[2023-08-15 18:52:24,307] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-08-15 18:52:24,307] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-08-15 18:52:24,307] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-08-15 18:52:24,310] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-08-15 18:52:24,310] 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}} [2023-08-15 18:52:24,310] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HW22CDRX2/1 [2023-08-15 18:52:24,462] multiqc [WARNING] MultiQC Version v1.15 now available! [2023-08-15 18:52:24,462] multiqc [INFO ] This is MultiQC v1.9 [2023-08-15 18:52:24,462] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HW22CDRX2/1 [2023-08-15 18:52:24,463] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HW22CDRX2/1 [2023-08-15 18:52:24,463] multiqc [INFO ] Template : default [2023-08-15 18:52:24,463] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-08-15 18:52:24,463] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HW22CDRX2/1 [2023-08-15 18:52:24,463] 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 [2023-08-15 18:52:24,463] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-36508951/tmp1375jj3v [2023-08-15 18:52:24,567] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HW22CDRX2_l01_n02_undetermined_fastqc.html [2023-08-15 18:52:24,569] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HW22CDRX2_l01_n02_undetermined_fastqc.html [2023-08-15 18:52:24,700] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HW22CDRX2_l01_n01_scN1update_fastqc.html [2023-08-15 18:52:24,702] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HW22CDRX2_l01_n01_scN1update_fastqc.html [2023-08-15 18:52:24,806] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HW22CDRX2_l01_n02_scN1update_fastqc.html [2023-08-15 18:52:24,808] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HW22CDRX2_l01_n02_scN1update_fastqc.html [2023-08-15 18:52:24,859] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HW22CDRX2_l01_n01_undetermined_fastqc.html [2023-08-15 18:52:24,861] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HW22CDRX2_l01_n01_undetermined_fastqc.html [2023-08-15 18:52:24,903] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HW22CDRX2_l01_n01_ScWTupdated_fastqc.html [2023-08-15 18:52:24,905] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HW22CDRX2_l01_n01_ScWTupdated_fastqc.html [2023-08-15 18:52:24,946] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HW22CDRX2_l01_n02_ScWTupdated_fastqc.html [2023-08-15 18:52:24,948] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HW22CDRX2_l01_n02_ScWTupdated_fastqc.html [2023-08-15 18:52:25,432] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-08-15 18:52:25,433] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-08-15 18:52:25,450] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-08-15 18:52:25,451] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-08-15 18:52:25,453] multiqc.modules.custom_content.custom_content [INFO ] demux_report-1: Found 3 samples (table) [2023-08-15 18:52:25,458] multiqc [DEBUG ] No samples found: conpair [2023-08-15 18:52:25,463] multiqc [DEBUG ] No samples found: peddy [2023-08-15 18:52:25,468] multiqc [DEBUG ] No samples found: somalier [2023-08-15 18:52:25,473] multiqc [DEBUG ] No samples found: methylQA [2023-08-15 18:52:25,480] multiqc [DEBUG ] No samples found: mosdepth [2023-08-15 18:52:25,484] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-08-15 18:52:25,487] multiqc [DEBUG ] No samples found: qualimap [2023-08-15 18:52:25,492] multiqc [DEBUG ] No samples found: preseq [2023-08-15 18:52:25,496] multiqc [DEBUG ] No samples found: quast [2023-08-15 18:52:25,501] multiqc [DEBUG ] No samples found: qorts [2023-08-15 18:52:25,506] multiqc [DEBUG ] No samples found: rna_seqc [2023-08-15 18:52:25,510] multiqc [DEBUG ] No samples found: rockhopper [2023-08-15 18:52:25,515] multiqc [DEBUG ] No samples found: rsem [2023-08-15 18:52:25,526] multiqc [DEBUG ] No samples found: rseqc [2023-08-15 18:52:25,530] multiqc [DEBUG ] No samples found: busco [2023-08-15 18:52:25,534] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-08-15 