [2019-09-24 09:22:19,078] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-127_S33_L005_R2_001_val_2.20bp-trim.fq.gz [2019-09-24 09:22:19,079] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-185_S19_L003_R2_001_val_2.20bp-trim_fastqc.html [2019-09-24 09:22:19,079] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-128_S34_L005_R2_001_val_2.20bp-trim_fastqc.html [2019-09-24 09:22:19,080] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-119_S31_L005_R1_001_val_1.20bp-trim.fq.gz [2019-09-24 09:22:19,080] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-42_S39_L005_R1_001_val_1.20bp-trim.fq.gz [2019-09-24 09:22:19,080] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-161_S8_L002_R2_001_val_2.20bp-trim_fastqc.html [2019-09-24 09:22:19,080] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-111_S29_L005_R1_001_val_1.20bp-trim.fq.gz [2019-09-24 09:22:19,081] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-104_S28_L005_R2_001_val_2.20bp-trim.fq.gz [2019-09-24 09:22:19,081] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-199_S24_L003_R1_001_val_1.20bp-trim_fastqc.html [2019-09-24 09:22:19,081] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-170_S13_L002_R1_001_val_1.20bp-trim.fq.gz [2019-09-24 09:22:19,081] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-214_S30_L004_R1_001_val_1.20bp-trim_fastqc.html [2019-09-24 09:22:19,082] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-187_S20_L003_R2_001_val_2.20bp-trim.fq.gz [2019-09-24 09:22:19,082] multiqc [DEBUG ] Ignoring 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[DEBUG ] Ignoring file as matched an ignore pattern: EPI-111_S29_L005_R2_001_val_2.20bp-trim_fastqc.html [2019-09-24 09:22:19,085] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-43_S40_L005_R2_001_val_2.20bp-trim.fq.gz [2019-09-24 09:22:19,086] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-185_S19_L003_R1_001_val_1.20bp-trim.fq.gz [2019-09-24 09:22:19,149] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-41_S38_L005_R2_001_val_2.20bp-trim_fastqc.html [2019-09-24 09:22:19,149] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-187_S20_L003_R1_001_val_1.20bp-trim.fq.gz [2019-09-24 09:22:19,149] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-160_S7_L002_R2_001_val_2.20bp-trim_fastqc.html [2019-09-24 09:22:19,149] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-209_S29_L004_R1_001_val_1.20bp-trim_fastqc.html [2019-09-24 09:22:19,150] multiqc [DEBUG ] Ignoring file as matched an ignore 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[2019-09-24 09:22:19,152] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-103_S27_L005_R2_001_val_2.20bp-trim_fastqc.html [2019-09-24 09:22:19,152] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-104_S28_L005_R2_001_val_2.20bp-trim_fastqc.html [2019-09-24 09:22:19,152] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-167_S10_L002_R2_001_val_2.20bp-trim_fastqc.html [2019-09-24 09:22:19,152] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-120_S32_L005_R2_001_val_2.20bp-trim.fq.gz [2019-09-24 09:22:19,152] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-113_S30_L005_R2_001_val_2.20bp-trim.fq.gz [2019-09-24 09:22:19,153] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-229_S36_L004_R1_001_val_1.20bp-trim.fq.gz [2019-09-24 09:22:19,153] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-188_S21_L003_R1_001_val_1.20bp-trim_fastqc.html [2019-09-24 09:22:19,153] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-44_S41_L005_R2_001_val_2.20bp-trim.fq.gz [2019-09-24 09:22:19,154] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-162_S9_L002_R1_001_val_1.20bp-trim_fastqc.html [2019-09-24 09:22:19,154] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-227_S35_L004_R2_001_val_2.20bp-trim.fq.gz [2019-09-24 09:22:19,154] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-205_S26_L004_R2_001_val_2.20bp-trim.fq.gz [2019-09-24 09:22:19,155] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-170_S13_L002_R1_001_val_1.20bp-trim_fastqc.html [2019-09-24 