[2019-09-03 16:27:04,792] multiqc [DEBUG ] No MultiQC config found: /home/rcorbett/python-2.7-venv/lib/python2.7/site-packages/multiqc_config.yaml [2019-09-03 16:27:04,792] multiqc [DEBUG ] No MultiQC config found: /home/rcorbett/.multiqc_config.yaml [2019-09-03 16:27:04,793] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2019-09-03 16:27:04,793] multiqc [DEBUG ] Command used: /home/rcorbett/python-2.7-venv/bin/multiqc -f -v . [2019-09-03 16:27:06,152] multiqc [DEBUG ] Latest MultiQC version is v1.7 [2019-09-03 16:27:06,153] multiqc [INFO ] This is MultiQC v1.7 [2019-09-03 16:27:06,153] multiqc [DEBUG ] Command : /home/rcorbett/python-2.7-venv/bin/multiqc -f -v . [2019-09-03 16:27:06,153] multiqc [DEBUG ] Working dir : /projects/rcorbettprj2/CGEN/GIAB2/multiqc3 [2019-09-03 16:27:06,153] multiqc [INFO ] Template : default [2019-09-03 16:27:06,153] multiqc [INFO ] Searching '.' [2019-09-03 16:27:06,154] 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, dedup, damageprofiler, picard, prokka, samblaster, samtools, 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, clusterflow, bcl2fastq, interop, flash [2019-09-03 16:27:06,157] multiqc [DEBUG ] Using temporary directory for creating report: /projects/bioSCRATCH/rcorbett/tmpAui55Y [2019-09-03 16:27:06,650] multiqc [DEBUG ] Ignoring directory as matched fn_ignore_dirs: ./multiqc_data [2019-09-03 16:27:07,135] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24143_round1.bam [2019-09-03 16:27:07,136] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24143_round2.bam [2019-09-03 16:27:07,136] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24143_round3.bam [2019-09-03 16:27:07,137] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24149_round1.bam [2019-09-03 16:27:07,137] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24149_round2.bam [2019-09-03 16:27:07,137] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24149_round3.bam [2019-09-03 16:27:07,138] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24385_round1.bam [2019-09-03 16:27:07,138] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24385_round2.bam [2019-09-03 16:27:07,139] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24385_round3.bam [2019-09-03 16:27:07,139] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pMTL_NA24143_round1.bam [2019-09-03 16:27:07,139] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pMTL_NA24143_round2.bam [2019-09-03 16:27:07,140] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pMTL_NA24143_round3.bam [2019-09-03 16:27:07,140] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pMTL_NA24149_round1.bam [2019-09-03 16:27:07,140] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pMTL_NA24149_round2.bam [2019-09-03 16:27:07,141] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pMTL_NA24149_round3.bam [2019-09-03 16:27:07,141] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pMTL_NA24385_round1.bam [2019-09-03 16:27:07,141] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pMTL_NA24385_round2.bam [2019-09-03 16:27:07,142] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pMTL_NA24385_round3.bam [2019-09-03 16:27:07,142] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pTOR_NA24143_round1.cram.bam [2019-09-03 16:27:07,142] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pTOR_NA24143_round2.cram.bam [2019-09-03 16:27:07,142] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pTOR_NA24143_round3.cram.bam [2019-09-03 16:27:07,143] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pTOR_NA24149_round1.cram.bam [2019-09-03 16:27:07,143] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pTOR_NA24149_round2.cram.bam [2019-09-03 16:27:07,143] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pTOR_NA24149_round3.cram.bam [2019-09-03 16:27:07,144] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pTOR_NA24385_round1.cram.bam [2019-09-03 16:27:07,144] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pTOR_NA24385_round2.cram.bam [2019-09-03 16:27:07,144] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pTOR_NA24385_round3.cram.bam [2019-09-03 16:27:07,145] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pBC_NA24143_round1.bam [2019-09-03 16:27:07,145] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pBC_NA24143_round2.bam [2019-09-03 16:27:07,145] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pBC_NA24143_round3.bam [2019-09-03 16:27:07,146] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pBC_NA24149_round1.bam [2019-09-03 16:27:07,146] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pBC_NA24149_round2.bam [2019-09-03 16:27:07,146] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pBC_NA24149_round3.bam [2019-09-03 16:27:07,147] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pBC_NA24385_round1.bam [2019-09-03 16:27:07,147] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pBC_NA24385_round2.bam [2019-09-03 16:27:07,147] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pBC_NA24385_round3.bam [2019-09-03 16:27:07,148] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pMTL_NA24143_round1.bam [2019-09-03 16:27:07,148] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pMTL_NA24143_round2.bam [2019-09-03 16:27:07,148] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pMTL_NA24143_round3.bam [2019-09-03 16:27:07,149] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pMTL_NA24149_round1.bam [2019-09-03 