[2023-08-22 02:29:38,076] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-08-22 02:29:38,076] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-08-22 02:29:38,077] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-08-22 02:29:38,079] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2023-08-22 02:29:38,079] multiqc [DEBUG ] New config 'report_section_order': {'general_stats': {'order': 1000}, 'demux_report': {'order': 900}, 'demux_report-1': {'order': 900}, 'demux_report-2': {'order': 900}, 'undetermined_barcodes': {'order': 800}, 'run_stats': {'order': 700}, 'fastqc': {'order': 500}} [2023-08-22 02:29:38,079] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2023-08-22 02:29:39,039] multiqc [WARNING] MultiQC Version v1.15 now available! [2023-08-22 02:29:39,040] multiqc [INFO ] This is MultiQC v1.9 [2023-08-22 02:29:39,040] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2023-08-22 02:29:39,040] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/f4/ffd0fa2dc89bb3c46dcaa35585fdad/merged [2023-08-22 02:29:39,040] multiqc [INFO ] Template : default [2023-08-22 02:29:39,040] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-08-22 02:29:39,040] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/f4/ffd0fa2dc89bb3c46dcaa35585fdad/merged [2023-08-22 02:29:39,040] 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 [2023-08-22 02:29:39,040] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-36747435/tmpgkig2596 [2023-08-22 02:29:39,169] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMNY2BGXT_n01_DO65_fastqc.html [2023-08-22 02:29:39,177] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMNY2BGXT_n01_DO65_fastqc.html [2023-08-22 02:29:39,241] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 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hicexplorer because it exceeded search pattern filesize limit: HMNY2BGXT_n01_HW13_fastqc.html [2023-08-22 02:29:40,577] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMNY2BGXT_n01_HW13_fastqc.html [2023-08-22 02:29:40,641] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMNY2BGXT_n01_JK203_fastqc.html [2023-08-22 02:29:40,649] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMNY2BGXT_n01_JK203_fastqc.html [2023-08-22 02:29:40,712] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMNY2BGXT_n01_YZ33_fastqc.html [2023-08-22 02:29:40,721] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMNY2BGXT_n01_YZ33_fastqc.html [2023-08-22 02:29:40,788] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMNY2BGXT_n01_undetermined_fastqc.html [2023-08-22 02:29:40,795] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMNY2BGXT_n01_undetermined_fastqc.html [2023-08-22 02:29:40,859] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-08-22 02:29:40,864] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-08-22 02:29:41,622] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-08-22 02:29:41,623] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-08-22 02:29:41,643] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 24 samples (table) [2023-08-22 02:29:41,645] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-08-22 02:29:41,655] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-08-22 02:29:41,660] multiqc [DEBUG ] No samples found: conpair [2023-08-22 02:29:41,666] multiqc [DEBUG ] No samples found: peddy [2023-08-22 02:29:41,672] multiqc [DEBUG ] No samples found: somalier [2023-08-22 02:29:41,677] multiqc [DEBUG ] No samples found: methylQA [2023-08-22 02:29:41,686] multiqc [DEBUG ] No samples found: mosdepth [2023-08-22 02:29:41,691] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-08-22 02:29:41,695] multiqc [DEBUG ] No samples found: qualimap [2023-08-22 02:29:41,700] multiqc [DEBUG ] No samples found: preseq [2023-08-22 02:29:41,705] multiqc [DEBUG ] No samples found: quast [2023-08-22 02:29:41,711] multiqc [DEBUG ] No samples found: qorts [2023-08-22 02:29:41,716] multiqc [DEBUG ] No samples found: rna_seqc [2023-08-22 02:29:41,722] multiqc [DEBUG ] No samples found: rockhopper [2023-08-22 02:29:41,727] multiqc [DEBUG ] No samples found: rsem [2023-08-22 02:29:41,740] multiqc [DEBUG ] No samples found: rseqc [2023-08-22 02:29:41,745] multiqc [DEBUG ] No samples found: busco [2023-08-22 02:29:41,751] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-08-22 02:29:41,756] multiqc [DEBUG ] No samples found: disambiguate [2023-08-22 02:29:41,762] multiqc [DEBUG ] No samples found: supernova [2023-08-22 02:29:41,776] multiqc [DEBUG ] No samples found: deeptools [2023-08-22 02:29:41,782] multiqc [DEBUG ] No samples found: sargasso [2023-08-22 02:29:41,787] multiqc [DEBUG ] No samples found: verifybamid [2023-08-22 02:29:41,792] multiqc [DEBUG ] No samples found: mirtrace [2023-08-22 02:29:41,798] multiqc [DEBUG ] No samples found: happy [2023-08-22 02:29:41,803] multiqc [DEBUG ] No samples found: mirtop [2023-08-22 02:29:41,810] multiqc [DEBUG ] No samples found: homer [2023-08-22 02:29:41,815] multiqc [DEBUG ] No samples found: macs2 [2023-08-22 02:29:41,820] multiqc [DEBUG ] No samples found: theta2 [2023-08-22 02:29:41,825] multiqc [DEBUG ] No samples found: snpeff [2023-08-22 02:29:41,833] multiqc [DEBUG ] No samples found: gatk [2023-08-22 02:29:41,838] multiqc [DEBUG ] No samples found: htseq [2023-08-22 02:29:41,844] multiqc [DEBUG ] No samples found: bcftools [2023-08-22 02:29:41,849] multiqc [DEBUG ] No samples found: featureCounts [2023-08-22 02:29:41,856] multiqc [DEBUG ] No samples found: fgbio [2023-08-22 02:29:41,872] multiqc [DEBUG ] No samples found: dragen [2023-08-22 02:29:41,877] multiqc [DEBUG ] No samples found: dedup [2023-08-22 02:29:41,883] multiqc [DEBUG ] No samples found: damageprofiler [2023-08-22 02:29:41,909] multiqc [DEBUG ] No samples found: biobambam2 [2023-08-22 02:29:41,914] multiqc [DEBUG ] No samples found: mtnucratio [2023-08-22 02:29:41,916] multiqc [DEBUG ] No samples found: picard [2023-08-22 02:29:41,922] multiqc [DEBUG ] No samples found: prokka [2023-08-22 02:29:41,927] multiqc [DEBUG ] No samples found: samblaster [2023-08-22 02:29:41,936] multiqc [DEBUG ] No samples found: samtools [2023-08-22 02:29:41,942] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-08-22 02:29:41,948] multiqc [DEBUG ] No samples found: bamtools [2023-08-22 02:29:41,952] multiqc [DEBUG ] No samples found: jellyfish [2023-08-22 02:29:41,961] multiqc [DEBUG ] No samples found: vcftools [2023-08-22 02:29:41,966] multiqc [DEBUG ] No samples found: longranger [2023-08-22 02:29:41,972] multiqc [DEBUG ] No samples found: stacks [2023-08-22 02:29:41,977] multiqc [DEBUG ] No samples found: varscan2 [2023-08-22 02:29:41,993] multiqc [DEBUG ] No samples found: bbmap [2023-08-22 02:29:41,999] multiqc [DEBUG ] No samples found: bismark [2023-08-22 02:29:42,005] multiqc [DEBUG ] No samples found: biscuit [2023-08-22 02:29:42,010] multiqc [DEBUG ] No samples found: hicexplorer [2023-08-22 02:29:42,015] multiqc [DEBUG ] No samples found: hicup [2023-08-22 02:29:42,021] multiqc [DEBUG ] No samples found: hicpro [2023-08-22 02:29:42,026] multiqc [DEBUG ] No samples found: salmon [2023-08-22 02:29:42,031] multiqc [DEBUG ] No samples found: kallisto [2023-08-22 02:29:42,036] multiqc [DEBUG ] No samples found: slamdunk [2023-08-22 02:29:42,042] multiqc [DEBUG ] No samples found: star [2023-08-22 02:29:42,047] multiqc [DEBUG ] No samples found: hisat2 [2023-08-22 02:29:42,052] multiqc [DEBUG ] No samples found: tophat [2023-08-22 02:29:42,060] multiqc [DEBUG ] No samples found: bowtie2 [2023-08-22 02:29:42,065] multiqc [DEBUG ] No samples found: bowtie1 [2023-08-22 02:29:42,070] multiqc [DEBUG ] No samples found: snpsplit [2023-08-22 02:29:42,078] multiqc [DEBUG ] No samples found: kat [2023-08-22 02:29:42,083] multiqc [DEBUG ] No samples found: leehom [2023-08-22 02:29:42,090] multiqc [DEBUG ] No samples found: adapterRemoval [2023-08-22 02:29:42,100] multiqc [DEBUG ] No samples found: clipandmerge [2023-08-22 02:29:42,113] multiqc [DEBUG ] No samples found: cutadapt [2023-08-22 02:29:42,118] multiqc [DEBUG ] No samples found: flexbar [2023-08-22 02:29:42,124] multiqc [DEBUG ] No samples found: kaiju [2023-08-22 