[2019-12-18 12:05:22,605] multiqc [DEBUG ] No MultiQC config found: /home/sam/.local/lib/python3.5/site-packages/multiqc-1.6-py3.5.egg/multiqc_config.yaml [2019-12-18 12:05:22,605] multiqc [DEBUG ] No MultiQC config found: /home/sam/.multiqc_config.yaml [2019-12-18 12:05:22,605] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2019-12-18 12:05:22,605] multiqc [DEBUG ] Command used: /usr/local/bin/multiqc . [2019-12-18 12:05:23,767] multiqc [WARNING] MultiQC Version v1.8 now available! [2019-12-18 12:05:23,768] multiqc [INFO ] This is MultiQC v1.6 [2019-12-18 12:05:23,768] multiqc [DEBUG ] Command : /usr/local/bin/multiqc . [2019-12-18 12:05:23,768] multiqc [DEBUG ] Working dir : /home/sam/analyses/20191218_cbai_fastp_RNAseq_trimming [2019-12-18 12:05:23,768] multiqc [INFO ] Template : default [2019-12-18 12:05:23,768] multiqc [INFO ] Searching '.' [2019-12-18 12:05:23,770] 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 [2019-12-18 12:05:23,770] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmplo8ol0xm [2019-12-18 12:05:23,949] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 304428_S1_L002_R2_001.fastp-trim.201912184416_fastqc.html [2019-12-18 12:05:23,950] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 304428_S1_L001_R1_001.fastp-trim.201912183855.report.html [2019-12-18 12:05:23,975] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329774_S1_L002_R2_001.fastp-trim.201912185239_fastqc.html [2019-12-18 12:05:23,983] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329775_S2_L002_R1_001.fastp-trim.201912185856.fq.gz [2019-12-18 12:05:23,983] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 304428_S1_L002_R1_001.fastp-trim.201912184416.fq.gz [2019-12-18 12:05:23,984] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329777_S4_L001_R1_001.fastp-trim.201912180900_fastqc.html [2019-12-18 12:05:24,015] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329775_S2_L001_R1_001.fastp-trim.201912185554_fastqc.html [2019-12-18 12:05:24,015] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329775_S2_L002_R1_001.fastp-trim.201912185856.report.html [2019-12-18 12:05:24,016] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329777_S4_L002_R1_001.fastp-trim.201912181245.report.html [2019-12-18 12:05:24,016] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329774_S1_L001_R1_001.fastp-trim.201912184855.fq.gz [2019-12-18 12:05:24,017] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 304428_S1_L002_R2_001.fastp-trim.201912184416.fq.gz [2019-12-18 12:05:24,017] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329774_S1_L002_R1_001.fastp-trim.201912185239_fastqc.html [2019-12-18 12:05:24,017] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329774_S1_L001_R2_001.fastp-trim.201912184855_fastqc.html [2019-12-18 12:05:24,017] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329777_S4_L001_R1_001.fastp-trim.201912180900.fq.gz [2019-12-18 12:05:24,017] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 304428_S1_L002_R1_001.fastp-trim.201912184416.report.html [2019-12-18 12:05:24,017] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329775_S2_L001_R2_001.fastp-trim.201912185554_fastqc.html [2019-12-18 12:05:24,036] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329776_S3_L001_R1_001.fastp-trim.201912180142_fastqc.html [2019-12-18 12:05:24,037] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329775_S2_L001_R1_001.fastp-trim.201912185554.fq.gz [2019-12-18 12:05:24,038] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329774_S1_L001_R1_001.fastp-trim.201912184855_fastqc.html [2019-12-18 12:05:24,038] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329776_S3_L001_R2_001.fastp-trim.201912180142.fq.gz [2019-12-18 12:05:24,061] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329776_S3_L002_R2_001.fastp-trim.201912180540_fastqc.html [2019-12-18 12:05:24,085] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 304428_S1_L001_R2_001.fastp-trim.201912183855_fastqc.html [2019-12-18 12:05:24,086] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329774_S1_L002_R1_001.fastp-trim.201912185239.fq.gz [2019-12-18 12:05:24,087] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329776_S3_L002_R1_001.fastp-trim.201912180540.fq.gz [2019-12-18 12:05:24,087] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329777_S4_L001_R2_001.fastp-trim.201912180900.fq.gz [2019-12-18 12:05:24,184] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329777_S4_L002_R1_001.fastp-trim.201912181245_fastqc.html [2019-12-18 12:05:24,207] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329775_S2_L002_R2_001.fastp-trim.201912185856_fastqc.html [2019-12-18 12:05:24,207] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329776_S3_L002_R1_001.fastp-trim.201912180540.report.html [2019-12-18 12:05:24,212] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329777_S4_L002_R2_001.fastp-trim.201912181245.fq.gz [2019-12-18 12:05:24,212] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329774_S1_L001_R1_001.fastp-trim.201912184855.report.html [2019-12-18 12:05:24,212] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329776_S3_L001_R2_001.fastp-trim.201912180142_fastqc.html [2019-12-18 12:05:24,219] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329776_S3_L001_R1_001.fastp-trim.201912180142.report.html [2019-12-18 12:05:24,219] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329775_S2_L001_R2_001.fastp-trim.201912185554.fq.gz [2019-12-18 12:05:24,226] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329774_S1_L002_R2_001.fastp-trim.201912185239.fq.gz [2019-12-18 12:05:24,226] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329776_S3_L002_R2_001.fastp-trim.201912180540.fq.gz [2019-12-18 12:05:24,226] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329777_S4_L001_R1_001.fastp-trim.201912180900.report.html [2019-12-18 12:05:24,227] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329775_S2_L002_R2_001.fastp-trim.201912185856.fq.gz [2019-12-18 12:05:24,227] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329776_S3_L001_R1_001.fastp-trim.201912180142.fq.gz [2019-12-18 12:05:24,227] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329775_S2_L001_R1_001.fastp-trim.201912185554.report.html [2019-12-18 12:05:24,227] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 304428_S1_L001_R2_001.fastp-trim.201912183855.fq.gz [2019-12-18 12:05:24,227] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 304428_S1_L002_R1_001.fastp-trim.201912184416_fastqc.html [2019-12-18 12:05:24,227] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 304428_S1_L001_R1_001.fastp-trim.201912183855.fq.gz [2019-12-18 12:05:24,227] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329777_S4_L002_R1_001.fastp-trim.201912181245.fq.gz [2019-12-18 12:05:24,228] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329776_S3_L002_R1_001.fastp-trim.201912180540_fastqc.html [2019-12-18 12:05:24,228] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329775_S2_L002_R1_001.fastp-trim.201912185856_fastqc.html [2019-12-18 12:05:24,228] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329774_S1_L002_R1_001.fastp-trim.201912185239.report.html [2019-12-18 12:05:24,228] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329777_S4_L001_R2_001.fastp-trim.201912180900_fastqc.html [2019-12-18 12:05:24,228] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 329774_S1_L001_R2_001.fastp-trim.201912184855.fq.gz [2019-12-18 12:05:25,129] multiqc [DEBUG ] No samples found: custom_content [2019-12-18 12:05:25,138] multiqc [DEBUG ] No samples found: conpair [2019-12-18 12:05:25,146] multiqc [DEBUG ] No samples found: peddy [2019-12-18 12:05:25,159] multiqc [DEBUG ] No samples found: methylQA [2019-12-18 12:05:25,165] multiqc [DEBUG ] No samples found: qualimap [2019-12-18 12:05:25,169] multiqc [DEBUG ] No samples found: preseq [2019-12-18 12:05:25,174] multiqc [DEBUG ] No samples found: quast [2019-12-18 12:05:25,178] multiqc [DEBUG ] No samples found: qorts [2019-12-18 12:05:25,183] multiqc [DEBUG ] No samples found: rna_seqc [2019-12-18 12:05:25,187] multiqc [DEBUG ] No samples found: rsem [2019-12-18 12:05:25,196] multiqc [DEBUG ] No samples found: rseqc [2019-12-18 12:05:25,200] multiqc [DEBUG ] No samples found: busco [2019-12-18 12:05:25,205] multiqc [DEBUG ] No samples found: goleft_indexcov [2019-12-18 12:05:25,209] multiqc [DEBUG ] No samples found: disambiguate [2019-12-18 12:05:25,214] multiqc [DEBUG ] No samples found: supernova [2019-12-18 12:05:25,220] multiqc [DEBUG ] No samples found: deeptools [2019-12-18 12:05:25,225] multiqc [DEBUG ] No samples found: sargasso [2019-12-18 12:05:25,229] multiqc [DEBUG ] No samples found: verifybamid [2019-12-18 12:05:25,234] multiqc [DEBUG ] No samples