16:27:07,149] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pMTL_NA24149_round2.bam [2019-09-03 16:27:07,149] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pMTL_NA24149_round3.bam [2019-09-03 16:27:07,150] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pMTL_NA24385_round1.bam [2019-09-03 16:27:07,150] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pMTL_NA24385_round2.bam [2019-09-03 16:27:07,150] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pMTL_NA24385_round3.bam [2019-09-03 16:27:07,151] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pTOR_NA24143_round1.cram.bam [2019-09-03 16:27:07,151] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pTOR_NA24143_round2.cram.bam [2019-09-03 16:27:07,151] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pTOR_NA24143_round3.cram.bam [2019-09-03 16:27:07,152] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pTOR_NA24149_round1.cram.bam [2019-09-03 16:27:07,152] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pTOR_NA24149_round2.cram.bam [2019-09-03 16:27:07,152] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pBC_NA24143_round1.bam [2019-09-03 16:27:07,153] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pTOR_NA24149_round3.cram.bam [2019-09-03 16:27:07,153] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pTOR_NA24385_round1.cram.bam [2019-09-03 16:27:07,153] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pTOR_NA24385_round2.cram.bam [2019-09-03 16:27:07,154] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pTOR_NA24385_round3.cram.bam [2019-09-03 16:27:07,154] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pBC_NA24143_round2.bam [2019-09-03 16:27:07,154] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pBC_NA24143_round3.bam [2019-09-03 16:27:07,155] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pBC_NA24149_round1.bam [2019-09-03 16:27:07,155] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pBC_NA24149_round2.bam [2019-09-03 16:27:07,155] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pBC_NA24149_round3.bam [2019-09-03 16:27:07,156] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pBC_NA24385_round1.bam [2019-09-03 16:27:07,156] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pBC_NA24385_round2.bam [2019-09-03 16:27:07,156] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pBC_NA24385_round3.bam [2019-09-03 16:27:07,157] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pMTL_NA24143_round1.bam [2019-09-03 16:27:07,157] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pMTL_NA24143_round2.bam [2019-09-03 16:27:07,157] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pMTL_NA24143_round3.bam [2019-09-03 16:27:07,158] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pMTL_NA24149_round1.bam [2019-09-03 16:27:07,158] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pMTL_NA24149_round2.bam [2019-09-03 16:27:07,158] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pMTL_NA24149_round3.bam [2019-09-03 16:27:07,159] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pMTL_NA24385_round1.bam [2019-09-03 16:27:07,159] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pMTL_NA24385_round2.bam [2019-09-03 16:27:07,159] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pMTL_NA24385_round3.bam [2019-09-03 16:27:07,160] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pTOR_NA24143_round1.cram.bam [2019-09-03 16:27:07,160] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pTOR_NA24143_round2.cram.bam [2019-09-03 16:27:07,160] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pTOR_NA24143_round3.cram.bam [2019-09-03 16:27:07,161] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pTOR_NA24149_round1.cram.bam [2019-09-03 16:27:07,161] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pTOR_NA24149_round2.cram.bam [2019-09-03 16:27:07,161] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pTOR_NA24149_round3.cram.bam [2019-09-03 16:27:07,162] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pTOR_NA24385_round1.cram.bam [2019-09-03 16:27:07,162] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pTOR_NA24385_round2.cram.bam [2019-09-03 16:27:07,162] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pTOR_NA24385_round3.cram.bam [2019-09-03 16:27:07,163] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24143_round1.bam.bai [2019-09-03 16:27:07,163] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24143_round2.bam.bai [2019-09-03 16:27:07,163] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24143_round3.bam.bai [2019-09-03 16:27:07,164] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24149_round1.bam.bai [2019-09-03 16:27:07,164] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24149_round2.bam.bai [2019-09-03 16:27:07,164] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24149_round3.bam.bai [2019-09-03 16:27:07,165] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24385_round1.bam.bai [2019-09-03 16:27:07,165] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24385_round2.bam.bai [2019-09-03 16:27:07,165] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pBC_NA24385_round3.bam.bai [2019-09-03 16:27:07,166] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pMTL_NA24143_round1.bam.bai [2019-09-03 16:27:07,166] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pMTL_NA24143_round2.bam.bai [2019-09-03 16:27:07,166] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pMTL_NA24143_round3.bam.bai [2019-09-03 16:27:07,167] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pMTL_NA24149_round1.bam.bai [2019-09-03 16:27:07,167] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pMTL_NA24149_round2.bam.bai [2019-09-03 16:27:07,167] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pMTL_NA24149_round3.bam.bai [2019-09-03 16:27:07,168] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pMTL_NA24385_round1.bam.bai [2019-09-03 16:27:07,168] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pMTL_NA24385_round2.bam.bai [2019-09-03 16:27:07,168] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pMTL_NA24385_round3.bam.bai [2019-09-03 16:27:07,169] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pBC_NA24143_round1.bam.bai [2019-09-03 16:27:07,169] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pTOR_NA24143_round1.cram.bam.bai [2019-09-03 16:27:07,169] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pTOR_NA24143_round2.cram.bam.bai [2019-09-03 16:27:07,170] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pTOR_NA24143_round3.cram.bam.bai [2019-09-03 16:27:07,170] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pTOR_NA24149_round1.cram.bam.bai [2019-09-03 16:27:07,170] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pTOR_NA24149_round2.cram.bam.bai [2019-09-03 16:27:07,171] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pTOR_NA24149_round3.cram.bam.bai [2019-09-03 16:27:07,171] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pTOR_NA24385_round1.cram.bam.bai [2019-09-03 16:27:07,171] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pTOR_NA24385_round2.cram.bam.bai [2019-09-03 16:27:07,172] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sBC_pTOR_NA24385_round3.cram.bam.bai [2019-09-03 16:27:07,172] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pBC_NA24143_round2.bam.bai [2019-09-03 16:27:07,172] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pBC_NA24143_round3.bam.bai [2019-09-03 16:27:07,172] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pBC_NA24149_round1.bam.bai [2019-09-03 16:27:07,173] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pBC_NA24149_round2.bam.bai [2019-09-03 16:27:07,173] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pBC_NA24149_round3.bam.bai [2019-09-03 16:27:07,173] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pBC_NA24385_round1.bam.bai [2019-09-03 16:27:07,174] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pBC_NA24385_round2.bam.bai [2019-09-03 16:27:07,174] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pBC_NA24385_round3.bam.bai [2019-09-03 16:27:07,174] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pMTL_NA24143_round1.bam.bai [2019-09-03 16:27:07,175] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pMTL_NA24143_round2.bam.bai [2019-09-03 16:27:07,175] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pMTL_NA24143_round3.bam.bai [2019-09-03 16:27:07,175] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pMTL_NA24149_round1.bam.bai [2019-09-03 16:27:07,176] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pMTL_NA24149_round2.bam.bai [2019-09-03 16:27:07,176] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pMTL_NA24149_round3.bam.bai [2019-09-03 16:27:07,176] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pMTL_NA24385_round1.bam.bai [2019-09-03 16:27:07,177] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pMTL_NA24385_round2.bam.bai [2019-09-03 16:27:07,177] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pMTL_NA24385_round3.bam.bai [2019-09-03 16:27:07,177] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pTOR_NA24143_round1.cram.bam.bai [2019-09-03 16:27:07,178] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pTOR_NA24143_round2.cram.bam.bai [2019-09-03 16:27:07,178] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pTOR_NA24143_round3.cram.bam.bai [2019-09-03 16:27:07,178] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pTOR_NA24149_round1.cram.bam.bai [2019-09-03 16:27:07,179] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pTOR_NA24149_round2.cram.bam.bai [2019-09-03 16:27:07,180] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pTOR_NA24149_round3.cram.bam.bai [2019-09-03 16:27:07,180] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pTOR_NA24385_round1.cram.bam.bai [2019-09-03 16:27:07,180] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pTOR_NA24385_round2.cram.bam.bai [2019-09-03 16:27:07,181] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sMTL_pTOR_NA24385_round3.cram.bam.bai [2019-09-03 16:27:07,181] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pBC_NA24143_round1.bam.bai [2019-09-03 16:27:07,181] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pBC_NA24143_round2.bam.bai [2019-09-03 16:27:07,182] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pBC_NA24143_round3.bam.bai [2019-09-03 16:27:07,182] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pBC_NA24149_round1.bam.bai [2019-09-03 16:27:07,183] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pBC_NA24149_round2.bam.bai [2019-09-03 16:27:07,183] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pBC_NA24149_round3.bam.bai [2019-09-03 16:27:07,183] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pBC_NA24385_round1.bam.bai [2019-09-03 16:27:07,184] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pBC_NA24385_round2.bam.bai [2019-09-03 