[2021-02-15 10:48:02,631] multiqc [DEBUG ] No MultiQC config found: /data/Bioinformatics_Softwere/Miniconda/.conda/envs/multiqc/lib/python3.6/site-packages/multiqc_config.yaml [2021-02-15 10:48:02,631] multiqc [DEBUG ] No MultiQC config found: /home/hatim/.multiqc_config.yaml [2021-02-15 10:48:02,632] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-02-15 10:48:02,632] multiqc [DEBUG ] Command used: /home/hatim/data/Bioinformatics_Softwere/Miniconda/.conda/envs/multiqc/bin/multiqc . [2021-02-15 10:48:02,907] multiqc [DEBUG ] Latest MultiQC version is v1.9 [2021-02-15 10:48:02,907] multiqc [INFO ] This is MultiQC v1.9 [2021-02-15 10:48:02,907] multiqc [DEBUG ] Command : /home/hatim/data/Bioinformatics_Softwere/Miniconda/.conda/envs/multiqc/bin/multiqc . [2021-02-15 10:48:02,907] multiqc [DEBUG ] Working dir : /data/Experments/E_37_SRA_Submission/Reads/Hert [2021-02-15 10:48:02,907] multiqc [INFO ] Template : default [2021-02-15 10:48:02,907] multiqc [DEBUG ] Running Python 3.6.12 | packaged by conda-forge | (default, Dec 9 2020, 00:36:02) [GCC 9.3.0] [2021-02-15 10:48:02,907] multiqc [INFO ] Searching : /data/Experments/E_37_SRA_Submission/Reads/Hert [2021-02-15 10:48:02,907] multiqc [DEBUG ] Analysing modules: custom_content, conpair, peddy, somalier, methylQA, mosdepth, phantompeakqualtools, qualimap, preseq, quast, qorts, rna_seqc, rockhopper, rsem, rseqc, busco, goleft_indexcov, disambiguate, supernova, deeptools, sargasso, verifybamid, mirtrace, happy, mirtop, homer, macs2, theta2, snpeff, gatk, htseq, bcftools, featureCounts, fgbio, dragen, dedup, damageprofiler, biobambam2, mtnucratio, picard, prokka, samblaster, samtools, sexdeterrmine, bamtools, jellyfish, vcftools, longranger, stacks, varscan2, bbmap, bismark, biscuit, hicexplorer, hicup, hicpro, salmon, kallisto, slamdunk, star, hisat2, tophat, bowtie2, bowtie1, snpsplit, kat, leehom, adapterRemoval, clipandmerge, cutadapt, flexbar, kaiju, kraken, malt, trimmomatic, sickle, skewer, sortmerna, biobloomtools, fastq_screen, afterqc, fastp, fastqc, pycoqc, minionqc, multivcfanalyzer, clusterflow, bcl2fastq, interop, ivar, flash, seqyclean [2021-02-15 10:48:02,907] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmphkk5k8u1 [2021-02-15 10:48:03,129] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Hert_BGI19_500_2.fq [2021-02-15 10:48:03,129] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Hert_171219.fastq [2021-02-15 10:48:03,240] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Hert_pycoQC.json [2021-02-15 10:48:03,262] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Hert_aber19_300_1.fq [2021-02-15 10:48:03,262] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Hert_BGI19_270_2.fq [2021-02-15 10:48:03,263] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Hert_BGI19_270_1.fq [2021-02-15 10:48:03,386] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Hert_BGI19_270_1_fastqc.html [2021-02-15 10:48:03,445] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Hert_BGI19_270_1_fastqc.html [2021-02-15 10:48:03,445] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: Hert_BGI19_270_1_fastqc.html [2021-02-15 10:48:03,445] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: Hert_BGI19_270_1_fastqc.html [2021-02-15 10:48:03,445] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: Hert_BGI19_270_1_fastqc.html [2021-02-15 10:48:03,445] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: Hert_BGI19_270_1_fastqc.html [2021-02-15 10:48:03,446] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: Hert_BGI19_270_1_fastqc.html [2021-02-15 10:48:03,452] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: Hert_BGI19_270_1_fastqc.html [2021-02-15 10:48:03,652] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Hert_aber19_300_2.fq [2021-02-15 