09:22:19,155] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-167_S10_L002_R1_001_val_1.20bp-trim_fastqc.html [2019-09-24 09:22:19,155] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-162_S9_L002_R2_001_val_2.20bp-trim_fastqc.html [2019-09-24 09:22:19,155] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 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[2019-09-24 09:22:19,159] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-227_S35_L004_R1_001_val_1.20bp-trim_fastqc.html [2019-09-24 09:22:19,160] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-181_S16_L003_R1_001_val_1.20bp-trim.fq.gz [2019-09-24 09:22:19,160] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-200_S25_L003_R1_001_val_1.20bp-trim_fastqc.html [2019-09-24 09:22:19,160] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-42_S39_L005_R2_001_val_2.20bp-trim.fq.gz [2019-09-24 09:22:19,160] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-208_S28_L004_R1_001_val_1.20bp-trim.fq.gz [2019-09-24 09:22:19,160] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-169_S12_L002_R1_001_val_1.20bp-trim.fq.gz [2019-09-24 09:22:19,160] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-209_S29_L004_R1_001_val_1.20bp-trim.fq.gz [2019-09-24 09:22:19,161] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-205_S26_L004_R1_001_val_1.20bp-trim.fq.gz [2019-09-24 09:22:19,161] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-199_S24_L003_R2_001_val_2.20bp-trim_fastqc.html [2019-09-24 09:22:19,161] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-208_S28_L004_R1_001_val_1.20bp-trim_fastqc.html [2019-09-24 09:22:19,161] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-169_S12_L002_R2_001_val_2.20bp-trim.fq.gz [2019-09-24 09:22:19,162] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-175_S14_L003_R1_001_val_1.20bp-trim.fq.gz [2019-09-24 09:22:19,162] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-220_S32_L004_R2_001_val_2.20bp-trim.fq.gz [2019-09-24 09:22:19,162] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-227_S35_L004_R2_001_val_2.20bp-trim_fastqc.html [2019-09-24 09:22:19,162] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-127_S33_L005_R1_001_val_1.20bp-trim_fastqc.html [2019-09-24 09:22:19,162] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-145_S38_L005_R2_001_val_2.20bp-trim.fq.gz [2019-09-24 09:22:19,163] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-44_S41_L005_R1_001_val_1.20bp-trim.fq.gz [2019-09-24 09:22:19,163] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-184_S18_L003_R2_001_val_2.20bp-trim.fq.gz [2019-09-24 09:22:19,163] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-44_S41_L005_R2_001_val_2.20bp-trim_fastqc.html [2019-09-24 09:22:19,163] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-181_S16_L003_R2_001_val_2.20bp-trim_fastqc.html [2019-09-24 09:22:19,164] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-181_S16_L003_R1_001_val_1.20bp-trim_fastqc.html [2019-09-24 09:22:19,164] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-135_S35_L005_R1_001_val_1.20bp-trim_fastqc.html [2019-09-24 09:22:19,173] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-41_S38_L005_R2_001_val_2.20bp-trim.fq.gz [2019-09-24 09:22:19,173] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-143_S37_L005_R1_001_val_1.20bp-trim.fq.gz [2019-09-24 09:22:19,173] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-120_S32_L005_R2_001_val_2.20bp-trim_fastqc.html [2019-09-24 09:22:19,173] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-230_S37_L004_R2_001_val_2.20bp-trim.fq.gz [2019-09-24 09:22:19,174] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-136_S36_L005_R2_001_val_2.20bp-trim_fastqc.html [2019-09-24 09:22:19,174] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-208_S28_L004_R2_001_val_2.20bp-trim_fastqc.html [2019-09-24 09:22:19,174] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-226_S34_L004_R1_001_val_1.20bp-trim_fastqc.html [2019-09-24 09:22:19,174] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-41_S38_L005_R1_001_val_1.20bp-trim.fq.gz [2019-09-24 