16:27:07,184] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pBC_NA24385_round3.bam.bai [2019-09-03 16:27:07,184] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pMTL_NA24143_round1.bam.bai [2019-09-03 16:27:07,184] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pMTL_NA24143_round2.bam.bai [2019-09-03 16:27:07,185] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pMTL_NA24143_round3.bam.bai [2019-09-03 16:27:07,185] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pMTL_NA24149_round1.bam.bai [2019-09-03 16:27:07,185] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pMTL_NA24149_round2.bam.bai [2019-09-03 16:27:07,186] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pMTL_NA24149_round3.bam.bai [2019-09-03 16:27:07,186] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pMTL_NA24385_round1.bam.bai [2019-09-03 16:27:07,186] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pMTL_NA24385_round2.bam.bai [2019-09-03 16:27:07,187] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pMTL_NA24385_round3.bam.bai [2019-09-03 16:27:07,187] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pTOR_NA24143_round1.cram.bam.bai [2019-09-03 16:27:07,187] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pTOR_NA24143_round2.cram.bam.bai [2019-09-03 16:27:07,188] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pTOR_NA24143_round3.cram.bam.bai [2019-09-03 16:27:07,188] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pTOR_NA24149_round1.cram.bam.bai [2019-09-03 16:27:07,188] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pTOR_NA24149_round2.cram.bam.bai [2019-09-03 16:27:07,189] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pTOR_NA24149_round3.cram.bam.bai [2019-09-03 16:27:07,189] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pTOR_NA24385_round1.cram.bam.bai [2019-09-03 16:27:07,189] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pTOR_NA24385_round2.cram.bam.bai [2019-09-03 16:27:07,190] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sTOR_pTOR_NA24385_round3.cram.bam.bai [2019-09-03 16:28:51,843] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: multiqc_report.html [2019-09-03 16:28:52,983] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:28:55,926] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:28:58,886] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:29:01,907] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:29:04,978] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:29:07,937] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:29:10,967] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:29:14,050] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:29:17,385] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:29:20,446] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:29:23,415] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:29:26,434] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:29:29,432] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:29:32,416] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:29:35,416] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:29:38,452] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:29:41,466] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:29:44,434] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:29:47,628] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:29:50,633] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:29:53,650] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:29:56,604] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:29:59,595] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:30:02,690] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:30:05,714] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:30:08,696] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:30:11,660] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:30:14,603] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:30:17,545] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:30:20,578] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:30:23,560] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:30:26,562] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:30:29,603] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:30:32,614] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:30:35,624] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:30:38,618] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:30:41,669] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:30:44,703] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:30:47,705] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:30:50,707] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:30:53,710] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:30:56,823] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:30:59,863] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:31:03,079] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:31:06,112] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:31:09,099] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:31:12,110] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:31:15,154] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:31:18,145] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:31:21,188] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:31:24,192] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