[2024-01-26 14:41:58,796] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-01-26 14:41:58,796] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-01-26 14:41:58,796] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-01-26 14:41:58,799] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-01-26 14:41:58,799] 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}} [2024-01-26 14:41:58,799] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-01-26 14:41:58,974] multiqc [WARNING] MultiQC Version v1.19 now available! [2024-01-26 14:41:58,974] multiqc [INFO ] This is MultiQC v1.9 [2024-01-26 14:41:58,975] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-01-26 14:41:58,975] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/14/2d6d3f380365358fe28ee920311615/merged [2024-01-26 14:41:58,975] multiqc [INFO ] Template : default [2024-01-26 14:41:58,975] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-01-26 14:41:58,975] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/14/2d6d3f380365358fe28ee920311615/merged [2024-01-26 14:41:58,975] 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 [2024-01-26 14:41:58,975] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-42309311/tmpooqs99s_ [2024-01-26 14:41:59,105] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVJ2YDRX3_n01_R13_macrophage_fastqc.html [2024-01-26 14:41:59,113] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVJ2YDRX3_n01_R13_macrophage_fastqc.html [2024-01-26 14:41:59,201] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVJ2YDRX3_n01_R14_macrophage_fastqc.html [2024-01-26 14:41:59,208] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVJ2YDRX3_n01_R14_macrophage_fastqc.html [2024-01-26 14:41:59,311] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVJ2YDRX3_n01_R15_macrophage_fastqc.html [2024-01-26 14:41:59,329] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVJ2YDRX3_n01_R15_macrophage_fastqc.html [2024-01-26 14:41:59,426] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVJ2YDRX3_n01_R16_macrophage_fastqc.html [2024-01-26 14:41:59,433] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVJ2YDRX3_n01_R16_macrophage_fastqc.html [2024-01-26 14:41:59,517] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVJ2YDRX3_n01_R17_macrophage_fastqc.html [2024-01-26 14:41:59,525] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVJ2YDRX3_n01_R17_macrophage_fastqc.html [2024-01-26 14:41:59,609] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVJ2YDRX3_n01_R18_macrophage_fastqc.html [2024-01-26 14:41:59,616] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVJ2YDRX3_n01_R18_macrophage_fastqc.html [2024-01-26 14:41:59,700] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVJ2YDRX3_n01_R19_macrophage_fastqc.html [2024-01-26 14:41:59,707] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVJ2YDRX3_n01_R19_macrophage_fastqc.html [2024-01-26 14:41:59,801] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVJ2YDRX3_n01_R20_macrophage_fastqc.html [2024-01-26 14:41:59,810] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVJ2YDRX3_n01_R20_macrophage_fastqc.html [2024-01-26 14:41:59,904] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVJ2YDRX3_n01_R21_macrophage_fastqc.html [2024-01-26 14:41:59,914] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVJ2YDRX3_n01_R21_macrophage_fastqc.html [2024-01-26 14:42:00,008] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVJ2YDRX3_n01_R22_macrophage_fastqc.html [2024-01-26 14:42:00,017] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVJ2YDRX3_n01_R22_macrophage_fastqc.html [2024-01-26 14:42:00,120] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVJ2YDRX3_n01_R23_macrophage_fastqc.html [2024-01-26 14:42:00,127] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVJ2YDRX3_n01_R23_macrophage_fastqc.html [2024-01-26 14:42:00,226] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVJ2YDRX3_n01_R24_macrophage_fastqc.html [2024-01-26 14:42:00,239] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVJ2YDRX3_n01_R24_macrophage_fastqc.html [2024-01-26 14:42:00,337] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVJ2YDRX3_n01_undetermined_fastqc.html [2024-01-26 14:42:00,347] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVJ2YDRX3_n01_undetermined_fastqc.html [2024-01-26 14:42:00,422] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-01-26 14:42:00,442] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-01-26 14:42:00,442] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-01-26 14:42:00,442] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-01-26 14:42:00,442] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-01-26 14:42:00,442] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-01-26 