[2023-09-20 23:43:33,996] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-09-20 23:43:33,996] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-09-20 23:43:33,997] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-09-20 23:43:33,999] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-09-20 23:43:33,999] 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}} [2023-09-20 23:43:33,999] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HWLGMBGXT/merged [2023-09-20 23:43:34,164] multiqc [WARNING] MultiQC Version v1.15 now available! [2023-09-20 23:43:34,164] multiqc [INFO ] This is MultiQC v1.9 [2023-09-20 23:43:34,164] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HWLGMBGXT/merged [2023-09-20 23:43:34,165] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HWLGMBGXT/merged [2023-09-20 23:43:34,165] multiqc [INFO ] Template : default [2023-09-20 23:43:34,165] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-09-20 23:43:34,165] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HWLGMBGXT/merged [2023-09-20 23:43:34,165] 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 [2023-09-20 23:43:34,165] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-37932959/tmpd3oss4c7 [2023-09-20 23:43:34,312] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWLGMBGXT_n01_AtbZIP26_ColAmpPoolHm-B_ae1_fastqc.html [2023-09-20 23:43:34,315] multiqc [DEBUG ] File ignored by longranger/invocation 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HWLGMBGXT_n01_AtbZIP65_ampCol-B_ae1_fastqc.html [2023-09-20 23:43:40,829] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWLGMBGXT_n01_AtbZIP65_ampCol-B_ae1_fastqc.html [2023-09-20 23:43:40,875] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWLGMBGXT_n01_AtbZIP29_ampCol-B_ae2_fastqc.html [2023-09-20 23:43:40,877] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWLGMBGXT_n01_AtbZIP29_ampCol-B_ae2_fastqc.html [2023-09-20 23:43:40,924] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWLGMBGXT_n01_AtbZIP63_ampCol-B_ae2_fastqc.html [2023-09-20 23:43:40,926] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWLGMBGXT_n01_AtbZIP63_ampCol-B_ae2_fastqc.html [2023-09-20 23:43:40,972] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWLGMBGXT_n01_AtbZIP64_ampCol-B_ae1_fastqc.html [2023-09-20 23:43:40,974] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWLGMBGXT_n01_AtbZIP64_ampCol-B_ae1_fastqc.html [2023-09-20 23:43:41,023] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWLGMBGXT_n01_AtbZIP26_ShaAmpPoolHm-B_ae1_fastqc.html [2023-09-20 23:43:41,025] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWLGMBGXT_n01_AtbZIP26_ShaAmpPoolHm-B_ae1_fastqc.html [2023-09-20 23:43:41,089] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWLGMBGXT_n01_AtbZIP47_ampCol-B_ae1_fastqc.html [2023-09-20 23:43:41,091] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWLGMBGXT_n01_AtbZIP47_ampCol-B_ae1_fastqc.html [2023-09-20 23:43:41,151] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWLGMBGXT_n01_AtbZIP71_ampCol-B_ae2_fastqc.html [2023-09-20 23:43:41,153] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWLGMBGXT_n01_AtbZIP71_ampCol-B_ae2_fastqc.html [2023-09-20 23:43:41,200] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWLGMBGXT_n01_AtbZIP79_ampCol-B_ae2_fastqc.html [2023-09-20 23:43:41,202] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWLGMBGXT_n01_AtbZIP79_ampCol-B_ae2_fastqc.html [2023-09-20 23:43:41,267] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWLGMBGXT_n01_AtbZIP75_ampCol-B_ae1_fastqc.html [2023-09-20 23:43:41,269] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWLGMBGXT_n01_AtbZIP75_ampCol-B_ae1_fastqc.html [2023-09-20 23:43:41,315] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWLGMBGXT_n01_AtbZIP69_ampCol-B_ae2_fastqc.html [2023-09-20 23:43:41,317] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWLGMBGXT_n01_AtbZIP69_ampCol-B_ae2_fastqc.html [2023-09-20 23:43:41,810] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-09-20 23:43:41,812] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-09-20 23:43:41,821] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-09-20 23:43:41,831] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-09-20 23:43:41,881] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 109 samples (table) [2023-09-20 23:43:41,886] multiqc [DEBUG ] No samples found: conpair [2023-09-20 23:43:41,891] multiqc [DEBUG ] No samples found: peddy [2023-09-20 23:43:41,896] multiqc [DEBUG ] No samples found: somalier [2023-09-20 23:43:41,901] multiqc [DEBUG ] No samples found: methylQA [2023-09-20 23:43:41,909] multiqc [DEBUG ] No samples found: mosdepth [2023-09-20 23:43:41,913] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-09-20 23:43:41,917] multiqc [DEBUG ] No samples found: qualimap [2023-09-20 23:43:41,922] multiqc [DEBUG ] No samples found: preseq [2023-09-20 23:43:41,927] multiqc [DEBUG ] No samples found: quast [2023-09-20 23:43:41,932] multiqc [DEBUG ] No samples found: qorts [2023-09-20 23:43:41,937] multiqc [DEBUG ] No samples found: rna_seqc [2023-09-20 23:43:41,942] multiqc [DEBUG ] No samples found: rockhopper [2023-09-20 23:43:41,947] multiqc [DEBUG ] No samples found: rsem [2023-09-20 23:43:41,958] multiqc [DEBUG ] No samples found: rseqc [2023-09-20 23:43:41,962] multiqc [DEBUG ] No samples found: busco [2023-09-20 23:43:41,967] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-09-20 23:43:41,971] multiqc [DEBUG ] No samples found: disambiguate [2023-09-20 23:43:41,976] multiqc [DEBUG ] No samples found: supernova [2023-09-20 23:43:41,988] multiqc [DEBUG ] No samples found: deeptools [2023-09-20 23:43:41,993] multiqc [DEBUG ] No samples found: sargasso [2023-09-20 23:43:41,998] multiqc [DEBUG ] No samples found: verifybamid [2023-09-20 23:43:42,002] multiqc [DEBUG ] No samples found: mirtrace [2023-09-20 23:43:42,007] multiqc [DEBUG ] No samples found: happy [2023-09-20 23:43:42,012] multiqc [DEBUG ] No samples found: mirtop [2023-09-20 23:43:42,018] multiqc [DEBUG ] No samples found: homer [2023-09-20 23:43:42,023] multiqc [DEBUG ] No samples found: macs2 [2023-09-20 23:43:42,027] multiqc [DEBUG ] No samples found: theta2 [2023-09-20 23:43:42,032] multiqc [DEBUG ] No samples found: snpeff [2023-09-20 23:43:42,039] multiqc [DEBUG ] No samples found: gatk [2023-09-20 23:43:42,044] multiqc [DEBUG ] No samples found: htseq [2023-09-20 23:43:42,049] multiqc [DEBUG ] No samples found: bcftools [2023-09-20 23:43:42,054] multiqc [DEBUG ] No samples found: featureCounts [2023-09-20 23:43:42,060] multiqc [DEBUG ] No samples found: fgbio [2023-09-20 23:43:42,073] multiqc [DEBUG ] No samples found: dragen [2023-09-20 23:43:42,077] multiqc [DEBUG ] No samples found: dedup [2023-09-20 23:43:42,082] multiqc [DEBUG ] No samples found: damageprofiler [2023-09-20 23:43:42,105] multiqc [DEBUG ] No samples found: biobambam2 [2023-09-20 23:43:42,109] multiqc [DEBUG ] No samples found: mtnucratio [2023-09-20 23:43:42,112] multiqc [DEBUG ] No samples found: picard [2023-09-20 23:43:42,117] multiqc [DEBUG ] No samples found: prokka [2023-09-20 23:43:42,121] multiqc [DEBUG ] No samples found: samblaster [2023-09-20 23:43:42,129] multiqc [DEBUG ] No samples found: samtools [2023-09-20 23:43:42,134] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-09-20 23:43:42,139] multiqc [DEBUG ] No samples found: bamtools [2023-09-20 23:43:42,144] multiqc [DEBUG ] No samples found: jellyfish [2023-09-20 23:43:42,151] multiqc [DEBUG ] No samples found: vcftools [2023-09-20 23:43:42,156] multiqc [DEBUG ] No samples found: longranger [2023-09-20 23:43:42,161] multiqc [DEBUG ] No samples found: stacks [2023-09-20 23:43:42,165] multiqc [DEBUG ] No samples found: varscan2 [2023-09-20 23:43:42,179] multiqc [DEBUG ] No samples found: bbmap [2023-09-20 23:43:42,184] multiqc [DEBUG ] No samples found: bismark [2023-09-20 23:43:42,189] multiqc [DEBUG ] No samples found: biscuit [2023-09-20 23:43:42,194] multiqc [DEBUG ] No samples found: hicexplorer [2023-09-20 23:43:42,199] multiqc [DEBUG ] No samples found: hicup [2023-09-20 23:43:42,203] multiqc [DEBUG ] No samples found: hicpro [2023-09-20 23:43:42,208] multiqc [DEBUG ] No samples found: salmon [2023-09-20 23:43:42,212] multiqc [DEBUG ] No samples found: kallisto [2023-09-20 23:43:42,217] multiqc [DEBUG ] No samples found: slamdunk [2023-09-20 23:43:42,222] multiqc [DEBUG ] No samples found: star [2023-09-20 23:43:42,227] multiqc [DEBUG ] No samples found: hisat2 [2023-09-20 23:43:42,231] multiqc [DEBUG ] No samples found: tophat [2023-09-20 23:43:42,236] multiqc [DEBUG ] No samples found: bowtie2 [2023-09-20 23:43:42,241] multiqc [DEBUG ] No samples found: bowtie1 [2023-09-20 23:43:42,245] multiqc [DEBUG ] No samples found: snpsplit [2023-09-20 23:43:42,250] multiqc [DEBUG ] No samples found: kat [2023-09-20 23:43:42,254] multiqc [DEBUG ] No samples