:31:27,289] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:31:30,250] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:31:33,233] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:31:36,207] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:31:39,177] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:31:42,112] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:31:45,157] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:31:48,119] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:31:51,095] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:31:54,074] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:31:57,022] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:31:59,974] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:32:03,182] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:32:06,175] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:32:09,207] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:32:12,197] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:32:15,146] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:32:18,110] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:32:21,170] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:32:24,193] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:32:27,612] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:32:30,499] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:32:33,442] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:32:36,346] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:32:39,277] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:32:42,232] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:32:45,164] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:32:48,084] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:32:51,108] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:32:54,074] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2019-09-03 16:32:58,073] multiqc [DEBUG ] No samples found: custom_content [2019-09-03 16:32:58,090] multiqc [DEBUG ] No samples found: conpair [2019-09-03 16:32:58,107] multiqc [DEBUG ] No samples found: peddy [2019-09-03 16:32:58,127] multiqc [DEBUG ] No samples found: methylQA [2019-09-03 16:32:58,146] multiqc [DEBUG ] No samples found: phantompeakqualtools [2019-09-03 16:33:10,549] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2019-09-03 16:33:14,721] multiqc.modules.qualimap.qualimap [INFO ] Found 81 BamQC reports [2019-09-03 16:33:14,735] multiqc [DEBUG ] No samples found: preseq [2019-09-03 16:33:14,751] multiqc [DEBUG ] No samples found: quast [2019-09-03 16:33:14,768] multiqc [DEBUG ] No samples found: qorts [2019-09-03 16:33:14,783] multiqc [DEBUG ] No samples found: rna_seqc [2019-09-03 16:33:14,799] multiqc [DEBUG ] No samples found: rsem [2019-09-03 16:33:14,832] multiqc [DEBUG ] No samples found: rseqc [2019-09-03 16:33:14,848] multiqc [DEBUG ] No samples found: busco [2019-09-03 16:33:14,864] multiqc [DEBUG ] No samples found: goleft_indexcov [2019-09-03 16:33:14,879] multiqc [DEBUG ] No samples found: disambiguate [2019-09-03 16:33:14,896] multiqc [DEBUG ] No samples found: supernova [2019-09-03 16:33:14,933] multiqc [DEBUG ] No samples found: deeptools [2019-09-03 16:33:14,948] multiqc [DEBUG ] No samples found: sargasso [2019-09-03 16:33:14,964] multiqc [DEBUG ] No samples found: verifybamid [2019-09-03 16:33:14,984] multiqc [DEBUG ] No samples found: mirtrace [2019-09-03 16:33:15,003] multiqc [DEBUG ] No samples found: happy [2019-09-03 16:33:15,026] multiqc [DEBUG ] No samples found: homer [2019-09-03 16:33:15,042] multiqc [DEBUG ] No samples found: macs2 [2019-09-03 16:33:15,058] multiqc [DEBUG ] No samples found: theta2 [2019-09-03 16:33:15,074] multiqc [DEBUG ] No samples found: snpeff [2019-09-03 16:33:15,096] multiqc [DEBUG ] No samples found: gatk [2019-09-03 16:33:15,111] multiqc [DEBUG ] No samples found: htseq [2019-09-03 16:33:15,128] multiqc [DEBUG ] No samples found: bcftools [2019-09-03 16:33:15,144] multiqc [DEBUG ] No samples found: featureCounts [2019-09-03 16:33:15,162] multiqc [DEBUG ] No samples found: dedup [2019-09-03 16:33:15,179] multiqc [DEBUG ] No samples found: damageprofiler [2019-09-03 16:33:15,835] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sMTL_pBC_NA24143_round2.bam.gc.summary.txt! Overwriting: sMTL_pBC_NA24143_round2 [2019-09-03 16:33:15,849] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sMTL_pBC_NA24143_round3.bam.gc.summary.txt! Overwriting: sMTL_pBC_NA24143_round3 [2019-09-03 16:33:15,863] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sBC_pBC_NA24385_round1.bam.gc.summary.txt! Overwriting: sBC_pBC_NA24385_round1 [2019-09-03 16:33:15,877] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sMTL_pBC_NA24149_round2.bam.gc.summary.txt! Overwriting: sMTL_pBC_NA24149_round2 [2019-09-03 16:33:15,891] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sMTL_pBC_NA24385_round1.bam.gc.summary.txt! Overwriting: sMTL_pBC_NA24385_round1 [2019-09-03 16:33:15,905] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sMTL_pBC_NA24385_round2.bam.gc.summary.txt! Overwriting: sMTL_pBC_NA24385_round2 [2019-09-03 16:33:15,911] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sBC_pBC_NA24143_round1.bam.gc.summary.txt! Overwriting: sBC_pBC_NA24143_round1 [2019-09-03 16:33:15,916] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sBC_pBC_NA24143_round2.bam.gc.summary.txt! Overwriting: sBC_pBC_NA24143_round2 [2019-09-03 16:33:15,922] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sBC_pBC_NA24149_round3.bam.gc.summary.txt! Overwriting: sBC_pBC_NA24149_round3 [2019-09-03 16:33:15,927] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sBC_pBC_NA24149_round1.bam.gc.summary.txt! Overwriting: sBC_pBC_NA24149_round1 [2019-09-03 16:33:15,932] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sMTL_pBC_NA24385_round3.bam.gc.summary.txt! Overwriting: sMTL_pBC_NA24385_round3 [2019-09-03 16:33:15,937] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sMTL_pBC_NA24149_round1.bam.gc.summary.txt! Overwriting: sMTL_pBC_NA24149_round1 [2019-09-03 16:33:15,942] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sTOR_pBC_NA24143_round3.bam.gc.summary.txt! Overwriting: sTOR_pBC_NA24143_round3 [2019-09-03 16:33:15,948] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sTOR_pBC_NA24149_round1.bam.gc.summary.txt! Overwriting: sTOR_pBC_NA24149_round1 [2019-09-03 16:33:15,953] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sMTL_pBC_NA24149_round3.bam.gc.summary.txt! Overwriting: sMTL_pBC_NA24149_round3 [2019-09-03 16:33:15,958] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sBC_pBC_NA24143_round3.bam.gc.summary.txt! Overwriting: sBC_pBC_NA24143_round3 [2019-09-03 16:33:15,963] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sBC_pBC_NA24149_round2.bam.gc.summary.txt! Overwriting: sBC_pBC_NA24149_round2 [2019-09-03 16:33:15,968] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sBC_pBC_NA24385_round3.bam.gc.summary.txt! Overwriting: sBC_pBC_NA24385_round3 [2019-09-03 16:33:15,974] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sMTL_pBC_NA24143_round1.bam.gc.summary.txt! Overwriting: sMTL_pBC_NA24143_round1 [2019-09-03 16:33:15,979] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sTOR_pBC_NA24143_round2.bam.gc.summary.txt! Overwriting: sTOR_pBC_NA24143_round2 [2019-09-03 16:33:15,984] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sBC_pTOR_NA24385_round1.cram.bam.gc.summary.txt! Overwriting: sBC_pTOR_NA24385_round1 [2019-09-03 16:33:15,989] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sTOR_pBC_NA24143_round1.bam.gc.summary.txt! Overwriting: sTOR_pBC_NA24143_round1 [2019-09-03 16:33:15,994] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sBC_pTOR_NA24143_round1.cram.bam.gc.summary.txt! Overwriting: sBC_pTOR_NA24143_round1 [2019-09-03 16:33:15,999] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sMTL_pTOR_NA24149_round2.cram.bam.gc.summary.txt! Overwriting: sMTL_pTOR_NA24149_round2 [2019-09-03 16:33:16,004] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sMTL_pTOR_NA24385_round1.cram.bam.gc.summary.txt! Overwriting: sMTL_pTOR_NA24385_round1 [2019-09-03 16:33:16,009] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sBC_pTOR_NA24385_round2.cram.bam.gc.summary.txt! Overwriting: sBC_pTOR_NA24385_round2 [2019-09-03 16:33:16,014] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sMTL_pTOR_NA24149_round1.cram.bam.gc.summary.txt! Overwriting: sMTL_pTOR_NA24149_round1 [2019-09-03 16:33:16,019] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sBC_pTOR_NA24385_round3.cram.bam.gc.summary.txt! Overwriting: sBC_pTOR_NA24385_round3 [2019-09-03 16:33:16,024] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sBC_pTOR_NA24149_round1.cram.bam.gc.summary.txt! Overwriting: sBC_pTOR_NA24149_round1 [2019-09-03 16:33:16,030] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sMTL_pTOR_NA24143_round3.cram.bam.gc.summary.txt! Overwriting: sMTL_pTOR_NA24143_round3 [2019-09-03 16:33:16,035] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sBC_pTOR_NA24149_round2.cram.bam.gc.summary.txt! Overwriting: sBC_pTOR_NA24149_round2 [2019-09-03 16:33:16,040] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sMTL_pTOR_NA24143_round2.cram.bam.gc.summary.txt! Overwriting: sMTL_pTOR_NA24143_round2 [2019-09-03 16:33:16,045] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sBC_pTOR_NA24143_round3.cram.bam.gc.summary.txt! Overwriting: sBC_pTOR_NA24143_round3 [2019-09-03 16:33:16,051] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sBC_pTOR_NA24149_round3.cram.bam.gc.summary.txt! Overwriting: sBC_pTOR_NA24149_round3 [2019-09-03 16:33:16,056] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sBC_pTOR_NA24143_round2.cram.bam.gc.summary.txt! Overwriting: sBC_pTOR_NA24143_round2 [2019-09-03 16:33:16,061] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sMTL_pTOR_NA24143_round1.cram.bam.gc.summary.txt! Overwriting: sMTL_pTOR_NA24143_round1 [2019-09-03 16:33:16,067] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sMTL_pTOR_NA24385_round2.cram.bam.gc.summary.txt! Overwriting: sMTL_pTOR_NA24385_round2 [2019-09-03 16:33:16,073] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sTOR_pTOR_NA24385_round3.cram.bam.gc.summary.txt! Overwriting: sTOR_pTOR_NA24385_round3 [2019-09-03 16:33:16,078] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sMTL_pTOR_NA24149_round3.cram.bam.gc.summary.txt! Overwriting: sMTL_pTOR_NA24149_round3 [2019-09-03 16:33:16,084] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sMTL_pTOR_NA24385_round3.cram.bam.gc.summary.txt! Overwriting: sMTL_pTOR_NA24385_round3 [2019-09-03 16:33:16,089] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sTOR_pTOR_NA24385_round1.cram.bam.gc.summary.txt! Overwriting: sTOR_pTOR_NA24385_round1 [2019-09-03 