[2020-03-20 12:31:41,795] multiqc [DEBUG ] No MultiQC config found: /home/sam/.local/lib/python3.5/site-packages/multiqc-1.8-py3.5.egg/multiqc_config.yaml [2020-03-20 12:31:41,795] multiqc [DEBUG ] No MultiQC config found: /home/sam/.multiqc_config.yaml [2020-03-20 12:31:41,795] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2020-03-20 12:31:41,795] multiqc [DEBUG ] Command used: /usr/local/bin/multiqc . [2020-03-20 12:31:47,630] multiqc [DEBUG ] Latest MultiQC version is v1.8 [2020-03-20 12:31:47,630] multiqc [INFO ] This is MultiQC v1.8 [2020-03-20 12:31:47,630] multiqc [DEBUG ] Command : /usr/local/bin/multiqc . [2020-03-20 12:31:47,630] multiqc [DEBUG ] Working dir : /home/sam/analyses/20200318_cbai_RNAseq_fastp_trimming [2020-03-20 12:31:47,630] multiqc [INFO ] Template : default [2020-03-20 12:31:47,630] multiqc [DEBUG ] Running Python 3.5.2 (default, Oct 8 2019, 13:06:37) [GCC 5.4.0 20160609] [2020-03-20 12:31:47,630] multiqc [INFO ] Searching : /home/sam/analyses/20200318_cbai_RNAseq_fastp_trimming [2020-03-20 12:31:47,631] 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, fgbio, dedup, damageprofiler, biobambam2, mtnucratio, picard, prokka, samblaster, samtools, sexdeterrmine, 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, mosdepth, clusterflow, bcl2fastq, interop, flash, seqyclean [2020-03-20 12:31:47,631] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpsrluvdy6 [2020-03-20 12:31:47,640] multiqc [DEBUG ] Ignoring directory as matched fn_ignore_dirs: ./multiqc_data [2020-03-20 12:31:47,643] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 73_R1_001.fastp-trim.202003182229_fastqc.html [2020-03-20 12:31:47,657] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 463_R1_001.fastp-trim.202003185732.report.json [2020-03-20 12:31:47,665] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 463_R1_001.fastp-trim.202003185732.report.json [2020-03-20 12:31:47,696] multiqc [DEBUG ] Ignoring file as 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[2020-03-20 12:31:48,496] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 463_R2_001.fastp-trim.202003185732.fq.gz [2020-03-20 12:31:48,496] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 151_R1_001.fastp-trim.202003180619.fq.gz [2020-03-20 12:31:48,496] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 118_R1_001.fastp-trim.202003184931.report.html [2020-03-20 12:31:48,496] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 73_R1_001.fastp-trim.202003182229.report.html [2020-03-20 12:31:48,496] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 445_R2_001.fastp-trim.202003185018_fastqc.html [2020-03-20 12:31:48,497] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 280_R1_001.fastp-trim.202003185124.fq.gz [2020-03-20 12:31:48,498] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 485_R1_001.fastp-trim.202003181245.report.html [2020-03-20 12:31:48,499] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 359_R1_001.fastp-trim.202003182247_fastqc.html [2020-03-20 12:31:48,499] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 222_R2_001.fastp-trim.202003182800_fastqc.html [2020-03-20 12:31:48,501] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 254_R1_001.fastp-trim.202003184228.report.json [2020-03-20 12:31:48,508] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 254_R1_001.fastp-trim.202003184228.report.json [2020-03-20 12:31:48,536] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 280_R1_001.fastp-trim.202003185124.report.html [2020-03-20 12:31:48,536] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 113_R2_001.fastp-trim.202003184225_fastqc.html [2020-03-20 12:31:48,538] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 221_R1_001.fastp-trim.202003182309.report.json [2020-03-20 12:31:48,544] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 221_R1_001.fastp-trim.202003182309.report.json [2020-03-20 12:31:48,572] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 349_R1_001.fastp-trim.202003181609.report.json [2020-03-20 12:31:48,578] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 349_R1_001.fastp-trim.202003181609.report.json [2020-03-20 12:31:48,604] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 73_R1_001.fastp-trim.202003182229.fq.gz [2020-03-20 12:31:48,604] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 72_R1_001.fastp-trim.202003181709.fq.gz [2020-03-20 12:31:48,605] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 427_R2_001.fastp-trim.202003184618_fastqc.html [2020-03-20 12:31:48,607] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 173_R2_001.fastp-trim.202003181159_fastqc.html [2020-03-20 12:31:48,607] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 221_R1_001.fastp-trim.202003182309.fq.gz [2020-03-20 12:31:48,610] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 113_R1_001.fastp-trim.202003184225.report.json [2020-03-20 12:31:48,616] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 113_R1_001.fastp-trim.202003184225.report.json [2020-03-20 12:31:48,643] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 127_R2_001.fastp-trim.202003185538_fastqc.html [2020-03-20 12:31:48,644] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 294_R1_001.fastp-trim.202003180701.fq.gz [2020-03-20 12:31:48,852] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 2.2.5 [2020-03-20 12:31:48,852] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 2.2.5 [2020-03-20 12:31:48,853] multiqc [DEBUG ] No samples found: custom_content [2020-03-20 12:31:48,857] multiqc [DEBUG ] No samples found: conpair [2020-03-20 12:31:48,861] multiqc [DEBUG ] No samples found: peddy [2020-03-20 12:31:48,865] multiqc [DEBUG ] No samples found: methylQA [2020-03-20 12:31:48,869] multiqc [DEBUG ] No samples found: phantompeakqualtools [2020-03-20 12:31:48,873] multiqc [DEBUG ] No samples found: qualimap [2020-03-20 12:31:48,877] multiqc [DEBUG ] No samples found: preseq [2020-03-20 12:31:48,881] multiqc [DEBUG ] No samples found: quast [2020-03-20 12:31:48,885] multiqc [DEBUG ] No samples found: qorts [2020-03-20 12:31:48,888] multiqc [DEBUG ] No samples found: rna_seqc [2020-03-20 12:31:48,892] multiqc [DEBUG ] No samples found: rsem [2020-03-20 12:31:48,898] multiqc [DEBUG ] No samples found: rseqc [2020-03-20 12:31:48,902] multiqc [DEBUG ] No samples found: busco [2020-03-20 12:31:48,905] multiqc [DEBUG ] No samples found: goleft_indexcov [2020-03-20 12:31:48,910] multiqc [DEBUG ] No samples found: disambiguate [2020-03-20 12:31:48,914] multiqc [DEBUG ] No samples found: supernova [2020-03-20 12:31:48,919] multiqc [DEBUG ] No samples found: deeptools [2020-03-20 12:31:48,923] multiqc [DEBUG ] No samples found: sargasso [2020-03-20 12:31:48,927] multiqc [DEBUG ] No samples found: verifybamid [2020-03-20 12:31:48,931] multiqc [DEBUG ] No samples found: mirtrace [2020-03-20 12:31:48,934] multiqc [DEBUG ] No samples found: happy [2020-03-20 12:31:48,939] multiqc [DEBUG ] No samples found: homer [2020-03-20 12:31:48,943] multiqc [DEBUG ] No samples found: macs2 [2020-03-20 12:31:48,946] multiqc [DEBUG ] No samples found: theta2 [2020-03-20 12:31:48,950] multiqc [DEBUG ] No samples found: snpeff [2020-03-20 12:31:48,955] multiqc [DEBUG ] No samples found: gatk [2020-03-20 12:31:48,959] multiqc [DEBUG ] No samples found: htseq [2020-03-20 12:31:48,963] multiqc [DEBUG ] No samples found: bcftools [2020-03-20 12:31:48,967] multiqc [DEBUG ] No samples found: featureCounts [2020-03-20 12:31:48,971] multiqc [DEBUG ] No samples found: fgbio [2020-03-20 12:31:48,974] multiqc [DEBUG ] No samples found: dedup [2020-03-20 12:31:48,978] multiqc [DEBUG ] No samples found: damageprofiler [2020-03-20 12:31:48,985] multiqc [DEBUG ] No samples found: biobambam2 [2020-03-20 12:31:48,989] multiqc [DEBUG ] No samples found: mtnucratio [2020-03-20 12:31:48,993] multiqc [DEBUG ] No samples found: picard [2020-03-20 12:31:48,996] multiqc [DEBUG ] No samples found: prokka [2020-03-20 12:31:49,000] multiqc [DEBUG ] No samples found: samblaster [2020-03-20 12:31:49,005] multiqc [DEBUG ] No samples found: samtools [2020-03-20 12:31:49,008] multiqc [DEBUG ] No samples found: sexdeterrmine [2020-03-20 12:31:49,012] multiqc [DEBUG ] No samples found: bamtools [2020-03-20 12:31:49,016] multiqc [DEBUG ] No samples found: jellyfish [2020-03-20 12:31:49,021] multiqc [DEBUG ] No samples found: vcftools [2020-03-20 12:31:49,025] multiqc [DEBUG ] No samples found: longranger [2020-03-20 12:31:49,028] multiqc [DEBUG ] No samples found: stacks [2020-03-20 12:31:49,034] multiqc [DEBUG ] No samples found: bbmap [2020-03-20 12:31:49,038] multiqc [DEBUG ] No samples found: bismark [2020-03-20 12:31:49,042] multiqc [DEBUG ] No samples found: biscuit [2020-03-20 12:31:49,046] multiqc [DEBUG ] No samples found: hicexplorer [2020-03-20 12:31:49,050] multiqc [DEBUG ] No samples found: hicup [2020-03-20 12:31:49,054] multiqc [DEBUG ] No samples found: hicpro [2020-03-20 12:31:49,058] multiqc [DEBUG ] No samples found: salmon [2020-03-20 12:31:49,061] multiqc [DEBUG ] No samples found: kallisto [2020-03-20 12:31:49,065] multiqc [DEBUG ] No samples found: slamdunk [2020-03-20 12:31:49,069] multiqc [DEBUG ] No samples found: star [2020-03-20 12:31:49,073] multiqc [DEBUG ] No samples found: hisat2 [2020-03-20 12:31:49,076] multiqc [DEBUG ] No samples found: tophat [2020-03-20 12:31:49,080] multiqc [DEBUG ] No samples found: bowtie2 [2020-03-20 12:31:49,084] multiqc [DEBUG ] No samples found: bowtie1 [2020-03-20 12:31:49,088] multiqc [DEBUG ] No samples found: kat [2020-03-20 12:31:49,091] multiqc [DEBUG ] No samples found: leehom [2020-03-20 12:31:49,095] multiqc [DEBUG ] No samples found: adapterRemoval [2020-03-20 12:31:49,099] multiqc [DEBUG ] No samples found: clipandmerge [2020-03-20 12:31:49,103] multiqc [DEBUG ] No samples found: cutadapt [2020-03-20 12:31:49,106] multiqc [DEBUG ] No samples found: flexbar [2020-03-20 12:31:49,110] multiqc [DEBUG ] No samples found: trimmomatic [2020-03-20 12:31:49,114] multiqc [DEBUG ] No samples found: skewer [2020-03-20 12:31:49,117] multiqc [DEBUG ] No samples found: sortmerna [2020-03-20 12:31:49,121] multiqc [DEBUG ] No samples found: biobloomtools [2020-03-20 12:31:49,125] multiqc [DEBUG ] No samples found: fastq_screen [2020-03-20 12:31:49,129] multiqc [DEBUG ] No samples found: afterqc [2020-03-20 12:31:49,133] multiqc [DEBUG ] No samples found: fastp [2020-03-20 12:31:58,483] multiqc.modules.fastqc.fastqc [INFO ] Found 48 reports [2020-03-20 12:32:00,115] multiqc [DEBUG ] No samples found: minionqc [2020-03-20 12:32:00,118] multiqc [DEBUG ] No samples found: mosdepth [2020-03-20 12:32:00,122] multiqc [DEBUG ] No samples found: clusterflow [2020-03-20 12:32:00,126] multiqc [DEBUG ] No samples found: bcl2fastq [2020-03-20 12:32:00,130] multiqc [DEBUG ] No samples found: interop [2020-03-20 12:32:00,134] multiqc [DEBUG ] No samples found: flash [2020-03-20 12:32:00,138] multiqc [DEBUG ] No samples found: seqyclean [2020-03-20 12:32:00,220] multiqc [INFO ] Compressing plot data [2020-03-20 12:32:01,037] multiqc [WARNING] Previous MultiQC output found! Adjusting filenames.. [2020-03-20 12:32:01,038] multiqc [WARNING] Use -f or --force to overwrite existing reports instead [2020-03-20 12:32:01,038] multiqc [INFO ] Report : multiqc_report_1.html [2020-03-20 12:32:01,038] multiqc [INFO ] Data : multiqc_data_1 [2020-03-20 12:32:01,038] multiqc [DEBUG ] Moving data file from '/tmp/tmpsrluvdy6/multiqc_data/multiqc_general_stats.txt' to '/home/sam/analyses/20200318_cbai_RNAseq_fastp_trimming/multiqc_data_1' [2020-03-20 12:32:01,039] multiqc [DEBUG ] Moving data file from '/tmp/tmpsrluvdy6/multiqc_data/multiqc_fastqc.txt' to '/home/sam/analyses/20200318_cbai_RNAseq_fastp_trimming/multiqc_data_1' [2020-03-20 12:32:01,039] multiqc [DEBUG ] Moving data file from '/tmp/tmpsrluvdy6/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/home/sam/analyses/20200318_cbai_RNAseq_fastp_trimming/multiqc_data_1' [2020-03-20 12:32:01,039] multiqc [DEBUG ] Moving data file from '/tmp/tmpsrluvdy6/multiqc_data/multiqc_sources.txt' to '/home/sam/analyses/20200318_cbai_RNAseq_fastp_trimming/multiqc_data_1' [2020-03-20 12:32:01,040] multiqc [DEBUG ] Moving data file from '/tmp/tmpsrluvdy6/multiqc_data/multiqc_data.json' to '/home/sam/analyses/20200318_cbai_RNAseq_fastp_trimming/multiqc_data_1' [2020-03-20 12:32:01,163] multiqc [INFO ] MultiQC complete