found: leehom [2023-09-20 23:43:42,259] multiqc [DEBUG ] No samples found: adapterRemoval [2023-09-20 23:43:42,263] multiqc [DEBUG ] No samples found: clipandmerge [2023-09-20 23:43:42,268] multiqc [DEBUG ] No samples found: cutadapt [2023-09-20 23:43:42,272] multiqc [DEBUG ] No samples found: flexbar [2023-09-20 23:43:42,277] multiqc [DEBUG ] No samples found: kaiju [2023-09-20 23:43:42,281] multiqc [DEBUG ] No samples found: kraken [2023-09-20 23:43:42,286] multiqc [DEBUG ] No samples found: malt [2023-09-20 23:43:42,291] multiqc [DEBUG ] No samples found: trimmomatic [2023-09-20 23:43:42,295] multiqc [DEBUG ] No samples found: sickle [2023-09-20 23:43:42,300] multiqc [DEBUG ] No samples found: skewer [2023-09-20 23:43:42,304] multiqc [DEBUG ] No samples found: sortmerna [2023-09-20 23:43:42,309] multiqc [DEBUG ] No samples found: biobloomtools [2023-09-20 23:43:42,314] multiqc [DEBUG ] No samples found: fastq_screen [2023-09-20 23:43:42,318] multiqc [DEBUG ] No samples found: afterqc [2023-09-20 23:43:42,323] multiqc [DEBUG ] No samples found: fastp [2023-09-20 23:43:52,344] multiqc.modules.fastqc.fastqc [INFO ] Found 109 reports [2023-09-20 23:44:16,127] multiqc [DEBUG ] No samples found: pycoqc [2023-09-20 23:44:16,132] multiqc [DEBUG ] No samples found: minionqc [2023-09-20 23:44:16,138] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-09-20 23:44:16,143] multiqc [DEBUG ] No samples found: clusterflow [2023-09-20 23:44:16,148] multiqc [DEBUG ] No samples found: bcl2fastq [2023-09-20 23:44:16,152] multiqc [DEBUG ] No samples found: interop [2023-09-20 23:44:16,158] multiqc [DEBUG ] No samples found: ivar [2023-09-20 23:44:16,162] multiqc [DEBUG ] No samples found: flash [2023-09-20 23:44:16,167] multiqc [DEBUG ] No samples found: seqyclean [2023-09-20 23:44:16,167] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-09-20 23:44:16,167] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-09-20 23:44:16,167] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-09-20 23:44:16,167] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2023-09-20 23:44:16,167] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2023-09-20 23:44:16,167] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2023-09-20 23:44:16,167] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2023-09-20 23:44:16,167] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2023-09-20 23:44:16,168] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2023-09-20 23:44:16,168] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-09-20 23:44:16,168] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-09-20 23:44:16,168] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-09-20 23:44:16,168] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-09-20 23:44:16,168] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-09-20 23:44:16,168] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-09-20 23:44:16,168] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-09-20 23:44:16,168] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-09-20 23:44:16,168] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-09-20 23:44:16,168] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-09-20 23:44:16,168] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-09-20 23:44:16,168] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-09-20 23:44:16,168] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-09-20 23:44:16,168] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-09-20 23:44:16,168] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-09-20 23:44:16,168] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-09-20 23:44:16,168] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-09-20 23:44:16,168] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-09-20 23:44:16,168] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-09-20 23:44:16,168] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-09-20 23:44:16,168] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-09-20 23:44:16,301] multiqc [INFO ] Compressing plot data [2023-09-20 23:44:16,358] multiqc [INFO ] Report : multiqc_report.html [2023-09-20 23:44:16,359] multiqc [INFO ] Data : multiqc_data [2023-09-20 23:44:16,359] multiqc [DEBUG ] Moving data file from '/state/partition1/job-37932959/tmpd3oss4c7/multiqc_data' to '/scratch/gencore/logs/html/HWLGMBGXT/merged/multiqc_data' [2023-09-20 23:44:16,497] multiqc [INFO ] MultiQC complete