16:33:16,095] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sTOR_pTOR_NA24385_round2.cram.bam.gc.summary.txt! Overwriting: sTOR_pTOR_NA24385_round2 [2019-09-03 16:33:16,100] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sTOR_pTOR_NA24143_round1.cram.bam.gc.summary.txt! Overwriting: sTOR_pTOR_NA24143_round1 [2019-09-03 16:33:16,105] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sTOR_pTOR_NA24149_round2.cram.bam.gc.summary.txt! Overwriting: sTOR_pTOR_NA24149_round2 [2019-09-03 16:33:16,111] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sTOR_pTOR_NA24149_round3.cram.bam.gc.summary.txt! Overwriting: sTOR_pTOR_NA24149_round3 [2019-09-03 16:33:16,116] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sTOR_pTOR_NA24149_round1.cram.bam.gc.summary.txt! Overwriting: sTOR_pTOR_NA24149_round1 [2019-09-03 16:33:16,121] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sTOR_pTOR_NA24143_round3.cram.bam.gc.summary.txt! Overwriting: sTOR_pTOR_NA24143_round3 [2019-09-03 16:33:16,126] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sTOR_pTOR_NA24143_round2.cram.bam.gc.summary.txt! Overwriting: sTOR_pTOR_NA24143_round2 [2019-09-03 16:33:16,131] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sTOR_pBC_NA24385_round1.bam.gc.summary.txt! Overwriting: sTOR_pBC_NA24385_round1 [2019-09-03 16:33:16,136] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sMTL_pMTL_NA24143_round2.bam.gc.summary.txt! Overwriting: sMTL_pMTL_NA24143_round2 [2019-09-03 16:33:16,141] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sMTL_pMTL_NA24143_round3.bam.gc.summary.txt! Overwriting: sMTL_pMTL_NA24143_round3 [2019-09-03 16:33:16,147] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sBC_pBC_NA24385_round2.bam.gc.summary.txt! Overwriting: sBC_pBC_NA24385_round2 [2019-09-03 16:33:16,152] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sTOR_pBC_NA24385_round3.bam.gc.summary.txt! Overwriting: sTOR_pBC_NA24385_round3 [2019-09-03 16:33:16,157] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sBC_pMTL_NA24385_round3.bam.gc.summary.txt! Overwriting: sBC_pMTL_NA24385_round3 [2019-09-03 16:33:16,162] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sTOR_pBC_NA24149_round2.bam.gc.summary.txt! Overwriting: sTOR_pBC_NA24149_round2 [2019-09-03 16:33:16,167] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sTOR_pBC_NA24149_round3.bam.gc.summary.txt! Overwriting: sTOR_pBC_NA24149_round3 [2019-09-03 16:33:16,173] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sTOR_pBC_NA24385_round2.bam.gc.summary.txt! Overwriting: sTOR_pBC_NA24385_round2 [2019-09-03 16:33:16,178] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sBC_pMTL_NA24143_round1.bam.gc.summary.txt! Overwriting: sBC_pMTL_NA24143_round1 [2019-09-03 16:33:16,183] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sMTL_pMTL_NA24149_round2.bam.gc.summary.txt! Overwriting: sMTL_pMTL_NA24149_round2 [2019-09-03 16:33:16,188] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sMTL_pMTL_NA24143_round1.bam.gc.summary.txt! Overwriting: sMTL_pMTL_NA24143_round1 [2019-09-03 16:33:16,193] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sBC_pMTL_NA24149_round1.bam.gc.summary.txt! Overwriting: sBC_pMTL_NA24149_round1 [2019-09-03 16:33:16,199] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sMTL_pMTL_NA24385_round1.bam.gc.summary.txt! Overwriting: sMTL_pMTL_NA24385_round1 [2019-09-03 16:33:16,204] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sMTL_pMTL_NA24149_round1.bam.gc.summary.txt! Overwriting: sMTL_pMTL_NA24149_round1 [2019-09-03 16:33:16,209] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sBC_pMTL_NA24143_round2.bam.gc.summary.txt! Overwriting: sBC_pMTL_NA24143_round2 [2019-09-03 16:33:16,215] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sMTL_pMTL_NA24385_round2.bam.gc.summary.txt! Overwriting: sMTL_pMTL_NA24385_round2 [2019-09-03 16:33:16,220] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sMTL_pMTL_NA24149_round3.bam.gc.summary.txt! Overwriting: sMTL_pMTL_NA24149_round3 [2019-09-03 16:33:16,225] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sBC_pMTL_NA24149_round2.bam.gc.summary.txt! Overwriting: sBC_pMTL_NA24149_round2 [2019-09-03 16:33:16,231] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sBC_pMTL_NA24143_round3.bam.gc.summary.txt! Overwriting: sBC_pMTL_NA24143_round3 [2019-09-03 16:33:16,236] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sTOR_pMTL_NA24149_round3.bam.gc.summary.txt! Overwriting: sTOR_pMTL_NA24149_round3 [2019-09-03 16:33:16,241] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sTOR_pMTL_NA24385_round3.bam.gc.summary.txt! Overwriting: sTOR_pMTL_NA24385_round3 [2019-09-03 16:33:16,246] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sTOR_pMTL_NA24149_round2.bam.gc.summary.txt! Overwriting: sTOR_pMTL_NA24149_round2 [2019-09-03 16:33:16,252] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sTOR_pMTL_NA24385_round2.bam.gc.summary.txt! Overwriting: sTOR_pMTL_NA24385_round2 [2019-09-03 16:33:16,257] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sTOR_pMTL_NA24385_round1.bam.gc.summary.txt! Overwriting: sTOR_pMTL_NA24385_round1 [2019-09-03 16:33:16,263] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sBC_pMTL_NA24149_round3.bam.gc.summary.txt! Overwriting: sBC_pMTL_NA24149_round3 [2019-09-03 16:33:16,269] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sBC_pMTL_NA24385_round1.bam.gc.summary.txt! Overwriting: sBC_pMTL_NA24385_round1 [2019-09-03 16:33:16,275] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sBC_pMTL_NA24385_round2.bam.gc.summary.txt! Overwriting: sBC_pMTL_NA24385_round2 [2019-09-03 16:33:16,282] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sTOR_pMTL_NA24149_round1.bam.gc.summary.txt! Overwriting: sTOR_pMTL_NA24149_round1 [2019-09-03 16:33:16,287] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sTOR_pMTL_NA24143_round3.bam.gc.summary.txt! Overwriting: sTOR_pMTL_NA24143_round3 [2019-09-03 16:33:16,293] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sMTL_pMTL_NA24385_round3.bam.gc.summary.txt! Overwriting: sMTL_pMTL_NA24385_round3 [2019-09-03 16:33:16,300] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sTOR_pMTL_NA24143_round2.bam.gc.summary.txt! Overwriting: sTOR_pMTL_NA24143_round2 [2019-09-03 16:33:16,306] multiqc.modules.picard.GcBiasMetrics [DEBUG ] Duplicate sample name found in sTOR_pMTL_NA24143_round1.bam.gc.summary.txt! Overwriting: sTOR_pMTL_NA24143_round1 [2019-09-03 16:33:16,416] multiqc.modules.picard.picard [INFO ] Found 81 GcBiasMetrics reports [2019-09-03 16:33:16,437] multiqc [DEBUG ] No samples found: prokka [2019-09-03 16:33:16,460] multiqc [DEBUG ] No samples found: samblaster [2019-09-03 16:33:17,559] multiqc.modules.samtools.samtools [INFO ] Found 81 stats reports [2019-09-03 16:33:17,579] multiqc [DEBUG ] No samples found: bamtools [2019-09-03 16:33:17,595] multiqc [DEBUG ] No samples found: jellyfish [2019-09-03 16:33:17,622] multiqc [DEBUG ] No samples found: vcftools [2019-09-03 16:33:17,643] multiqc [DEBUG ] No samples found: longranger [2019-09-03 16:33:17,662] multiqc [DEBUG ] No samples found: stacks [2019-09-03 16:33:17,708] multiqc [DEBUG ] No samples found: bbmap [2019-09-03 16:33:17,726] multiqc [DEBUG ] No samples found: bismark [2019-09-03 16:33:17,745] multiqc [DEBUG ] No samples found: biscuit [2019-09-03 16:33:17,763] multiqc [DEBUG ] No samples found: hicexplorer [2019-09-03 16:33:17,781] multiqc [DEBUG ] No samples found: hicup [2019-09-03 16:33:17,807] multiqc [DEBUG ] No samples found: hicpro [2019-09-03 16:33:17,828] multiqc [DEBUG ] No samples found: salmon [2019-09-03 16:33:17,849] multiqc [DEBUG ] No samples found: kallisto [2019-09-03 16:33:17,869] multiqc [DEBUG ] No samples found: slamdunk [2019-09-03 16:33:17,891] multiqc [DEBUG ] No samples found: star [2019-09-03 16:33:17,912] multiqc [DEBUG ] No samples found: hisat2 [2019-09-03 16:33:17,934] multiqc [DEBUG ] No samples found: tophat [2019-09-03 16:33:17,952] multiqc [DEBUG ] No samples found: bowtie2 [2019-09-03 16:33:17,976] multiqc [DEBUG ] No samples found: bowtie1 [2019-09-03 16:33:17,995] multiqc [DEBUG ] No samples found: kat [2019-09-03 16:33:18,015] multiqc [DEBUG ] No samples found: leehom [2019-09-03 16:33:18,034] multiqc [DEBUG ] No samples found: adapterRemoval [2019-09-03 16:33:18,058] multiqc [DEBUG ] No samples found: clipandmerge [2019-09-03 16:33:18,080] multiqc [DEBUG ] No samples found: cutadapt [2019-09-03 16:33:18,102] multiqc [DEBUG ] No samples found: flexbar [2019-09-03 16:33:18,122] multiqc [DEBUG ] No samples found: trimmomatic [2019-09-03 16:33:18,144] multiqc [DEBUG ] No samples found: skewer [2019-09-03 16:33:18,167] multiqc [DEBUG ] No samples found: sortmerna [2019-09-03 16:33:18,189] multiqc [DEBUG ] No samples found: biobloomtools [2019-09-03 16:33:18,212] multiqc [DEBUG ] No samples found: fastq_screen [2019-09-03 16:33:18,233] multiqc [DEBUG ] No samples found: afterqc [2019-09-03 16:33:18,251] multiqc [DEBUG ] No samples found: fastp [2019-09-03 16:33:18,276] multiqc [DEBUG ] No samples found: fastqc [2019-09-03 16:33:18,296] multiqc [DEBUG ] No samples found: minionqc [2019-09-03 16:33:18,318] multiqc [DEBUG ] No samples found: clusterflow [2019-09-03 16:33:18,352] multiqc [DEBUG ] No samples found: bcl2fastq [2019-09-03 16:33:18,375] multiqc [DEBUG ] No samples found: interop [2019-09-03 16:33:18,397] multiqc [DEBUG ] No samples found: flash [2019-09-03 16:33:18,951] multiqc [INFO ] Compressing plot data [2019-09-03 16:33:54,749] multiqc [WARNING] Deleting : multiqc_report.html (-f was specified) [2019-09-03 16:33:54,768] multiqc [WARNING] Deleting : multiqc_data (-f was specified) [2019-09-03 16:33:54,798] multiqc [INFO ] Report : multiqc_report.html [2019-09-03 16:33:54,799] multiqc [INFO ] Data : multiqc_data [2019-09-03 16:33:54,804] multiqc [DEBUG ] Moving data file from '/projects/bioSCRATCH/rcorbett/tmpAui55Y/multiqc_data/multiqc_picard_gcbias.txt' to '/projects/rcorbettprj2/CGEN/GIAB2/multiqc3/multiqc_data' [2019-09-03 16:33:54,815] multiqc [DEBUG ] Moving data file from '/projects/bioSCRATCH/rcorbett/tmpAui55Y/multiqc_data/multiqc_samtools_stats.txt' to '/projects/rcorbettprj2/CGEN/GIAB2/multiqc3/multiqc_data' [2019-09-03 16:33:54,828] multiqc [DEBUG ] Moving data file from '/projects/bioSCRATCH/rcorbett/tmpAui55Y/multiqc_data/multiqc_general_stats.txt' to '/projects/rcorbettprj2/CGEN/GIAB2/multiqc3/multiqc_data' [2019-09-03 16:33:54,842] multiqc [DEBUG ] Moving data file from '/projects/bioSCRATCH/rcorbett/tmpAui55Y/multiqc_data/multiqc_sources.txt' to '/projects/rcorbettprj2/CGEN/GIAB2/multiqc3/multiqc_data' [2019-09-03 16:33:54,855] multiqc [DEBUG ] Moving data file from '/projects/bioSCRATCH/rcorbett/tmpAui55Y/multiqc_data/multiqc_data.json' to '/projects/rcorbettprj2/CGEN/GIAB2/multiqc3/multiqc_data' [2019-09-03 16:33:56,176] multiqc [INFO ] MultiQC complete