[2021-02-15 10:27:35,517] multiqc [DEBUG ] No MultiQC config found: /data/Bioinformatics_Softwere/Miniconda/.conda/envs/multiqc/lib/python3.6/site-packages/multiqc_config.yaml [2021-02-15 10:27:35,517] multiqc [DEBUG ] No MultiQC config found: /home/hatim/.multiqc_config.yaml [2021-02-15 10:27:35,518] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-02-15 10:27:35,518] multiqc [DEBUG ] Command used: /home/hatim/data/Bioinformatics_Softwere/Miniconda/.conda/envs/multiqc/bin/multiqc -f . [2021-02-15 10:27:38,938] multiqc [DEBUG ] Latest MultiQC version is v1.9 [2021-02-15 10:27:38,939] multiqc [INFO ] This is MultiQC v1.9 [2021-02-15 10:27:38,939] multiqc [DEBUG ] Command : /home/hatim/data/Bioinformatics_Softwere/Miniconda/.conda/envs/multiqc/bin/multiqc -f . [2021-02-15 10:27:38,939] multiqc [DEBUG ] Working dir : /data/Experments/E_37_SRA_Submission/Reads/CM1 [2021-02-15 10:27:38,939] multiqc [INFO ] Template : default [2021-02-15 10:27:38,939] 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 10:27:38,939] multiqc [INFO ] Searching : /data/Experments/E_37_SRA_Submission/Reads/CM1 [2021-02-15 10:27:38,939] 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 10:27:38,940] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmprxgsocie [2021-02-15 10:27:39,160] multiqc [DEBUG ] Ignoring directory as matched fn_ignore_dirs: ./multiqc_data [2021-02-15 10:27:39,172] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CM1_BGI19_500_1.fq [2021-02-15 10:27:39,289] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: CM1_aber19_300_2_fastqc.html [2021-02-15 10:27:39,338] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: CM1_aber19_300_2_fastqc.html [2021-02-15 10:27:39,338] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: CM1_aber19_300_2_fastqc.html [2021-02-15 10:27:39,338] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: CM1_aber19_300_2_fastqc.html [2021-02-15 10:27:39,338] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: CM1_aber19_300_2_fastqc.html [2021-02-15 10:27:39,338] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: CM1_aber19_300_2_fastqc.html [2021-02-15 10:27:39,338] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: CM1_aber19_300_2_fastqc.html [2021-02-15 10:27:39,347] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: CM1_aber19_300_2_fastqc.html [2021-02-15 10:27:39,726] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CM1_091219_P.fastq [2021-02-15 10:27:39,823] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: CM1_aber19_300_1_fastqc.html [2021-02-15 10:27:39,870] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: CM1_aber19_300_1_fastqc.html [2021-02-15 10:27:39,870] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: CM1_aber19_300_1_fastqc.html [2021-02-15 10:27:39,870] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: CM1_aber19_300_1_fastqc.html [2021-02-15 10:27:39,870] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: CM1_aber19_300_1_fastqc.html [2021-02-15 10:27:39,871] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: CM1_aber19_300_1_fastqc.html [2021-02-15 10:27:39,871] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: CM1_aber19_300_1_fastqc.html [2021-02-15 10:27:39,879] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: CM1_aber19_300_1_fastqc.html [2021-02-15 10:27:40,293] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: multiqc_report.html [2021-02-15 10:27:40,496] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: CM1_BGI19_270_1_fastqc.html [2021-02-15 10:27:40,600] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: CM1_BGI19_270_1_fastqc.html [2021-02-15 10:27:40,601] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: CM1_BGI19_270_1_fastqc.html [2021-02-15 10:27:40,601] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: CM1_BGI19_270_1_fastqc.html [2021-02-15 10:27:40,601] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: CM1_BGI19_270_1_fastqc.html [2021-02-15 10:27:40,601] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: CM1_BGI19_270_1_fastqc.html [2021-02-15 10:27:40,601] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: CM1_BGI19_270_1_fastqc.html [2021-02-15 10:27:40,606] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: CM1_BGI19_270_1_fastqc.html [2021-02-15 10:27:40,865] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: pycoQC_output.CM1_091219_P.html [2021-02-15 10:27:40,865] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: pycoQC_output.CM1_130120.html [2021-02-15 10:27:40,866] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: pycoQC_output.CM1_091219_S.html [2021-02-15 10:27:41,133] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: pycoQC_output.CM1_130120.json [2021-02-15 10:27:41,152] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: pycoqc_CM1_091219_P.html [2021-02-15 10:27:41,241] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: CM1_BGI19_500_1_fastqc.html [2021-02-15 10:27:41,287] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: CM1_BGI19_500_1_fastqc.html [2021-02-15 10:27:41,288] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: CM1_BGI19_500_1_fastqc.html [2021-02-15 10:27:41,288] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: CM1_BGI19_500_1_fastqc.html [2021-02-15 10:27:41,288] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: CM1_BGI19_500_1_fastqc.html [2021-02-15 10:27:41,288] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: CM1_BGI19_500_1_fastqc.html [2021-02-15 10:27:41,288] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: CM1_BGI19_500_1_fastqc.html [2021-02-15 10:27:41,292] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: CM1_BGI19_500_1_fastqc.html [2021-02-15 10:27:41,468] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CM1_BGI19_500_2.fq [2021-02-15 10:27:41,468] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: pycoqc_CM1_130120.html [2021-02-15 10:27:41,468] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: pycoQC_output.CM1_200120.html [2021-02-15 10:27:41,469] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CM1_BGI19_270_2.fq [2021-02-15 10:27:41,469] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CM1_aber19_300_1.fq [2021-02-15 10:27:41,469] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: pycoqc_CM1_091219_S.html [2021-02-15 10:27:41,469] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CM1_BGI19_270_1.fq [2021-02-15 10:27:41,469] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CM1_130120.fastq [2021-02-15 10:27:41,469] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CM1_200120.fastq [2021-02-15 10:27:41,470] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: pycoqc_CM1_200120.html [2021-02-15 10:27:41,569] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: pycoQC_output.CM1_200120.json [2021-02-15 10:27:41,702] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: pycoQC_output.CM1_091219_P.json [2021-02-15 10:27:41,812] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: pycoQC_output.CM1_091219_S.json [2021-02-15 10:27:41,831] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CM1_aber19_300_2.fq [2021-02-15 10:27:41,919] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: CM1_BGI19_270_2_fastqc.html [2021-02-15 10:27:41,965] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: CM1_BGI19_270_2_fastqc.html [2021-02-15 10:27:41,965] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: CM1_BGI19_270_2_fastqc.html [2021-02-15 10:27:41,965] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: CM1_BGI19_270_2_fastqc.html [2021-02-15 10:27:41,965] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: CM1_BGI19_270_2_fastqc.html [2021-02-15 10:27:41,965] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: CM1_BGI19_270_2_fastqc.html [2021-02-15 10:27:41,965] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: CM1_BGI19_270_2_fastqc.html [2021-02-15 10:27:41,969] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: CM1_BGI19_270_2_fastqc.html [2021-02-15 10:27:42,233] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: CM1_BGI19_500_2_fastqc.html [2021-02-15 10:27:42,279] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: CM1_BGI19_500_2_fastqc.html [2021-02-15 10:27:42,279] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: CM1_BGI19_500_2_fastqc.html [2021-02-15 10:27:42,279] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: CM1_BGI19_500_2_fastqc.html [2021-02-15 10:27:42,279] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: CM1_BGI19_500_2_fastqc.html [2021-02-15 10:27:42,279] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: CM1_BGI19_500_2_fastqc.html [2021-02-15 10:27:42,279] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: CM1_BGI19_500_2_fastqc.html [2021-02-15 10:27:42,283] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: CM1_BGI19_500_2_fastqc.html [2021-02-15 10:27:42,464] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CM1_091219_S.fastq [2021-02-15 10:27:43,759] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.4 [2021-02-15 10:27:43,768] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.4 [2021-02-15 10:27:43,781] multiqc [DEBUG ] No samples found: custom_content [2021-02-15 10:27:43,801] multiqc [DEBUG ] No samples found: conpair [2021-02-15 10:27:43,828] multiqc [DEBUG ] No samples found: peddy [2021-02-15 10:27:43,851] multiqc [DEBUG ] No samples found: somalier [2021-02-15 10:27:43,871] multiqc [DEBUG ] No samples found: methylQA [2021-02-15 10:27:43,928] multiqc [DEBUG ] No samples found: mosdepth [2021-02-15 10:27:43,967] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-02-15 10:27:43,983] multiqc [DEBUG ] No samples found: qualimap [2021-02-15 10:27:44,024] multiqc [DEBUG ] No samples found: preseq [2021-02-15 10:27:44,060] multiqc [DEBUG ] No samples found: quast [2021-02-15 10:27:44,084] multiqc [DEBUG ] No samples found: qorts [2021-02-15 10:27:44,116] multiqc [DEBUG ] No samples found: rna_seqc [2021-02-15 10:27:44,135] multiqc [DEBUG ] No samples found: rockhopper [2021-02-15 10:27:44,149] multiqc [DEBUG ] No samples found: rsem [2021-02-15 10:27:44,219] multiqc [DEBUG ] No samples found: rseqc [2021-02-15 10:27:44,237] multiqc [DEBUG ] No samples found: busco [2021-02-15 10:27:44,250] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-02-15 10:27:44,262] multiqc [DEBUG ] No samples found: disambiguate [2021-02-15 10:27:44,274] multiqc [DEBUG ] No samples found: supernova [2021-02-15 10:27:44,319] multiqc [DEBUG ] No samples found: deeptools [2021-02-15 10:27:44,331] multiqc [DEBUG ] No samples found: sargasso [2021-02-15 10:27:44,344] multiqc [DEBUG ] No samples found: verifybamid [2021-02-15 10:27:44,357] multiqc [DEBUG ] No samples found: mirtrace [2021-02-15 10:27:44,369] multiqc [DEBUG ] No samples found: happy [2021-02-15 10:27:44,381] multiqc [DEBUG ] No samples found: mirtop [2021-02-15 10:27:44,402] multiqc [DEBUG ] No samples found: homer [2021-02-15 10:27:44,422] multiqc [DEBUG ] No samples found: macs2 [2021-02-15 10:27:44,437] multiqc [DEBUG ] No samples found: theta2 [2021-02-15 10:27:44,455] multiqc [DEBUG ] No samples found: snpeff [2021-02-15 10:27:44,475] multiqc [DEBUG ] No samples found: gatk [2021-02-15 10:27:44,488] multiqc [DEBUG ] No samples found: htseq [2021-02-15 10:27:44,504] multiqc [DEBUG ] No samples found: bcftools [2021-02-15 10:27:44,516] multiqc [DEBUG ] No samples found: featureCounts [2021-02-15 10:27:44,535] multiqc [DEBUG ] No samples found: fgbio [2021-02-15 10:27:44,575] multiqc [DEBUG ] No samples found: dragen [2021-02-15 10:27:44,588] multiqc [DEBUG ] No samples found: dedup [2021-02-15 10:27:44,600] multiqc [DEBUG ] No samples found: damageprofiler [2021-02-15 10:27:44,680] multiqc [DEBUG ] No samples found: biobambam2 [2021-02-15 10:27:44,693] multiqc [DEBUG ] No samples found: mtnucratio [2021-02-15 10:27:44,696] multiqc [DEBUG ] No samples found: picard [2021-02-15 10:27:44,709] multiqc [DEBUG ] No samples found: prokka [2021-02-15 10:27:44,721] multiqc [DEBUG ] No samples found: samblaster [2021-02-15 10:27:44,747] multiqc [DEBUG ] No samples found: samtools [2021-02-15 10:27:44,760] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-02-15 10:27:44,776] multiqc [DEBUG ] No samples found: bamtools [2021-02-15 10:27:44,789] multiqc [DEBUG ] No samples found: jellyfish [2021-02-15 10:27:44,815] multiqc [DEBUG ] No samples found: vcftools [2021-02-15 10:27:44,829] multiqc [DEBUG ] No samples found: longranger [2021-02-15 10:27:44,841] multiqc [DEBUG ] No samples found: stacks [2021-02-15 10:27:44,854] multiqc [DEBUG ] No samples found: varscan2 [2021-02-15 10:27:44,906] multiqc [DEBUG ] No samples found: bbmap [2021-02-15 10:27:44,918] multiqc [DEBUG ] No samples found: bismark [2021-02-15 10:27:44,930] multiqc [DEBUG ] No samples found: biscuit [2021-02-15 10:27:44,943] multiqc [DEBUG ] No samples found: hicexplorer [2021-02-15 10:27:44,956] multiqc [DEBUG ] No samples found: hicup [2021-02-15 10:27:44,967] multiqc [DEBUG ] No samples found: hicpro [2021-02-15 10:27:44,980] multiqc [DEBUG ] No samples found: salmon [2021-02-15 10:27:44,992] multiqc [DEBUG ] No samples found: kallisto [2021-02-15 10:27:45,006] multiqc [DEBUG ] No samples found: slamdunk [2021-02-15 10:27:45,019] multiqc [DEBUG ] No samples found: star [2021-02-15 10:27:45,032] multiqc [DEBUG ] No samples found: hisat2 [2021-02-15 10:27:45,044] multiqc [DEBUG ] No samples found: tophat [2021-02-15 10:27:45,058] multiqc [DEBUG ] No samples found: bowtie2 [2021-02-15 10:27:45,071] multiqc [DEBUG ] No samples found: bowtie1 [2021-02-15 10:27:45,083] multiqc [DEBUG ] No samples found: snpsplit [2021-02-15 10:27:45,095] multiqc [DEBUG ] No samples found: kat [2021-02-15 10:27:45,107] multiqc [DEBUG ] No samples found: leehom [2021-02-15 10:27:45,119] multiqc [DEBUG ] No samples found: adapterRemoval [2021-02-15 10:27:45,133] multiqc [DEBUG ] No samples found: clipandmerge [2021-02-15 10:27:45,147] multiqc [DEBUG ] No samples found: cutadapt [2021-02-15 10:27:45,161] multiqc [DEBUG ] No samples found: flexbar [2021-02-15 10:27:45,173] multiqc [DEBUG ] No samples found: kaiju [2021-02-15 10:27:45,186] multiqc [DEBUG ] No samples found: kraken [2021-02-15 10:27:45,205] multiqc [DEBUG ] No samples found: malt [2021-02-15 10:27:45,219] multiqc [DEBUG ] No samples found: trimmomatic [2021-02-15 10:27:45,236] multiqc [DEBUG ] No samples found: sickle [2021-02-15 10:27:45,250] multiqc [DEBUG ] No samples found: skewer [2021-02-15 10:27:45,263] multiqc [DEBUG ] No samples found: sortmerna [2021-02-15 10:27:45,281] multiqc [DEBUG ] No samples found: biobloomtools [2021-02-15 10:27:45,297] multiqc [DEBUG ] No samples found: fastq_screen [2021-02-15 10:27:45,317] multiqc [DEBUG ] No samples found: afterqc [2021-02-15 10:27:45,333] multiqc [DEBUG ] No samples found: fastp [2021-02-15 10:27:45,596] multiqc.modules.fastqc.fastqc [INFO ] Found 6 reports [2021-02-15 10:27:46,714] multiqc.modules.pycoqc.pycoqc [INFO ] Found 4 reports [2021-02-15 10:27:46,740] multiqc [DEBUG ] No samples found: minionqc [2021-02-15 10:27:46,754] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-02-15 10:27:46,768] multiqc [DEBUG ] No samples found: clusterflow [2021-02-15 10:27:46,781] multiqc [DEBUG ] No samples found: bcl2fastq [2021-02-15 10:27:46,793] multiqc [DEBUG ] No samples found: interop [2021-02-15 10:27:46,805] multiqc [DEBUG ] No samples found: ivar [2021-02-15 10:27:46,818] multiqc [DEBUG ] No samples found: flash [2021-02-15 10:27:46,831] multiqc [DEBUG ] No samples found: seqyclean [2021-02-15 10:27:46,846] multiqc [INFO ] Compressing plot data [2021-02-15 10:27:47,073] multiqc [WARNING] Deleting : multiqc_report.html (-f was specified) [2021-02-15 10:27:47,079] multiqc [WARNING] Deleting : multiqc_data (-f was specified) [2021-02-15 10:27:47,108] multiqc [INFO ] Report : multiqc_report.html [2021-02-15 10:27:47,108] multiqc [INFO ] Data : multiqc_data [2021-02-15 10:27:47,108] multiqc [DEBUG ] Moving data file from '/tmp/tmprxgsocie/multiqc_data' to '/data/Experments/E_37_SRA_Submission/Reads/CM1/multiqc_data' [2021-02-15 10:27:47,491] multiqc [INFO ] MultiQC complete