14:42:00,443] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-01-26 14:42:01,542] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-01-26 14:42:01,545] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-01-26 14:42:01,562] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 13 samples (table) [2024-01-26 14:42:01,564] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-01-26 14:42:01,574] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-01-26 14:42:01,581] multiqc [DEBUG ] No samples found: conpair [2024-01-26 14:42:01,591] multiqc [DEBUG ] No samples found: peddy [2024-01-26 14:42:01,599] multiqc [DEBUG ] No samples found: somalier [2024-01-26 14:42:01,607] multiqc [DEBUG ] No samples found: methylQA [2024-01-26 14:42:01,624] multiqc [DEBUG ] No samples found: mosdepth [2024-01-26 14:42:01,634] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-01-26 14:42:01,638] multiqc [DEBUG ] No samples found: qualimap [2024-01-26 14:42:01,644] multiqc [DEBUG ] No samples found: preseq [2024-01-26 14:42:01,652] multiqc [DEBUG ] No samples found: quast [2024-01-26 14:42:01,659] multiqc [DEBUG ] No samples found: qorts [2024-01-26 14:42:01,665] multiqc [DEBUG ] No samples found: rna_seqc [2024-01-26 14:42:01,671] multiqc [DEBUG ] No samples found: rockhopper [2024-01-26 14:42:01,678] multiqc [DEBUG ] No samples found: rsem [2024-01-26 14:42:01,693] multiqc [DEBUG ] No samples found: rseqc [2024-01-26 14:42:01,699] multiqc [DEBUG ] No samples found: busco [2024-01-26 14:42:01,705] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-01-26 14:42:01,711] multiqc [DEBUG ] No samples found: disambiguate [2024-01-26 14:42:01,718] multiqc [DEBUG ] No samples found: supernova [2024-01-26 14:42:01,736] multiqc [DEBUG ] No samples found: deeptools [2024-01-26 14:42:01,742] multiqc [DEBUG ] No samples found: sargasso [2024-01-26 14:42:01,748] multiqc [DEBUG ] No samples found: verifybamid [2024-01-26 14:42:01,754] multiqc [DEBUG ] No samples found: mirtrace [2024-01-26 14:42:01,760] multiqc [DEBUG ] No samples found: happy [2024-01-26 14:42:01,767] multiqc [DEBUG ] No samples found: mirtop [2024-01-26 14:42:01,775] multiqc [DEBUG ] No samples found: homer [2024-01-26 14:42:01,781] multiqc [DEBUG ] No samples found: macs2 [2024-01-26 14:42:01,787] multiqc [DEBUG ] No samples found: theta2 [2024-01-26 14:42:01,795] multiqc [DEBUG ] No samples found: snpeff [2024-01-26 14:42:01,804] multiqc [DEBUG ] No samples found: gatk [2024-01-26 14:42:01,810] multiqc [DEBUG ] No samples found: htseq [2024-01-26 14:42:01,817] multiqc [DEBUG ] No samples found: bcftools [2024-01-26 14:42:01,824] multiqc [DEBUG ] No samples found: featureCounts [2024-01-26 14:42:01,832] multiqc [DEBUG ] No samples found: fgbio [2024-01-26 14:42:01,851] multiqc [DEBUG ] No samples found: dragen [2024-01-26 14:42:01,858] multiqc [DEBUG ] No samples found: dedup [2024-01-26 14:42:01,864] multiqc [DEBUG ] No samples found: damageprofiler [2024-01-26 14:42:01,895] multiqc [DEBUG ] No samples found: biobambam2 [2024-01-26 14:42:01,901] multiqc [DEBUG ] No samples found: mtnucratio [2024-01-26 14:42:01,904] multiqc [DEBUG ] No samples found: picard [2024-01-26 14:42:01,910] multiqc [DEBUG ] No samples found: prokka [2024-01-26 14:42:01,915] multiqc [DEBUG ] No samples found: samblaster [2024-01-26 14:42:01,928] multiqc [DEBUG ] No samples found: samtools [2024-01-26 14:42:01,935] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-01-26 14:42:01,942] multiqc [DEBUG ] No samples found: bamtools [2024-01-26 14:42:01,948] multiqc [DEBUG ] No samples found: jellyfish [2024-01-26 14:42:01,957] multiqc [DEBUG ] No samples found: vcftools [2024-01-26 14:42:01,963] multiqc [DEBUG ] No samples found: longranger [2024-01-26 14:42:01,970] multiqc [DEBUG ] No samples found: stacks [2024-01-26 14:42:01,977] multiqc [DEBUG ] No samples found: varscan2 [2024-01-26 14:42:01,996] multiqc [DEBUG ] No samples found: bbmap [2024-01-26 14:42:02,002] multiqc [DEBUG ] No samples found: bismark [2024-01-26 14:42:02,009] multiqc [DEBUG ] No samples found: biscuit [2024-01-26 14:42:02,015] multiqc [DEBUG ] No samples found: hicexplorer [2024-01-26 14:42:02,022] multiqc [DEBUG ] No samples found: hicup [2024-01-26 14:42:02,029] multiqc [DEBUG ] No samples found: hicpro [2024-01-26 14:42:02,035] multiqc [DEBUG ] No samples found: salmon [2024-01-26 14:42:02,040] multiqc [DEBUG ] No samples found: kallisto [2024-01-26 14:42:02,047] multiqc [DEBUG ] No samples found: slamdunk [2024-01-26 14:42:02,053] multiqc [DEBUG ] No samples found: star [2024-01-26 14:42:02,059] multiqc [DEBUG ] No samples found: hisat2 [2024-01-26 14:42:02,065] multiqc [DEBUG ] No samples found: tophat [2024-01-26 14:42:02,071] multiqc [DEBUG ] No samples found: bowtie2 [2024-01-26 14:42:02,077] multiqc [DEBUG ] No samples found: bowtie1 [2024-01-26 14:42:02,084] multiqc [DEBUG ] No samples found: snpsplit [2024-01-26 14:42:02,090] multiqc [DEBUG ] No samples found: kat [2024-01-26 14:42:02,096] multiqc [DEBUG ] No samples found: leehom [2024-01-26 14:42:02,101] multiqc [DEBUG ] No samples found: adapterRemoval [2024-01-26 14:42:02,107] multiqc [DEBUG ] No samples found: clipandmerge [2024-01-26 14:42:02,113] multiqc [DEBUG ] No samples found: cutadapt [2024-01-26 14:42:02,119] multiqc [DEBUG ] No samples found: flexbar [2024-01-26 14:42:02,125] multiqc [DEBUG ] No samples found: kaiju [2024-01-26 14:42:02,132] multiqc [DEBUG ] No samples found: kraken [2024-01-26 14:42:02,138] multiqc [DEBUG ] No samples found: malt [2024-01-26 14:42:02,145] multiqc [DEBUG ] No samples found: trimmomatic [2024-01-26 14:42:02,151] multiqc [DEBUG ] No samples found: sickle [2024-01-26 14:42:02,157] multiqc [DEBUG ] No samples found: skewer [2024-01-26 14:42:02,164] multiqc [DEBUG ] No samples found: sortmerna [2024-01-26 14:42:02,172] multiqc [DEBUG ] No samples found: biobloomtools [2024-01-26 14:42:02,178] multiqc [DEBUG ] No samples found: fastq_screen [2024-01-26 14:42:02,184] multiqc [DEBUG ] No samples found: afterqc [2024-01-26 14:42:02,191] multiqc [DEBUG ] No samples found: fastp [2024-01-26 14:42:02,672] multiqc.modules.fastqc.fastqc [INFO ] Found 13 reports [2024-01-26 14:42:02,913] multiqc [DEBUG ] No samples found: pycoqc [2024-01-26 14:42:02,919] multiqc [DEBUG ] No samples found: minionqc [2024-01-26 14:42:02,925] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-01-26 14:42:02,931] multiqc [DEBUG ] No samples found: clusterflow [2024-01-26 14:42:02,938] multiqc [DEBUG ] No samples found: bcl2fastq [2024-01-26 14:42:02,944] multiqc [DEBUG ] No samples found: interop [2024-01-26 14:42:02,951] multiqc [DEBUG ] No samples found: ivar [2024-01-26 14:42:02,957] multiqc [DEBUG ] No samples found: flash [2024-01-26 14:42:02,963] multiqc [DEBUG ] No samples found: seqyclean [2024-01-26 14:42:02,963] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-01-26 14:42:02,963] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-01-26 14:42:02,963] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-01-26 14:42:02,963] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-01-26 14:42:02,963] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-01-26 14:42:02,963] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-01-26 14:42:02,963] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-01-26 14:42:02,963] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-01-26 14:42:02,963] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-01-26 14:42:02,963] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-01-26 14:42:02,963] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-01-26 14:42:02,963] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-01-26 14:42:02,963] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-01-26 14:42:02,963] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-01-26 14:42:02,963] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-01-26 14:42:02,963] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-01-26 14:42:02,963] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-01-26 14:42:02,964] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-01-26 14:42:02,964] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-01-26 14:42:02,964] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-01-26 14:42:02,964] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-01-26 14:42:02,964] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-01-26 14:42:02,964] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-01-26 14:42:02,964] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-01-26 14:42:02,964] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-01-26 14:42:02,964] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-01-26 14:42:02,964] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-01-26 14:42:02,964] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-01-26 14:42:02,964] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-01-26 14:42:02,964] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-01-26 14:42:02,981] multiqc [INFO ] Compressing plot data [2024-01-26 14:42:03,209] multiqc [INFO ] Report : multiqc_report.html [2024-01-26 14:42:03,209] multiqc [INFO ] Data : multiqc_data [2024-01-26 14:42:03,209] multiqc [DEBUG ] Moving data file from '/state/partition1/job-42309311/tmpooqs99s_/multiqc_data' to '/vast/gencore/GENEFLOW/work/14/2d6d3f380365358fe28ee920311615/merged/multiqc_data' [2024-01-26 14:42:03,402] multiqc [INFO ] MultiQC complete