09:22:19,174] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-41_S38_L005_R1_001_val_1.20bp-trim_fastqc.html [2019-09-24 09:22:19,174] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-152_S3_L002_R1_001_val_1.20bp-trim.fq.gz [2019-09-24 09:22:19,181] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-200_S25_L003_R1_001_val_1.20bp-trim.fq.gz [2019-09-24 09:22:19,181] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-181_S16_L003_R2_001_val_2.20bp-trim.fq.gz [2019-09-24 09:22:19,182] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-167_S10_L002_R1_001_val_1.20bp-trim.fq.gz [2019-09-24 09:22:19,182] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-230_S37_L004_R1_001_val_1.20bp-trim_fastqc.html [2019-09-24 09:22:19,182] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-184_S18_L003_R1_001_val_1.20bp-trim.fq.gz [2019-09-24 09:22:19,182] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-205_S26_L004_R1_001_val_1.20bp-trim_fastqc.html [2019-09-24 09:22:19,182] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-194_S23_L003_R1_001_val_1.20bp-trim.fq.gz [2019-09-24 09:22:19,182] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-170_S13_L002_R2_001_val_2.20bp-trim.fq.gz [2019-09-24 09:22:19,183] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-199_S24_L003_R2_001_val_2.20bp-trim.fq.gz [2019-09-24 09:22:19,183] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-161_S8_L002_R1_001_val_1.20bp-trim.fq.gz [2019-09-24 09:22:19,184] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-168_S11_L002_R2_001_val_2.20bp-trim.fq.gz [2019-09-24 09:22:19,184] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-206_S27_L004_R2_001_val_2.20bp-trim_fastqc.html [2019-09-24 09:22:19,184] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-128_S34_L005_R1_001_val_1.20bp-trim_fastqc.html [2019-09-24 09:22:19,184] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-43_S40_L005_R2_001_val_2.20bp-trim_fastqc.html [2019-09-24 09:22:19,184] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-169_S12_L002_R1_001_val_1.20bp-trim_fastqc.html [2019-09-24 09:22:19,185] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-221_S33_L004_R1_001_val_1.20bp-trim_fastqc.html [2019-09-24 09:22:19,185] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-209_S29_L004_R2_001_val_2.20bp-trim.fq.gz [2019-09-24 09:22:19,185] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-113_S30_L005_R1_001_val_1.20bp-trim_fastqc.html [2019-09-24 09:22:19,185] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-120_S32_L005_R1_001_val_1.20bp-trim_fastqc.html [2019-09-24 09:22:19,186] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-119_S31_L005_R2_001_val_2.20bp-trim.fq.gz [2019-09-24 09:22:19,186] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-188_S21_L003_R2_001_val_2.20bp-trim_fastqc.html [2019-09-24 09:22:19,186] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-193_S22_L003_R2_001_val_2.20bp-trim_fastqc.html [2019-09-24 09:22:19,186] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-151_S2_L002_R1_001_val_1.20bp-trim_fastqc.html [2019-09-24 09:22:19,195] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-215_S31_L004_R1_001_val_1.20bp-trim_fastqc.html [2019-09-24 09:22:19,195] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-154_S5_L002_R2_001_val_2.20bp-trim.fq.gz [2019-09-24 09:22:19,196] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-111_S29_L005_R2_001_val_2.20bp-trim.fq.gz [2019-09-24 09:22:19,196] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-153_S4_L002_R2_001_val_2.20bp-trim_fastqc.html [2019-09-24 09:22:19,196] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-135_S35_L005_R1_001_val_1.20bp-trim.fq.gz [2019-09-24 09:22:19,196] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-176_S15_L003_R2_001_val_2.20bp-trim.fq.gz [2019-09-24 09:22:19,197] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-206_S27_L004_R1_001_val_1.20bp-trim.fq.gz [2019-09-24 09:22:19,197] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-154_S5_L002_R1_001_val_1.20bp-trim_fastqc.html [2019-09-24 