found: mirtrace [2019-12-18 12:05:25,239] multiqc [DEBUG ] No samples found: happy [2019-12-18 12:05:25,252] multiqc [DEBUG ] No samples found: homer [2019-12-18 12:05:25,262] multiqc [DEBUG ] No samples found: macs2 [2019-12-18 12:05:25,266] multiqc [DEBUG ] No samples found: theta2 [2019-12-18 12:05:25,281] multiqc [DEBUG ] No samples found: snpeff [2019-12-18 12:05:25,288] multiqc [DEBUG ] No samples found: gatk [2019-12-18 12:05:25,292] multiqc [DEBUG ] No samples found: htseq [2019-12-18 12:05:25,298] multiqc [DEBUG ] No samples found: bcftools [2019-12-18 12:05:25,302] multiqc [DEBUG ] No samples found: featureCounts [2019-12-18 12:05:25,306] multiqc [DEBUG ] No samples found: dedup [2019-12-18 12:05:25,316] multiqc [DEBUG ] No samples found: picard [2019-12-18 12:05:25,320] multiqc [DEBUG ] No samples found: prokka [2019-12-18 12:05:25,325] multiqc [DEBUG ] No samples found: samblaster [2019-12-18 12:05:25,331] multiqc [DEBUG ] No samples found: samtools [2019-12-18 12:05:25,335] multiqc [DEBUG ] No samples found: bamtools [2019-12-18 12:05:25,340] multiqc [DEBUG ] No samples found: jellyfish [2019-12-18 12:05:25,346] multiqc [DEBUG ] No samples found: vcftools [2019-12-18 12:05:25,351] multiqc [DEBUG ] No samples found: longranger [2019-12-18 12:05:25,360] multiqc [DEBUG ] No samples found: bbmap [2019-12-18 12:05:25,365] multiqc [DEBUG ] No samples found: bismark [2019-12-18 12:05:25,369] multiqc [DEBUG ] No samples found: hicexplorer [2019-12-18 12:05:25,373] multiqc [DEBUG ] No samples found: hicup [2019-12-18 12:05:25,378] multiqc [DEBUG ] No samples found: hicpro [2019-12-18 12:05:25,384] multiqc [DEBUG ] No samples found: salmon [2019-12-18 12:05:25,388] multiqc [DEBUG ] No samples found: kallisto [2019-12-18 12:05:25,393] multiqc [DEBUG ] No samples found: slamdunk [2019-12-18 12:05:25,397] multiqc [DEBUG ] No samples found: star [2019-12-18 12:05:25,401] multiqc [DEBUG ] No samples found: hisat2 [2019-12-18 12:05:25,406] multiqc [DEBUG ] No samples found: tophat [2019-12-18 12:05:25,410] multiqc [DEBUG ] No samples found: bowtie2 [2019-12-18 12:05:25,415] multiqc [DEBUG ] No samples found: bowtie1 [2019-12-18 12:05:25,419] multiqc [DEBUG ] No samples found: kat [2019-12-18 12:05:25,423] multiqc [DEBUG ] No samples found: leehom [2019-12-18 12:05:25,427] multiqc [DEBUG ] No samples found: adapterRemoval [2019-12-18 12:05:25,432] multiqc [DEBUG ] No samples found: clipandmerge [2019-12-18 12:05:25,437] multiqc [DEBUG ] No samples found: cutadapt [2019-12-18 12:05:25,441] multiqc [DEBUG ] No samples found: flexbar [2019-12-18 12:05:25,445] multiqc [DEBUG ] No samples found: trimmomatic [2019-12-18 12:05:25,449] multiqc [DEBUG ] No samples found: skewer [2019-12-18 12:05:25,454] multiqc [DEBUG ] No samples found: sortmerna [2019-12-18 12:05:25,458] multiqc [DEBUG ] No samples found: biobloomtools [2019-12-18 12:05:25,464] multiqc [DEBUG ] No samples found: fastq_screen [2019-12-18 12:05:25,468] multiqc [DEBUG ] No samples found: afterqc [2019-12-18 12:05:25,472] multiqc [DEBUG ] No samples found: fastp [2019-12-18 12:05:30,101] multiqc.modules.fastqc.fastqc [INFO ] Found 18 reports [2019-12-18 12:05:30,489] multiqc [DEBUG ] No samples found: clusterflow [2019-12-18 12:05:30,493] multiqc [DEBUG ] No samples found: bcl2fastq [2019-12-18 12:05:30,568] multiqc [DEBUG ] No samples found: interop [2019-12-18 12:05:30,603] multiqc [INFO ] Compressing plot data [2019-12-18 12:05:30,969] multiqc [INFO ] Report : multiqc_report.html [2019-12-18 12:05:30,969] multiqc [INFO ] Data : multiqc_data [2019-12-18 12:05:30,969] multiqc [DEBUG ] Moving data file from '/tmp/tmplo8ol0xm/multiqc_data/multiqc_general_stats.txt' to '/home/sam/analyses/20191218_cbai_fastp_RNAseq_trimming/multiqc_data' [2019-12-18 12:05:30,969] multiqc [DEBUG ] Moving data file from '/tmp/tmplo8ol0xm/multiqc_data/multiqc_fastqc.txt' to '/home/sam/analyses/20191218_cbai_fastp_RNAseq_trimming/multiqc_data' [2019-12-18 12:05:30,970] multiqc [DEBUG ] Moving data file from '/tmp/tmplo8ol0xm/multiqc_data/multiqc_sources.txt' to '/home/sam/analyses/20191218_cbai_fastp_RNAseq_trimming/multiqc_data' [2019-12-18 12:05:30,970] multiqc [DEBUG ] Moving data file from '/tmp/tmplo8ol0xm/multiqc_data/multiqc_data.json' to '/home/sam/analyses/20191218_cbai_fastp_RNAseq_trimming/multiqc_data' [2019-12-18 12:05:31,206] multiqc [INFO ] MultiQC complete