[2023-05-24 01:43:51,037] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-05-24 01:43:51,038] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-05-24 01:43:51,038] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-05-24 01:43:51,040] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-05-24 01:43:51,040] 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}} [2023-05-24 01:43:51,040] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HG2CHAFX5/merged [2023-05-24 01:43:56,217] multiqc [WARNING] MultiQC Version v1.14 now available! [2023-05-24 01:43:56,218] multiqc [INFO ] This is MultiQC v1.9 [2023-05-24 01:43:56,218] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HG2CHAFX5/merged [2023-05-24 01:43:56,218] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HG2CHAFX5/merged [2023-05-24 01:43:56,218] multiqc [INFO ] Template : default [2023-05-24 01:43:56,218] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-05-24 01:43:56,218] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HG2CHAFX5/merged [2023-05-24 01:43:56,218] 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 [2023-05-24 01:43:56,218] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-33833831/tmpd4bortd0 [2023-05-24 01:43:56,323] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-05-24 01:43:56,325] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-05-24 01:43:56,654] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HG2CHAFX5_n01_7_fastqc.html [2023-05-24 01:43:56,656] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HG2CHAFX5_n01_7_fastqc.html [2023-05-24 01:43:56,711] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HG2CHAFX5_n01_Donor2_bot10_fastqc.html [2023-05-24 01:43:56,713] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HG2CHAFX5_n01_Donor2_bot10_fastqc.html [2023-05-24 01:43:56,766] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HG2CHAFX5_n01_Donor3_presort_fastqc.html [2023-05-24 01:43:56,768] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HG2CHAFX5_n01_Donor3_presort_fastqc.html [2023-05-24 01:43:56,820] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HG2CHAFX5_n01_4_fastqc.html [2023-05-24 01:43:56,822] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HG2CHAFX5_n01_4_fastqc.html [2023-05-24 01:43:56,875] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HG2CHAFX5_n01_Donor2_top10_fastqc.html [2023-05-24 01:43:56,877] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HG2CHAFX5_n01_Donor2_top10_fastqc.html [2023-05-24 01:43:56,929] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HG2CHAFX5_n01_1_fastqc.html [2023-05-24 01:43:56,931] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HG2CHAFX5_n01_1_fastqc.html [2023-05-24 01:43:56,982] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HG2CHAFX5_n01_undetermined_fastqc.html [2023-05-24 01:43:56,984] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HG2CHAFX5_n01_undetermined_fastqc.html [2023-05-24 01:43:57,029] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HG2CHAFX5_n01_5_fastqc.html [2023-05-24 01:43:57,031] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HG2CHAFX5_n01_5_fastqc.html [2023-05-24 01:43:57,087] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HG2CHAFX5_n01_3_fastqc.html [2023-05-24 01:43:57,088] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HG2CHAFX5_n01_3_fastqc.html [2023-05-24 01:43:57,139] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HG2CHAFX5_n01_8_fastqc.html [2023-05-24 01:43:57,141] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HG2CHAFX5_n01_8_fastqc.html [2023-05-24 01:43:57,195] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HG2CHAFX5_n01_2_fastqc.html [2023-05-24 01:43:57,196] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HG2CHAFX5_n01_2_fastqc.html [2023-05-24 01:43:57,247] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HG2CHAFX5_n01_9_fastqc.html [2023-05-24 01:43:57,249] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HG2CHAFX5_n01_9_fastqc.html [2023-05-24 01:43:57,303] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HG2CHAFX5_n01_Donor3_top10_fastqc.html [2023-05-24 01:43:57,305] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HG2CHAFX5_n01_Donor3_top10_fastqc.html [2023-05-24 01:43:57,355] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HG2CHAFX5_n01_10_fastqc.html [2023-05-24 01:43:57,357] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HG2CHAFX5_n01_10_fastqc.html [2023-05-24 01:43:57,409] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HG2CHAFX5_n01_Donor2_presort_fastqc.html [2023-05-24 01:43:57,411] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HG2CHAFX5_n01_Donor2_presort_fastqc.html [2023-05-24 01:43:57,465] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HG2CHAFX5_n01_11_fastqc.html [2023-05-24 01:43:57,467] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HG2CHAFX5_n01_11_fastqc.html [2023-05-24 