09:22:19,197] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-167_S10_L002_R2_001_val_2.20bp-trim.fq.gz [2019-09-24 09:22:19,197] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-168_S11_L002_R2_001_val_2.20bp-trim_fastqc.html [2019-09-24 09:22:19,197] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-159_S6_L002_R1_001_val_1.20bp-trim.fq.gz [2019-09-24 09:22:19,197] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-160_S7_L002_R2_001_val_2.20bp-trim.fq.gz [2019-09-24 09:22:19,198] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-215_S31_L004_R1_001_val_1.20bp-trim.fq.gz [2019-09-24 09:22:19,198] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-229_S36_L004_R2_001_val_2.20bp-trim.fq.gz [2019-09-24 09:22:19,198] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-168_S11_L002_R1_001_val_1.20bp-trim.fq.gz [2019-09-24 09:22:19,198] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-136_S36_L005_R2_001_val_2.20bp-trim.fq.gz [2019-09-24 09:22:19,199] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-127_S33_L005_R1_001_val_1.20bp-trim.fq.gz [2019-09-24 09:22:19,199] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-160_S7_L002_R1_001_val_1.20bp-trim.fq.gz [2019-09-24 09:22:19,199] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-214_S30_L004_R2_001_val_2.20bp-trim.fq.gz [2019-09-24 09:22:19,199] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-221_S33_L004_R1_001_val_1.20bp-trim.fq.gz [2019-09-24 09:22:19,199] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-185_S19_L003_R2_001_val_2.20bp-trim.fq.gz [2019-09-24 09:22:19,200] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-184_S18_L003_R1_001_val_1.20bp-trim_fastqc.html [2019-09-24 09:22:19,200] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-205_S26_L004_R2_001_val_2.20bp-trim_fastqc.html [2019-09-24 09:22:19,200] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-229_S36_L004_R1_001_val_1.20bp-trim_fastqc.html [2019-09-24 09:22:19,200] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-220_S32_L004_R1_001_val_1.20bp-trim.fq.gz [2019-09-24 09:22:19,201] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-193_S22_L003_R2_001_val_2.20bp-trim.fq.gz [2019-09-24 09:22:19,201] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-159_S6_L002_R2_001_val_2.20bp-trim_fastqc.html [2019-09-24 09:22:19,201] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-135_S35_L005_R2_001_val_2.20bp-trim.fq.gz [2019-09-24 09:22:19,201] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-143_S37_L005_R2_001_val_2.20bp-trim.fq.gz [2019-09-24 09:22:19,201] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-162_S9_L002_R2_001_val_2.20bp-trim.fq.gz [2019-09-24 09:22:19,202] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-229_S36_L004_R2_001_val_2.20bp-trim_fastqc.html [2019-09-24 09:22:19,202] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-145_S38_L005_R2_001_val_2.20bp-trim_fastqc.html [2019-09-24 09:22:19,202] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-214_S30_L004_R2_001_val_2.20bp-trim_fastqc.html [2019-09-24 09:22:19,202] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-227_S35_L004_R1_001_val_1.20bp-trim.fq.gz [2019-09-24 09:22:19,203] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-170_S13_L002_R2_001_val_2.20bp-trim_fastqc.html [2019-09-24 09:22:19,203] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-226_S34_L004_R1_001_val_1.20bp-trim.fq.gz [2019-09-24 09:22:19,203] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-220_S32_L004_R2_001_val_2.20bp-trim_fastqc.html [2019-09-24 09:22:19,203] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-206_S27_L004_R2_001_val_2.20bp-trim.fq.gz [2019-09-24 09:22:19,204] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-200_S25_L003_R2_001_val_2.20bp-trim_fastqc.html [2019-09-24 09:22:19,204] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-161_S8_L002_R1_001_val_1.20bp-trim_fastqc.html [2019-09-24 09:22:19,204] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-188_S21_L003_R2_001_val_2.20bp-trim.fq.gz [2019-09-24 