02:29:42,130] multiqc [DEBUG ] No samples found: kraken [2023-08-22 02:29:42,135] multiqc [DEBUG ] No samples found: malt [2023-08-22 02:29:42,140] multiqc [DEBUG ] No samples found: trimmomatic [2023-08-22 02:29:42,146] multiqc [DEBUG ] No samples found: sickle [2023-08-22 02:29:42,152] multiqc [DEBUG ] No samples found: skewer [2023-08-22 02:29:42,157] multiqc [DEBUG ] No samples found: sortmerna [2023-08-22 02:29:42,162] multiqc [DEBUG ] No samples found: biobloomtools [2023-08-22 02:29:42,167] multiqc [DEBUG ] No samples found: fastq_screen [2023-08-22 02:29:42,173] multiqc [DEBUG ] No samples found: afterqc [2023-08-22 02:29:42,178] multiqc [DEBUG ] No samples found: fastp [2023-08-22 02:29:43,638] multiqc.modules.fastqc.fastqc [INFO ] Found 24 reports [2023-08-22 02:29:44,163] multiqc [DEBUG ] No samples found: pycoqc [2023-08-22 02:29:44,168] multiqc [DEBUG ] No samples found: minionqc [2023-08-22 02:29:44,174] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-08-22 02:29:44,179] multiqc [DEBUG ] No samples found: clusterflow [2023-08-22 02:29:44,185] multiqc [DEBUG ] No samples found: bcl2fastq [2023-08-22 02:29:44,190] multiqc [DEBUG ] No samples found: interop [2023-08-22 02:29:44,196] multiqc [DEBUG ] No samples found: ivar [2023-08-22 02:29:44,201] multiqc [DEBUG ] No samples found: flash [2023-08-22 02:29:44,206] multiqc [DEBUG ] No samples found: seqyclean [2023-08-22 02:29:44,206] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-08-22 02:29:44,206] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-08-22 02:29:44,206] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-08-22 02:29:44,206] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2023-08-22 02:29:44,206] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2023-08-22 02:29:44,206] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2023-08-22 02:29:44,206] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2023-08-22 02:29:44,206] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2023-08-22 02:29:44,206] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2023-08-22 02:29:44,206] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-08-22 02:29:44,206] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-08-22 02:29:44,206] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-08-22 02:29:44,207] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-08-22 02:29:44,207] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-08-22 02:29:44,207] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-08-22 02:29:44,207] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-08-22 02:29:44,207] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-08-22 02:29:44,207] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-08-22 02:29:44,207] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-08-22 02:29:44,207] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-08-22 02:29:44,207] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-08-22 02:29:44,207] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-08-22 02:29:44,207] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-08-22 02:29:44,207] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-08-22 02:29:44,207] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-08-22 02:29:44,207] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-08-22 02:29:44,207] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-08-22 02:29:44,207] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-08-22 02:29:44,207] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-08-22 02:29:44,207] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-08-22 02:29:44,237] multiqc [INFO ] Compressing plot data [2023-08-22 02:29:44,578] multiqc [INFO ] Report : multiqc_report.html [2023-08-22 02:29:44,579] multiqc [INFO ] Data : multiqc_data [2023-08-22 02:29:44,579] multiqc [DEBUG ] Moving data file from '/state/partition1/job-36747435/tmpgkig2596/multiqc_data' to '/vast/gencore/GENEFLOW/work/f4/ffd0fa2dc89bb3c46dcaa35585fdad/merged/multiqc_data' [2023-08-22 02:29:44,756] multiqc [INFO ] MultiQC complete