18:52:25,539] multiqc [DEBUG ] No samples found: disambiguate [2023-08-15 18:52:25,544] multiqc [DEBUG ] No samples found: supernova [2023-08-15 18:52:25,554] multiqc [DEBUG ] No samples found: deeptools [2023-08-15 18:52:25,559] multiqc [DEBUG ] No samples found: sargasso [2023-08-15 18:52:25,563] multiqc [DEBUG ] No samples found: verifybamid [2023-08-15 18:52:25,568] multiqc [DEBUG ] No samples found: mirtrace [2023-08-15 18:52:25,573] multiqc [DEBUG ] No samples found: happy [2023-08-15 18:52:25,577] multiqc [DEBUG ] No samples found: mirtop [2023-08-15 18:52:25,583] multiqc [DEBUG ] No samples found: homer [2023-08-15 18:52:25,587] multiqc [DEBUG ] No samples found: macs2 [2023-08-15 18:52:25,591] multiqc [DEBUG ] No samples found: theta2 [2023-08-15 18:52:25,596] multiqc [DEBUG ] No samples found: snpeff [2023-08-15 18:52:25,603] multiqc [DEBUG ] No samples found: gatk [2023-08-15 18:52:25,607] multiqc [DEBUG ] No samples found: htseq [2023-08-15 18:52:25,613] multiqc [DEBUG ] No samples found: bcftools [2023-08-15 18:52:25,616] multiqc [DEBUG ] No samples found: featureCounts [2023-08-15 18:52:25,622] multiqc [DEBUG ] No samples found: fgbio [2023-08-15 18:52:25,633] multiqc [DEBUG ] No samples found: dragen [2023-08-15 18:52:25,637] multiqc [DEBUG ] No samples found: dedup [2023-08-15 18:52:25,641] multiqc [DEBUG ] No samples found: damageprofiler [2023-08-15 18:52:25,661] multiqc [DEBUG ] No samples found: biobambam2 [2023-08-15 18:52:25,666] multiqc [DEBUG ] No samples found: mtnucratio [2023-08-15 18:52:25,669] multiqc [DEBUG ] No samples found: picard [2023-08-15 18:52:25,674] multiqc [DEBUG ] No samples found: prokka [2023-08-15 18:52:25,678] multiqc [DEBUG ] No samples found: samblaster [2023-08-15 18:52:25,686] multiqc [DEBUG ] No samples found: samtools [2023-08-15 18:52:25,691] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-08-15 18:52:25,696] multiqc [DEBUG ] No samples found: bamtools [2023-08-15 18:52:25,699] multiqc [DEBUG ] No samples found: jellyfish [2023-08-15 18:52:25,706] multiqc [DEBUG ] No samples found: vcftools [2023-08-15 18:52:25,711] multiqc [DEBUG ] No samples found: longranger [2023-08-15 18:52:25,716] multiqc [DEBUG ] No samples found: stacks [2023-08-15 18:52:25,720] multiqc [DEBUG ] No samples found: varscan2 [2023-08-15 18:52:25,731] multiqc [DEBUG ] No samples found: bbmap [2023-08-15 18:52:25,736] multiqc [DEBUG ] No samples found: bismark [2023-08-15 18:52:25,742] multiqc [DEBUG ] No samples found: biscuit [2023-08-15 18:52:25,747] multiqc [DEBUG ] No samples found: hicexplorer [2023-08-15 18:52:25,751] multiqc [DEBUG ] No samples found: hicup [2023-08-15 18:52:25,756] multiqc [DEBUG ] No samples found: hicpro [2023-08-15 18:52:25,760] multiqc [DEBUG ] No samples found: salmon [2023-08-15 18:52:25,764] multiqc [DEBUG ] No samples found: kallisto [2023-08-15 18:52:25,769] multiqc [DEBUG ] No samples found: slamdunk [2023-08-15 18:52:25,773] multiqc [DEBUG ] No samples found: star [2023-08-15 18:52:25,778] multiqc [DEBUG ] No samples found: hisat2 [2023-08-15 18:52:25,782] multiqc [DEBUG ] No samples found: tophat [2023-08-15 18:52:25,787] multiqc [DEBUG ] No samples found: bowtie2 [2023-08-15 18:52:25,792] multiqc [DEBUG ] No samples found: bowtie1 [2023-08-15 18:52:25,797] multiqc [DEBUG ] No samples found: snpsplit [2023-08-15 18:52:25,801] multiqc [DEBUG ] No samples found: kat [2023-08-15 18:52:25,805] multiqc [DEBUG ] No samples found: leehom [2023-08-15 18:52:25,809] multiqc [DEBUG ] No samples found: adapterRemoval [2023-08-15 18:52:25,813] multiqc [DEBUG ] No samples found: clipandmerge [2023-08-15 18:52:25,818] multiqc [DEBUG ] No samples found: cutadapt [2023-08-15 18:52:25,822] multiqc [DEBUG ] No samples found: flexbar [2023-08-15 18:52:25,827] multiqc [DEBUG ] No samples found: kaiju [2023-08-15 18:52:25,832] multiqc [DEBUG ] No samples found: kraken [2023-08-15 18:52:25,836] multiqc [DEBUG ] No samples found: malt [2023-08-15 18:52:25,841] multiqc [DEBUG ] No samples found: trimmomatic [2023-08-15 18:52:25,845] multiqc [DEBUG ] No samples found: sickle [2023-08-15 18:52:25,850] multiqc [DEBUG ] No samples found: skewer [2023-08-15 18:52:25,854] multiqc [DEBUG ] No samples found: sortmerna [2023-08-15 18:52:25,858] multiqc [DEBUG ] No samples found: biobloomtools [2023-08-15 18:52:25,862] multiqc [DEBUG ] No samples found: fastq_screen [2023-08-15 18:52:25,866] multiqc [DEBUG ] No samples found: afterqc [2023-08-15 18:52:25,871] multiqc [DEBUG ] No samples found: fastp [2023-08-15 18:52:26,086] multiqc.modules.fastqc.fastqc [INFO ] Found 6 reports [2023-08-15 18:52:26,154] multiqc [DEBUG ] No samples found: pycoqc [2023-08-15 18:52:26,159] multiqc [DEBUG ] No samples found: minionqc [2023-08-15 18:52:26,164] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-08-15 18:52:26,169] multiqc [DEBUG ] No samples found: clusterflow [2023-08-15 18:52:26,174] multiqc [DEBUG ] No samples found: bcl2fastq [2023-08-15 18:52:26,178] multiqc [DEBUG ] No samples found: interop [2023-08-15 18:52:26,182] multiqc [DEBUG ] No samples found: ivar [2023-08-15 18:52:26,187] multiqc [DEBUG ] No samples found: flash [2023-08-15 18:52:26,191] multiqc [DEBUG ] No samples found: seqyclean [2023-08-15 18:52:26,191] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-08-15 18:52:26,191] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2023-08-15 18:52:26,191] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-08-15 18:52:26,191] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Lane 1 Demultiplexing Report'. [2023-08-15 18:52:26,191] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 1 Demultiplexing Report'. [2023-08-15 18:52:26,191] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Lane 1 Demultiplexing Report'. [2023-08-15 18:52:26,191] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Lane 1 Demultiplexing Report'. [2023-08-15 18:52:26,191] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Lane 1 Demultiplexing Report'. [2023-08-15 18:52:26,191] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Lane 1 Demultiplexing Report'. [2023-08-15 18:52:26,191] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Lane 1 Demultiplexing Report'. [2023-08-15 18:52:26,191] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-08-15 18:52:26,192] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-08-15 18:52:26,192] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-08-15 18:52:26,192] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-08-15 18:52:26,192] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-08-15 18:52:26,192] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-08-15 18:52:26,192] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-08-15 18:52:26,192] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Lane Statistics'. [2023-08-15 18:52:26,192] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2023-08-15 18:52:26,192] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Lane Statistics'. [2023-08-15 18:52:26,192] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Lane Statistics'. [2023-08-15 18:52:26,192] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Lane Statistics'. [2023-08-15 18:52:26,192] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Lane Statistics'. [2023-08-15 18:52:26,192] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Lane Statistics'. [2023-08-15 18:52:26,192] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-08-15 18:52:26,192] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-08-15 18:52:26,192] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-08-15 18:52:26,192] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-08-15 18:52:26,192] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-08-15 18:52:26,192] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-08-15 18:52:26,192] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-08-15 18:52:26,201] multiqc [INFO ] Compressing plot data [2023-08-15 18:52:26,297] multiqc [INFO ] Report : multiqc_report.html [2023-08-15 18:52:26,297] multiqc [INFO ] Data : multiqc_data [2023-08-15 18:52:26,297] multiqc [DEBUG ] Moving data file from '/state/partition1/job-36508951/tmp1375jj3v/multiqc_data' to '/scratch/gencore/logs/html/HW22CDRX2/1/multiqc_data' [2023-08-15 18:52:26,414] multiqc [INFO ] MultiQC complete