09:22:19,205] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-220_S32_L004_R1_001_val_1.20bp-trim_fastqc.html [2019-09-24 09:22:19,205] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: EPI-226_S34_L004_R2_001_val_2.20bp-trim_fastqc.html [2019-09-24 09:22:20,119] multiqc [DEBUG ] No samples found: custom_content [2019-09-24 09:22:20,128] multiqc [DEBUG ] No samples found: conpair [2019-09-24 09:22:20,136] multiqc [DEBUG ] No samples found: peddy [2019-09-24 09:22:20,149] multiqc [DEBUG ] No samples found: methylQA [2019-09-24 09:22:20,154] multiqc [DEBUG ] No samples found: qualimap [2019-09-24 09:22:20,159] multiqc [DEBUG ] No samples found: preseq [2019-09-24 09:22:20,164] multiqc [DEBUG ] No samples found: quast [2019-09-24 09:22:20,199] multiqc [DEBUG ] No samples found: qorts [2019-09-24 09:22:20,203] multiqc [DEBUG ] No samples found: rna_seqc [2019-09-24 09:22:20,208] multiqc [DEBUG ] No samples found: rsem [2019-09-24 09:22:20,230] multiqc [DEBUG ] No samples found: rseqc [2019-09-24 09:22:20,235] multiqc [DEBUG ] No samples found: busco [2019-09-24 09:22:20,239] multiqc [DEBUG ] No samples found: goleft_indexcov [2019-09-24 09:22:20,243] multiqc [DEBUG ] No samples found: disambiguate [2019-09-24 09:22:20,248] multiqc [DEBUG ] No samples found: supernova [2019-09-24 09:22:20,254] multiqc [DEBUG ] No samples found: deeptools [2019-09-24 09:22:20,258] multiqc [DEBUG ] No samples found: sargasso [2019-09-24 09:22:20,263] multiqc [DEBUG ] No samples found: verifybamid [2019-09-24 09:22:20,267] multiqc [DEBUG ] No samples found: mirtrace [2019-09-24 09:22:20,271] multiqc [DEBUG ] No samples found: happy [2019-09-24 09:22:20,283] multiqc [DEBUG ] No samples found: homer [2019-09-24 09:22:20,287] multiqc [DEBUG ] No samples found: macs2 [2019-09-24 09:22:20,292] multiqc [DEBUG ] No samples found: theta2 [2019-09-24 09:22:20,305] multiqc [DEBUG ] No samples found: snpeff [2019-09-24 09:22:20,311] multiqc [DEBUG ] No samples found: gatk [2019-09-24 09:22:20,316] multiqc [DEBUG ] No samples found: htseq [2019-09-24 09:22:20,321] multiqc [DEBUG ] No samples found: bcftools [2019-09-24 09:22:20,325] multiqc [DEBUG ] No samples found: featureCounts [2019-09-24 09:22:20,330] multiqc [DEBUG ] No samples found: dedup [2019-09-24 09:22:20,339] multiqc [DEBUG ] No samples found: picard [2019-09-24 09:22:20,343] multiqc [DEBUG ] No samples found: prokka [2019-09-24 09:22:20,348] multiqc [DEBUG ] No samples found: samblaster [2019-09-24 09:22:20,354] multiqc [DEBUG ] No samples found: samtools [2019-09-24 09:22:20,358] multiqc [DEBUG ] No samples found: bamtools [2019-09-24 09:22:20,362] multiqc [DEBUG ] No samples found: jellyfish [2019-09-24 09:22:20,368] multiqc [DEBUG ] No samples found: vcftools [2019-09-24 09:22:20,373] multiqc [DEBUG ] No samples found: longranger [2019-09-24 09:22:20,381] multiqc [DEBUG ] No samples found: bbmap [2019-09-24 09:22:20,386] multiqc [DEBUG ] No samples found: bismark [2019-09-24 09:22:20,390] multiqc [DEBUG ] No samples found: hicexplorer [2019-09-24 09:22:20,394] multiqc [DEBUG ] No samples found: hicup [2019-09-24 09:22:20,399] multiqc [DEBUG ] No samples found: hicpro [2019-09-24 09:22:20,403] multiqc [DEBUG ] No samples found: salmon [2019-09-24 09:22:20,408] multiqc [DEBUG ] No samples found: kallisto [2019-09-24 09:22:20,412] multiqc [DEBUG ] No samples found: slamdunk [2019-09-24 09:22:20,417] multiqc [DEBUG ] No samples found: star [2019-09-24 09:22:20,421] multiqc [DEBUG ] No samples found: hisat2 [2019-09-24 09:22:20,425] multiqc [DEBUG ] No samples found: tophat [2019-09-24 09:22:20,430] multiqc [DEBUG ] No samples found: bowtie2 [2019-09-24 09:22:20,434] multiqc [DEBUG ] No samples found: bowtie1 [2019-09-24 09:22:20,438] multiqc [DEBUG ] No samples found: kat [2019-09-24 09:22:20,443] multiqc [DEBUG ] No samples found: leehom [2019-09-24 09:22:20,447] multiqc [DEBUG ] No samples found: adapterRemoval [2019-09-24 09:22:20,451] multiqc [DEBUG ] No samples found: clipandmerge [2019-09-24 09:22:20,456] multiqc [DEBUG ] No samples found: cutadapt [2019-09-24 09:22:20,460] multiqc [DEBUG ] No samples found: flexbar [2019-09-24 09:22:20,465] multiqc [DEBUG ] No samples found: trimmomatic [2019-09-24 09:22:20,469] multiqc [DEBUG ] No samples found: skewer [2019-09-24 09:22:20,473] multiqc [DEBUG ] No samples found: sortmerna [2019-09-24 09:22:20,477] multiqc [DEBUG ] No samples found: biobloomtools [2019-09-24 09:22:20,482] multiqc [DEBUG ] No samples found: fastq_screen [2019-09-24 09:22:20,486] multiqc [DEBUG ] No samples found: afterqc [2019-09-24 09:22:20,494] multiqc.modules.fastp.fastp [WARNING] Could not parse sample name from fastp command: fastp.json [2019-09-24 09:22:20,494] multiqc.modules.fastp.fastp [DEBUG ] fastp JSON did not have a 'adapter_cutting' key, skipping: 'fastp.json' [2019-09-24 09:22:20,494] multiqc.modules.fastp.fastp [DEBUG ] Could not calculate 'pct_adapter': fastp.json [2019-09-24 09:22:20,495] multiqc.modules.fastp.fastp [INFO ] Found 1 reports [2019-09-24 09:22:23,513] multiqc.modules.fastqc.fastqc [INFO ] Found 104 reports [2019-09-24 09:22:37,136] multiqc [DEBUG ] No samples found: clusterflow [2019-09-24 09:22:37,141] multiqc [DEBUG ] No samples found: bcl2fastq [2019-09-24 09:22:37,145] multiqc [DEBUG ] No samples found: interop [2019-09-24 09:22:37,348] multiqc [INFO ] Compressing plot data [2019-09-24 09:22:37,445] multiqc [INFO ] Report : multiqc_report.html [2019-09-24 09:22:37,446] multiqc [INFO ] Data : multiqc_data [2019-09-24 09:22:37,446] multiqc [DEBUG ] Moving data file from '/tmp/tmp1_wibq6w/multiqc_data/mqc_fastqc_per_base_n_content_plot_1.txt' to '/home/sam/analyses/20190923_pgen_fastp_EPI_trimming/multiqc_data' [2019-09-24 09:22:37,446] multiqc [DEBUG ] Moving data file from '/tmp/tmp1_wibq6w/multiqc_data/mqc_fastqc_sequence_length_distribution_plot_1.txt' to '/home/sam/analyses/20190923_pgen_fastp_EPI_trimming/multiqc_data' [2019-09-24 09:22:37,447] multiqc [DEBUG ] Moving data file from '/tmp/tmp1_wibq6w/multiqc_data/multiqc_general_stats.txt' to '/home/sam/analyses/20190923_pgen_fastp_EPI_trimming/multiqc_data' [2019-09-24 09:22:37,447] multiqc [DEBUG ] Moving data file from '/tmp/tmp1_wibq6w/multiqc_data/multiqc_fastqc.txt' to '/home/sam/analyses/20190923_pgen_fastp_EPI_trimming/multiqc_data' [2019-09-24 09:22:37,447] multiqc [DEBUG ] Moving data file from '/tmp/tmp1_wibq6w/multiqc_data/multiqc_sources.txt' to '/home/sam/analyses/20190923_pgen_fastp_EPI_trimming/multiqc_data' [2019-09-24 09:22:37,448] multiqc [DEBUG ] Moving data file from '/tmp/tmp1_wibq6w/multiqc_data/mqc_fastqc_sequence_counts_plot_1.txt' to '/home/sam/analyses/20190923_pgen_fastp_EPI_trimming/multiqc_data' [2019-09-24 09:22:37,448] multiqc [DEBUG ] Moving data file from '/tmp/tmp1_wibq6w/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Counts.txt' to '/home/sam/analyses/20190923_pgen_fastp_EPI_trimming/multiqc_data' [2019-09-24 09:22:37,448] multiqc [DEBUG ] Moving data file from '/tmp/tmp1_wibq6w/multiqc_data/mqc_fastqc_per_sequence_quality_scores_plot_1.txt' to '/home/sam/analyses/20190923_pgen_fastp_EPI_trimming/multiqc_data' [2019-09-24 09:22:37,449] multiqc [DEBUG ] Moving data file from '/tmp/tmp1_wibq6w/multiqc_data/multiqc_data.json' to '/home/sam/analyses/20190923_pgen_fastp_EPI_trimming/multiqc_data' [2019-09-24 09:22:37,450] multiqc [DEBUG ] Moving data file from '/tmp/tmp1_wibq6w/multiqc_data/mqc_fastqc_per_base_sequence_quality_plot_1.txt' to '/home/sam/analyses/20190923_pgen_fastp_EPI_trimming/multiqc_data' [2019-09-24 09:22:37,450] multiqc [DEBUG ] Moving data file from '/tmp/tmp1_wibq6w/multiqc_data/mqc_fastqc_sequence_duplication_levels_plot_1.txt' to '/home/sam/analyses/20190923_pgen_fastp_EPI_trimming/multiqc_data' [2019-09-24 09:22:37,451] multiqc [DEBUG ] Moving data file from '/tmp/tmp1_wibq6w/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Percentages.txt' to '/home/sam/analyses/20190923_pgen_fastp_EPI_trimming/multiqc_data' [2019-09-24 09:22:37,451] multiqc [DEBUG ] Moving data file from '/tmp/tmp1_wibq6w/multiqc_data/multiqc_fastp.txt' to '/home/sam/analyses/20190923_pgen_fastp_EPI_trimming/multiqc_data' [2019-09-24 09:22:37,693] multiqc [INFO ] MultiQC complete