01:43:57,520] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HG2CHAFX5_n01_Donor3_bot10_fastqc.html [2023-05-24 01:43:57,522] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HG2CHAFX5_n01_Donor3_bot10_fastqc.html [2023-05-24 01:43:57,575] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HG2CHAFX5_n01_6_fastqc.html [2023-05-24 01:43:57,576] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HG2CHAFX5_n01_6_fastqc.html [2023-05-24 01:43:58,104] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-05-24 01:43:58,105] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-05-24 01:43:58,113] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-05-24 01:43:58,121] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 18 samples (table) [2023-05-24 01:43:58,131] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-05-24 01:43:58,135] multiqc [DEBUG ] No samples found: conpair [2023-05-24 01:43:58,140] multiqc [DEBUG ] No samples found: peddy [2023-05-24 01:43:58,145] multiqc [DEBUG ] No samples found: somalier [2023-05-24 01:43:58,149] multiqc [DEBUG ] No samples found: methylQA [2023-05-24 01:43:58,157] multiqc [DEBUG ] No samples found: mosdepth [2023-05-24 01:43:58,162] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-05-24 01:43:58,165] multiqc [DEBUG ] No samples found: qualimap [2023-05-24 01:43:58,170] multiqc [DEBUG ] No samples found: preseq [2023-05-24 01:43:58,174] multiqc [DEBUG ] No samples found: quast [2023-05-24 01:43:58,179] multiqc [DEBUG ] No samples found: qorts [2023-05-24 01:43:58,184] multiqc [DEBUG ] No samples found: rna_seqc [2023-05-24 01:43:58,188] multiqc [DEBUG ] No samples found: rockhopper [2023-05-24 01:43:58,193] multiqc [DEBUG ] No samples found: rsem [2023-05-24 01:43:58,204] multiqc [DEBUG ] No samples found: rseqc [2023-05-24 01:43:58,208] multiqc [DEBUG ] No samples found: busco [2023-05-24 01:43:58,212] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-05-24 01:43:58,217] multiqc [DEBUG ] No samples found: disambiguate [2023-05-24 01:43:58,221] multiqc [DEBUG ] No samples found: supernova [2023-05-24 01:43:58,234] multiqc [DEBUG ] No samples found: deeptools [2023-05-24 01:43:58,238] multiqc [DEBUG ] No samples found: sargasso [2023-05-24 01:43:58,243] multiqc [DEBUG ] No samples found: verifybamid [2023-05-24 01:43:58,248] multiqc [DEBUG ] No samples found: mirtrace [2023-05-24 01:43:58,252] multiqc [DEBUG ] No samples found: happy [2023-05-24 01:43:58,257] multiqc [DEBUG ] No samples found: mirtop [2023-05-24 01:43:58,263] multiqc [DEBUG ] No samples found: homer [2023-05-24 01:43:58,267] multiqc [DEBUG ] No samples found: macs2 [2023-05-24 01:43:58,271] multiqc [DEBUG ] No samples found: theta2 [2023-05-24 01:43:58,276] multiqc [DEBUG ] No samples found: snpeff [2023-05-24 01:43:58,283] multiqc [DEBUG ] No samples found: gatk [2023-05-24 01:43:58,287] multiqc [DEBUG ] No samples found: htseq [2023-05-24 01:43:58,292] multiqc [DEBUG ] No samples found: bcftools [2023-05-24 01:43:58,297] multiqc [DEBUG ] No samples found: featureCounts [2023-05-24 01:43:58,303] multiqc [DEBUG ] No samples found: fgbio [2023-05-24 01:43:58,315] multiqc [DEBUG ] No samples found: dragen [2023-05-24 01:43:58,320] multiqc [DEBUG ] No samples found: dedup [2023-05-24 01:43:58,324] multiqc [DEBUG ] No samples found: damageprofiler [2023-05-24 01:43:58,346] multiqc [DEBUG ] No samples found: biobambam2 [2023-05-24 01:43:58,351] multiqc [DEBUG ] No samples found: mtnucratio [2023-05-24 01:43:58,353] multiqc [DEBUG ] No samples found: picard [2023-05-24 01:43:58,358] multiqc [DEBUG ] No samples found: prokka [2023-05-24 01:43:58,362] multiqc [DEBUG ] No samples found: samblaster [2023-05-24 01:43:58,370] multiqc [DEBUG ] No samples found: samtools [2023-05-24 01:43:58,375] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-05-24 01:43:58,379] multiqc [DEBUG ] No samples found: bamtools [2023-05-24 01:43:58,383] multiqc [DEBUG ] No samples found: jellyfish [2023-05-24 01:43:58,390] multiqc [DEBUG ] No samples found: vcftools [2023-05-24 01:43:58,395] multiqc [DEBUG ] No samples found: longranger [2023-05-24 01:43:58,400] multiqc [DEBUG ] No samples found: stacks [2023-05-24 01:43:58,404] multiqc [DEBUG ] No samples found: varscan2 [2023-05-24 01:43:58,417] multiqc [DEBUG ] No samples found: bbmap [2023-05-24 01:43:58,422] multiqc [DEBUG ] No samples found: bismark [2023-05-24 01:43:58,426] multiqc [DEBUG ] No samples found: biscuit [2023-05-24 01:43:58,431] multiqc [DEBUG ] No samples found: hicexplorer [2023-05-24 01:43:58,436] multiqc [DEBUG ] No samples found: hicup [2023-05-24 01:43:58,440] multiqc [DEBUG ] No samples found: hicpro [2023-05-24 01:43:58,444] multiqc [DEBUG ] No samples found: salmon [2023-05-24 01:43:58,449] multiqc [DEBUG ] No samples found: kallisto [2023-05-24 01:43:58,453] multiqc [DEBUG ] No samples found: slamdunk [2023-05-24 01:43:58,458] multiqc [DEBUG ] No samples