10:48:03,802] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Hert_aber19_300_2_fastqc.html [2021-02-15 10:48:03,865] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Hert_aber19_300_2_fastqc.html [2021-02-15 10:48:03,866] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: Hert_aber19_300_2_fastqc.html [2021-02-15 10:48:03,866] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: Hert_aber19_300_2_fastqc.html [2021-02-15 10:48:03,866] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: Hert_aber19_300_2_fastqc.html [2021-02-15 10:48:03,866] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: Hert_aber19_300_2_fastqc.html [2021-02-15 10:48:03,866] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: Hert_aber19_300_2_fastqc.html [2021-02-15 10:48:03,874] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: Hert_aber19_300_2_fastqc.html [2021-02-15 10:48:04,205] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Hert_BGI19_500_1.fq [2021-02-15 10:48:04,360] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Hert_BGI19_270_2_fastqc.html [2021-02-15 10:48:04,417] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Hert_BGI19_270_2_fastqc.html [2021-02-15 10:48:04,417] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: Hert_BGI19_270_2_fastqc.html [2021-02-15 10:48:04,417] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: Hert_BGI19_270_2_fastqc.html [2021-02-15 10:48:04,417] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: Hert_BGI19_270_2_fastqc.html [2021-02-15 10:48:04,418] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: Hert_BGI19_270_2_fastqc.html [2021-02-15 10:48:04,418] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: Hert_BGI19_270_2_fastqc.html [2021-02-15 10:48:04,422] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: Hert_BGI19_270_2_fastqc.html [2021-02-15 10:48:04,743] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Hert_aber19_300_1_fastqc.html [2021-02-15 10:48:04,814] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Hert_aber19_300_1_fastqc.html [2021-02-15 10:48:04,814] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: Hert_aber19_300_1_fastqc.html [2021-02-15 10:48:04,814] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: Hert_aber19_300_1_fastqc.html [2021-02-15 10:48:04,815] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: Hert_aber19_300_1_fastqc.html [2021-02-15 10:48:04,815] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: Hert_aber19_300_1_fastqc.html [2021-02-15 10:48:04,815] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: Hert_aber19_300_1_fastqc.html [2021-02-15 10:48:04,824] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: Hert_aber19_300_1_fastqc.html [2021-02-15 10:48:05,205] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Hert_pycoQC.html [2021-02-15 10:48:05,324] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Hert_BGI19_500_2_fastqc.html [2021-02-15 10:48:05,384] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Hert_BGI19_500_2_fastqc.html [2021-02-15 10:48:05,384] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: Hert_BGI19_500_2_fastqc.html [2021-02-15 10:48:05,384] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: Hert_BGI19_500_2_fastqc.html [2021-02-15 10:48:05,384] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: Hert_BGI19_500_2_fastqc.html [2021-02-15 10:48:05,384] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: Hert_BGI19_500_2_fastqc.html [2021-02-15 10:48:05,384] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: Hert_BGI19_500_2_fastqc.html [2021-02-15 10:48:05,389] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: Hert_BGI19_500_2_fastqc.html [2021-02-15 10:48:05,750] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Hert_BGI19_500_1_fastqc.html [2021-02-15 10:48:05,809] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Hert_BGI19_500_1_fastqc.html [2021-02-15 10:48:05,809] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: Hert_BGI19_500_1_fastqc.html [2021-02-15 10:48:05,809] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: Hert_BGI19_500_1_fastqc.html [2021-02-15 10:48:05,809] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: Hert_BGI19_500_1_fastqc.html [2021-02-15 10:48:05,809] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: Hert_BGI19_500_1_fastqc.html [2021-02-15 10:48:05,809] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: Hert_BGI19_500_1_fastqc.html [2021-02-15 10:48:05,813] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: Hert_BGI19_500_1_fastqc.html [2021-02-15 10:48:06,860] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.4 [2021-02-15 10:48:06,864] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.4 [2021-02-15 10:48:06,873] multiqc [DEBUG ] No samples found: custom_content [2021-02-15 10:48:06,887] multiqc [DEBUG ] No samples found: conpair [2021-02-15 10:48:06,905] multiqc [DEBUG ] No samples found: peddy [2021-02-15 10:48:06,923] multiqc [DEBUG ] No samples found: somalier [2021-02-15 10:48:06,940] multiqc [DEBUG ] No samples found: methylQA [2021-02-15 10:48:06,970] multiqc [DEBUG ] No samples found: mosdepth [2021-02-15 10:48:06,983] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-02-15 10:48:06,990] multiqc [DEBUG ] No samples found: qualimap [2021-02-15 10:48:07,011] multiqc [DEBUG ] No samples found: preseq [2021-02-15 10:48:07,033] multiqc [DEBUG ] No samples found: quast [2021-02-15 10:48:07,056] multiqc [DEBUG ] No samples found: qorts [2021-02-15 10:48:07,083] multiqc [DEBUG ] No samples found: rna_seqc [2021-02-15 10:48:07,111] multiqc [DEBUG ] No samples found: rockhopper [2021-02-15 10:48:07,126] multiqc [DEBUG ] No samples found: rsem [2021-02-15 10:48:07,178] multiqc [DEBUG ] No samples found: rseqc [2021-02-15 10:48:07,202] multiqc [DEBUG ] No samples found: busco [2021-02-15 10:48:07,218] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-02-15 10:48:07,234] multiqc [DEBUG ] No samples found: disambiguate [2021-02-15 10:48:07,252] multiqc [DEBUG ] No samples found: supernova [2021-02-15 10:48:07,308] multiqc [DEBUG ] No samples found: deeptools [2021-02-15 10:48:07,323] multiqc [DEBUG ] No samples found: sargasso [2021-02-15 10:48:07,337] multiqc [DEBUG ] No samples found: verifybamid [2021-02-15 10:48:07,352] multiqc [DEBUG ] No samples found: mirtrace [2021-02-15 10:48:07,371] multiqc [DEBUG ] No samples found: happy [2021-02-15 10:48:07,385] multiqc [DEBUG ] No samples found: mirtop [2021-02-15 10:48:07,418] multiqc [DEBUG ] No samples found: homer [2021-02-15 10:48:07,434] multiqc [DEBUG ] No samples found: macs2 [2021-02-15 10:48:07,449] multiqc [DEBUG ] No samples found: theta2 [2021-02-15 10:48:07,463] multiqc [DEBUG ] No samples found: snpeff [2021-02-15 10:48:07,484] multiqc [DEBUG ] No samples found: gatk [2021-02-15 10:48:07,497] multiqc [DEBUG ] No samples found: htseq [2021-02-15 10:48:07,513] multiqc [DEBUG ] No samples found: bcftools [2021-02-15 10:48:07,530] multiqc [DEBUG ] No samples found: featureCounts [2021-02-15 10:48:07,562] multiqc [DEBUG ] No samples found: fgbio [2021-02-15 10:48:07,621] multiqc [DEBUG ] No samples found: dragen [2021-02-15 10:48:07,643] multiqc [DEBUG ] No samples found: dedup [2021-02-15 10:48:07,656] multiqc [DEBUG ] No samples found: damageprofiler [2021-02-15 10:48:07,765] multiqc [DEBUG ] No samples found: biobambam2 [2021-02-15 10:48:07,781] multiqc [DEBUG ] No samples found: mtnucratio [2021-02-15 10:48:07,784] multiqc [DEBUG ] No samples found: picard [2021-02-15 10:48:07,797] multiqc [DEBUG ] No samples found: prokka [2021-02-15 10:48:07,813] multiqc [DEBUG ] No samples found: samblaster [2021-02-15 10:48:07,851] multiqc [DEBUG ] No samples found: samtools [2021-02-15 