[2021-02-15 10:49:39,452] multiqc [DEBUG ] No MultiQC config found: /data/Bioinformatics_Softwere/Miniconda/.conda/envs/multiqc/lib/python3.6/site-packages/multiqc_config.yaml [2021-02-15 10:49:39,452] multiqc [DEBUG ] No MultiQC config found: /home/hatim/.multiqc_config.yaml [2021-02-15 10:49:39,453] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-02-15 10:49:39,453] multiqc [DEBUG ] Command used: /home/hatim/data/Bioinformatics_Softwere/Miniconda/.conda/envs/multiqc/bin/multiqc . [2021-02-15 10:49:39,701] multiqc [DEBUG ] Latest MultiQC version is v1.9 [2021-02-15 10:49:39,701] multiqc [INFO ] This is MultiQC v1.9 [2021-02-15 10:49:39,701] multiqc [DEBUG ] Command : /home/hatim/data/Bioinformatics_Softwere/Miniconda/.conda/envs/multiqc/bin/multiqc . [2021-02-15 10:49:39,701] multiqc [DEBUG ] Working dir : /data/Experments/E_37_SRA_Submission/Reads/Hyrax [2021-02-15 10:49:39,702] multiqc [INFO ] Template : default [2021-02-15 10:49:39,702] 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 10:49:39,702] multiqc [INFO ] Searching : /data/Experments/E_37_SRA_Submission/Reads/Hyrax [2021-02-15 10:49:39,702] 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 10:49:39,702] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmp4v44o6rh [2021-02-15 10:49:39,978] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Hyrax_aber19_300_1.fq [2021-02-15 10:49:40,112] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Hyrax_BGI19_270_1_fastqc.html [2021-02-15 10:49:40,169] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Hyrax_BGI19_270_1_fastqc.html [2021-02-15 10:49:40,169] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: Hyrax_BGI19_270_1_fastqc.html [2021-02-15 10:49:40,169] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: Hyrax_BGI19_270_1_fastqc.html [2021-02-15 10:49:40,169] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: Hyrax_BGI19_270_1_fastqc.html [2021-02-15 10:49:40,169] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: Hyrax_BGI19_270_1_fastqc.html [2021-02-15 10:49:40,169] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: Hyrax_BGI19_270_1_fastqc.html [2021-02-15 10:49:40,180] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: Hyrax_BGI19_270_1_fastqc.html [2021-02-15 10:49:40,550] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Hyrax_BGI19_500_2.fq [2021-02-15 10:49:40,661] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Hyrax_aber19_300_1_fastqc.html [2021-02-15 10:49:40,718] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Hyrax_aber19_300_1_fastqc.html [2021-02-15 10:49:40,718] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: Hyrax_aber19_300_1_fastqc.html [2021-02-15 10:49:40,718] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: Hyrax_aber19_300_1_fastqc.html [2021-02-15 10:49:40,718] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: Hyrax_aber19_300_1_fastqc.html [2021-02-15 10:49:40,718] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: Hyrax_aber19_300_1_fastqc.html [2021-02-15 10:49:40,718] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: Hyrax_aber19_300_1_fastqc.html [2021-02-15 10:49:40,722] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: Hyrax_aber19_300_1_fastqc.html [2021-02-15 10:49:40,944] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Hyrax_BGI19_270_2.fq [2021-02-15 10:49:40,944] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Hyrax_181219.fastq [2021-02-15 10:49:40,944] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Hyrax_pycoQC.html [2021-02-15 10:49:41,095] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Hyrax_BGI19_270_2_fastqc.html [2021-02-15 10:49:41,156] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Hyrax_BGI19_270_2_fastqc.html [2021-02-15 10:49:41,156] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: Hyrax_BGI19_270_2_fastqc.html [2021-02-15 10:49:41,156] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: Hyrax_BGI19_270_2_fastqc.html [2021-02-15 10:49:41,156] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: Hyrax_BGI19_270_2_fastqc.html [2021-02-15 10:49:41,156] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: Hyrax_BGI19_270_2_fastqc.html [2021-02-15 10:49:41,156] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: Hyrax_BGI19_270_2_fastqc.html [2021-02-15 10:49:41,170] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: Hyrax_BGI19_270_2_fastqc.html [2021-02-15 10:49:41,651] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Hyrax_BGI19_500_1_fastqc.html [2021-02-15 10:49:41,705] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Hyrax_BGI19_500_1_fastqc.html [2021-02-15 10:49:41,705] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: Hyrax_BGI19_500_1_fastqc.html [2021-02-15 10:49:41,705] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: Hyrax_BGI19_500_1_fastqc.html [2021-02-15 10:49:41,705] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: Hyrax_BGI19_500_1_fastqc.html [2021-02-15 10:49:41,705] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: Hyrax_BGI19_500_1_fastqc.html [2021-02-15 10:49:41,705] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: Hyrax_BGI19_500_1_fastqc.html [2021-02-15 10:49:41,710] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: Hyrax_BGI19_500_1_fastqc.html [2021-02-15 10:49:42,017] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Hyrax_aber19_300_2_fastqc.html [2021-02-15 10:49:42,074] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Hyrax_aber19_300_2_fastqc.html [2021-02-15 10:49:42,074] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: Hyrax_aber19_300_2_fastqc.html [2021-02-15 10:49:42,074] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: Hyrax_aber19_300_2_fastqc.html [2021-02-15 10:49:42,074] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: Hyrax_aber19_300_2_fastqc.html [2021-02-15 10:49:42,074] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: Hyrax_aber19_300_2_fastqc.html [2021-02-15 10:49:42,074] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: Hyrax_aber19_300_2_fastqc.html [2021-02-15 10:49:42,079] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: Hyrax_aber19_300_2_fastqc.html [2021-02-15 10:49:42,385] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Hyrax_pycoQC.json [2021-02-15 10:49:42,533] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Hyrax_BGI19_500_2_fastqc.html [2021-02-15 10:49:42,586] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Hyrax_BGI19_500_2_fastqc.html [2021-02-15 10:49:42,586] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: Hyrax_BGI19_500_2_fastqc.html [2021-02-15 10:49:42,586] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: Hyrax_BGI19_500_2_fastqc.html [2021-02-15 10:49:42,586] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: Hyrax_BGI19_500_2_fastqc.html [2021-02-15 10:49:42,586] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: Hyrax_BGI19_500_2_fastqc.html [2021-02-15 10:49:42,586] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: Hyrax_BGI19_500_2_fastqc.html [2021-02-15 10:49:42,590] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: Hyrax_BGI19_500_2_fastqc.html [2021-02-15 10:49:42,792] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Hyrax_BGI19_270_1.fq [2021-02-15 10:49:42,793] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Hyrax_aber19_300_2.fq [2021-02-15 10:49:42,793] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Hyrax_BGI19_500_1.fq [2021-02-15 10:49:43,814] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.4 [2021-02-15 10:49:43,818] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.4 [2021-02-15 10:49:43,826] multiqc [DEBUG ] No samples found: custom_content [2021-02-15 10:49:43,840] multiqc [DEBUG ] No samples found: conpair [2021-02-15 10:49:43,855] multiqc [DEBUG ] No samples found: peddy [2021-02-15 10:49:43,869] multiqc [DEBUG ] No samples found: somalier [2021-02-15 10:49:43,882] multiqc [DEBUG ] No samples found: methylQA [2021-02-15 10:49:43,913] multiqc [DEBUG ] No samples found: mosdepth [2021-02-15 10:49:43,927] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-02-15 10:49:43,935] multiqc [DEBUG ] No samples found: qualimap [2021-02-15 10:49:43,950] multiqc [DEBUG ] No samples found: preseq [2021-02-15 10:49:43,963] multiqc [DEBUG ] No samples found: quast [2021-02-15 10:49:43,975] multiqc [DEBUG ] No samples found: qorts [2021-02-15 10:49:43,987] multiqc [DEBUG ] No samples found: rna_seqc [2021-02-15 10:49:43,999] multiqc [DEBUG ] No samples found: rockhopper [2021-02-15 10:49:44,016] multiqc [DEBUG ] No samples found: rsem [2021-02-15 10:49:44,064] multiqc [DEBUG ] No samples found: rseqc [2021-02-15 10:49:44,079] multiqc [DEBUG ] No samples found: busco [2021-02-15 10:49:44,092] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-02-15 10:49:44,104] multiqc [DEBUG ] No samples found: disambiguate [2021-02-15 10:49:44,115] multiqc [DEBUG ] No samples found: supernova [2021-02-15 10:49:44,156] multiqc [DEBUG ] No samples found: deeptools [2021-02-15 10:49:44,167] multiqc [DEBUG ] No samples found: sargasso [2021-02-15 10:49:44,179] multiqc [DEBUG ] No samples found: verifybamid [2021-02-15 10:49:44,189] multiqc [DEBUG ] No samples found: mirtrace [2021-02-15 10:49:44,201] multiqc [DEBUG ] No samples found: happy [2021-02-15 10:49:44,215] multiqc [DEBUG ] No samples found: mirtop [2021-02-15 10:49:44,235] multiqc [DEBUG ] No samples found: homer [2021-02-15 10:49:44,246] multiqc [DEBUG ] No samples found: macs2 [2021-02-15 10:49:44,257] multiqc [DEBUG ] No samples found: theta2 [2021-02-15 10:49:44,269] multiqc [DEBUG ] No samples found: snpeff [2021-02-15 10:49:44,287] multiqc [DEBUG ] No samples found: gatk [2021-02-15 10:49:44,298] multiqc [DEBUG ] No samples found: htseq [2021-02-15 10:49:44,312] multiqc [DEBUG ] No samples found: bcftools [2021-02-15 10:49:44,325] multiqc [DEBUG ] No samples found: featureCounts [2021-02-15 10:49:44,343] multiqc [DEBUG ] No samples found: fgbio [2021-02-15 10:49:44,381] multiqc [DEBUG ] No samples found: dragen [2021-02-15 10:49:44,392] multiqc [DEBUG ] No samples found: dedup [2021-02-15 10:49:44,404] multiqc [DEBUG ] No samples found: damageprofiler [2021-02-15 10:49:44,477] multiqc [DEBUG ] No samples found: biobambam2 [2021-02-15 10:49:44,490] multiqc [DEBUG ] No samples found: mtnucratio [2021-02-15 10:49:44,493] multiqc [DEBUG ] No samples found: picard [2021-02-15 10:49:44,505] multiqc [DEBUG ] No samples found: prokka [2021-02-15 10:49:44,516] multiqc [DEBUG ] No samples found: samblaster [2021-02-15 10:49:44,540] multiqc [DEBUG ] No samples found: samtools [2021-02-15 10:49:44,552] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-02-15 10:49:44,568] multiqc [DEBUG ] No samples found: bamtools [2021-02-15 10:49:44,581] multiqc [DEBUG ] No samples found: jellyfish [2021-02-15 10:49:44,607] multiqc [DEBUG ] No samples found: vcftools [2021-02-15 10:49:44,618] multiqc [DEBUG ] No samples found: longranger [2021-02-15 10:49:44,630] multiqc [DEBUG ] No samples found: stacks [2021-02-15 10:49:44,642] multiqc [DEBUG ] No samples found: varscan2 [2021-02-15 10:49:44,695] multiqc [DEBUG ] No samples found: bbmap [2021-02-15 10:49:44,721] multiqc [DEBUG ] No samples found: bismark [2021-02-15 10:49:44,733] multiqc [DEBUG ] No samples found: biscuit [2021-02-15 10:49:44,746] multiqc [DEBUG ] No samples found: hicexplorer [2021-02-15 10:49:44,758] multiqc [DEBUG ] No samples found: hicup [2021-02-15 10:49:44,769] multiqc [DEBUG ] No samples found: hicpro [2021-02-15 10:49:44,786] multiqc [DEBUG ] No samples found: salmon [2021-02-15 10:49:44,801] multiqc [DEBUG ] No samples found: kallisto [2021-02-15 10:49:44,814] multiqc [DEBUG ] No samples found: slamdunk [2021-02-15 10:49:44,827] multiqc [DEBUG ] No samples found: star [2021-02-15 10:49:44,839] multiqc [DEBUG ] No samples found: hisat2 [2021-02-15 10:49:44,851] multiqc [DEBUG ] No samples found: tophat [2021-02-15 10:49:44,863] multiqc [DEBUG ] No samples found: bowtie2 [2021-02-15 10:49:44,875] multiqc [DEBUG ] No samples found: bowtie1 [2021-02-15 10:49:44,888] multiqc [DEBUG ] No samples found: snpsplit [2021-02-15 10:49:44,901] multiqc [DEBUG ] No samples found: kat [2021-02-15 10:49:44,914] multiqc [DEBUG ] No samples found: leehom [2021-02-15 10:49:44,926] multiqc [DEBUG ] No samples found: adapterRemoval [2021-02-15 10:49:44,939] multiqc [DEBUG ] No samples found: clipandmerge [2021-02-15 10:49:44,952] multiqc [DEBUG ] No samples found: cutadapt [2021-02-15 10:49:44,965] multiqc [DEBUG ] No samples found: flexbar [2021-02-15 10:49:44,977] multiqc [DEBUG ] No samples found: kaiju [2021-02-15 10:49:44,988] multiqc [DEBUG ] No samples found: kraken [2021-02-15 10:49:45,000] multiqc [DEBUG ] No samples found: malt [2021-02-15 10:49:45,011] multiqc [DEBUG ] No samples found: trimmomatic [2021-02-15 10:49:45,023] multiqc [DEBUG ] No samples found: sickle [2021-02-15 10:49:45,038] multiqc [DEBUG ] No samples found: skewer [2021-02-15 10:49:45,050] multiqc [DEBUG ] No samples found: sortmerna [2021-02-15 10:49:45,062] multiqc [DEBUG ] No samples found: biobloomtools [2021-02-15 10:49:45,075] multiqc [DEBUG ] No samples found: fastq_screen [2021-02-15 10:49:45,088] multiqc [DEBUG ] No samples found: afterqc [2021-02-15 10:49:45,100] multiqc [DEBUG ] No samples found: fastp [2021-02-15 10:49:45,423] multiqc.modules.fastqc.fastqc [INFO ] Found 6 reports [2021-02-15 10:49:46,286] multiqc.modules.pycoqc.pycoqc [INFO ] Found 1 reports [2021-02-15 10:49:46,303] multiqc [DEBUG ] No samples found: minionqc [2021-02-15 10:49:46,315] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-02-15 10:49:46,327] multiqc [DEBUG ] No samples found: clusterflow [2021-02-15 10:49:46,339] multiqc [DEBUG ] No samples found: bcl2fastq [2021-02-15 10:49:46,351] multiqc [DEBUG ] No samples found: interop [2021-02-15 10:49:46,362] multiqc [DEBUG ] No samples found: ivar [2021-02-15 10:49:46,375] multiqc [DEBUG ] No samples found: flash [2021-02-15 10:49:46,387] multiqc [DEBUG ] No samples found: seqyclean [2021-02-15 10:49:46,397] multiqc [INFO ] Compressing plot data [2021-02-15 10:49:46,573] multiqc [INFO ] Report : multiqc_report.html [2021-02-15 10:49:46,574] multiqc [INFO ] Data : multiqc_data [2021-02-15 10:49:46,574] multiqc [DEBUG ] Moving data file from '/tmp/tmp4v44o6rh/multiqc_data' to '/data/Experments/E_37_SRA_Submission/Reads/Hyrax/multiqc_data' [2021-02-15 10:49:46,879] multiqc [INFO ] MultiQC complete