found: star [2023-05-24 01:43:58,466] multiqc [DEBUG ] No samples found: hisat2 [2023-05-24 01:43:58,471] multiqc [DEBUG ] No samples found: tophat [2023-05-24 01:43:58,475] multiqc [DEBUG ] No samples found: bowtie2 [2023-05-24 01:43:58,479] multiqc [DEBUG ] No samples found: bowtie1 [2023-05-24 01:43:58,484] multiqc [DEBUG ] No samples found: snpsplit [2023-05-24 01:43:58,488] multiqc [DEBUG ] No samples found: kat [2023-05-24 01:43:58,492] multiqc [DEBUG ] No samples found: leehom [2023-05-24 01:43:58,497] multiqc [DEBUG ] No samples found: adapterRemoval [2023-05-24 01:43:58,501] multiqc [DEBUG ] No samples found: clipandmerge [2023-05-24 01:43:58,505] multiqc [DEBUG ] No samples found: cutadapt [2023-05-24 01:43:58,509] multiqc [DEBUG ] No samples found: flexbar [2023-05-24 01:43:58,514] multiqc [DEBUG ] No samples found: kaiju [2023-05-24 01:43:58,518] multiqc [DEBUG ] No samples found: kraken [2023-05-24 01:43:58,523] multiqc [DEBUG ] No samples found: malt [2023-05-24 01:43:58,527] multiqc [DEBUG ] No samples found: trimmomatic [2023-05-24 01:43:58,531] multiqc [DEBUG ] No samples found: sickle [2023-05-24 01:43:58,536] multiqc [DEBUG ] No samples found: skewer [2023-05-24 01:43:58,540] multiqc [DEBUG ] No samples found: sortmerna [2023-05-24 01:43:58,544] multiqc [DEBUG ] No samples found: biobloomtools [2023-05-24 01:43:58,549] multiqc [DEBUG ] No samples found: fastq_screen [2023-05-24 01:43:58,553] multiqc [DEBUG ] No samples found: afterqc [2023-05-24 01:43:58,558] multiqc [DEBUG ] No samples found: fastp [2023-05-24 01:43:58,945] multiqc.modules.fastqc.fastqc [INFO ] Found 18 reports [2023-05-24 01:43:59,126] multiqc [DEBUG ] No samples found: pycoqc [2023-05-24 01:43:59,131] multiqc [DEBUG ] No samples found: minionqc [2023-05-24 01:43:59,135] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-05-24 01:43:59,139] multiqc [DEBUG ] No samples found: clusterflow [2023-05-24 01:43:59,144] multiqc [DEBUG ] No samples found: bcl2fastq [2023-05-24 01:43:59,149] multiqc [DEBUG ] No samples found: interop [2023-05-24 01:43:59,153] multiqc [DEBUG ] No samples found: ivar [2023-05-24 01:43:59,158] multiqc [DEBUG ] No samples found: flash [2023-05-24 01:43:59,162] multiqc [DEBUG ] No samples found: seqyclean [2023-05-24 01:43:59,162] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-05-24 01:43:59,162] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-05-24 01:43:59,162] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-05-24 01:43:59,162] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2023-05-24 01:43:59,162] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2023-05-24 01:43:59,162] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2023-05-24 01:43:59,162] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2023-05-24 01:43:59,162] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2023-05-24 01:43:59,162] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2023-05-24 01:43:59,162] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-05-24 01:43:59,162] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-05-24 01:43:59,162] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-05-24 01:43:59,162] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-05-24 01:43:59,162] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-05-24 01:43:59,163] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-05-24 01:43:59,163] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-05-24 01:43:59,163] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-05-24 01:43:59,163] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-05-24 01:43:59,163] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-05-24 01:43:59,163] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-05-24 01:43:59,163] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-05-24 01:43:59,163] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-05-24 01:43:59,163] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-05-24 01:43:59,163] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-05-24 01:43:59,163] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-05-24 01:43:59,163] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-05-24 01:43:59,163] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-05-24 01:43:59,163] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-05-24 01:43:59,163] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-05-24 01:43:59,163] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-05-24 01:43:59,184] multiqc [INFO ] Compressing plot data [2023-05-24 01:43:59,419] multiqc [INFO ] Report : multiqc_report.html [2023-05-24 01:43:59,419] multiqc [INFO ] Data : multiqc_data [2023-05-24 01:43:59,419] multiqc [DEBUG ] Moving data file from '/state/partition1/job-33833831/tmpd4bortd0/multiqc_data' to '/scratch/gencore/logs/html/HG2CHAFX5/merged/multiqc_data' [2023-05-24 01:43:59,544] multiqc [INFO ] MultiQC complete