10:48:07,864] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-02-15 10:48:07,883] multiqc [DEBUG ] No samples found: bamtools [2021-02-15 10:48:07,896] multiqc [DEBUG ] No samples found: jellyfish [2021-02-15 10:48:07,923] multiqc [DEBUG ] No samples found: vcftools [2021-02-15 10:48:07,935] multiqc [DEBUG ] No samples found: longranger [2021-02-15 10:48:07,951] multiqc [DEBUG ] No samples found: stacks [2021-02-15 10:48:07,969] multiqc [DEBUG ] No samples found: varscan2 [2021-02-15 10:48:08,024] multiqc [DEBUG ] No samples found: bbmap [2021-02-15 10:48:08,039] multiqc [DEBUG ] No samples found: bismark [2021-02-15 10:48:08,063] multiqc [DEBUG ] No samples found: biscuit [2021-02-15 10:48:08,091] multiqc [DEBUG ] No samples found: hicexplorer [2021-02-15 10:48:08,119] multiqc [DEBUG ] No samples found: hicup [2021-02-15 10:48:08,139] multiqc [DEBUG ] No samples found: hicpro [2021-02-15 10:48:08,157] multiqc [DEBUG ] No samples found: salmon [2021-02-15 10:48:08,174] multiqc [DEBUG ] No samples found: kallisto [2021-02-15 10:48:08,187] multiqc [DEBUG ] No samples found: slamdunk [2021-02-15 10:48:08,201] multiqc [DEBUG ] No samples found: star [2021-02-15 10:48:08,214] multiqc [DEBUG ] No samples found: hisat2 [2021-02-15 10:48:08,227] multiqc [DEBUG ] No samples found: tophat [2021-02-15 10:48:08,241] multiqc [DEBUG ] No samples found: bowtie2 [2021-02-15 10:48:08,257] multiqc [DEBUG ] No samples found: bowtie1 [2021-02-15 10:48:08,270] multiqc [DEBUG ] No samples found: snpsplit [2021-02-15 10:48:08,282] multiqc [DEBUG ] No samples found: kat [2021-02-15 10:48:08,294] multiqc [DEBUG ] No samples found: leehom [2021-02-15 10:48:08,310] multiqc [DEBUG ] No samples found: adapterRemoval [2021-02-15 10:48:08,322] multiqc [DEBUG ] No samples found: clipandmerge [2021-02-15 10:48:08,336] multiqc [DEBUG ] No samples found: cutadapt [2021-02-15 10:48:08,348] multiqc [DEBUG ] No samples found: flexbar [2021-02-15 10:48:08,363] multiqc [DEBUG ] No samples found: kaiju [2021-02-15 10:48:08,381] multiqc [DEBUG ] No samples found: kraken [2021-02-15 10:48:08,394] multiqc [DEBUG ] No samples found: malt [2021-02-15 10:48:08,407] multiqc [DEBUG ] No samples found: trimmomatic [2021-02-15 10:48:08,429] multiqc [DEBUG ] No samples found: sickle [2021-02-15 10:48:08,443] multiqc [DEBUG ] No samples found: skewer [2021-02-15 10:48:08,456] multiqc [DEBUG ] No samples found: sortmerna [2021-02-15 10:48:08,468] multiqc [DEBUG ] No samples found: biobloomtools [2021-02-15 10:48:08,480] multiqc [DEBUG ] No samples found: fastq_screen [2021-02-15 10:48:08,492] multiqc [DEBUG ] No samples found: afterqc [2021-02-15 10:48:08,506] multiqc [DEBUG ] No samples found: fastp [2021-02-15 10:48:08,827] multiqc.modules.fastqc.fastqc [INFO ] Found 6 reports [2021-02-15 10:48:09,698] multiqc.modules.pycoqc.pycoqc [INFO ] Found 1 reports [2021-02-15 10:48:09,716] multiqc [DEBUG ] No samples found: minionqc [2021-02-15 10:48:09,730] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-02-15 10:48:09,742] multiqc [DEBUG ] No samples found: clusterflow [2021-02-15 10:48:09,754] multiqc [DEBUG ] No samples found: bcl2fastq [2021-02-15 10:48:09,766] multiqc [DEBUG ] No samples found: interop [2021-02-15 10:48:09,778] multiqc [DEBUG ] No samples found: ivar [2021-02-15 10:48:09,793] multiqc [DEBUG ] No samples found: flash [2021-02-15 10:48:09,807] multiqc [DEBUG ] No samples found: seqyclean [2021-02-15 10:48:09,817] multiqc [INFO ] Compressing plot data [2021-02-15 10:48:09,998] multiqc [INFO ] Report : multiqc_report.html [2021-02-15 10:48:09,998] multiqc [INFO ] Data : multiqc_data [2021-02-15 10:48:09,998] multiqc [DEBUG ] Moving data file from '/tmp/tmphkk5k8u1/multiqc_data' to '/data/Experments/E_37_SRA_Submission/Reads/Hert/multiqc_data' [2021-02-15 10:48:10,387] multiqc [INFO ] MultiQC complete