[2024-02-24 17:25:22,105] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-02-24 17:25:22,105] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-02-24 17:25:22,106] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-02-24 17:25:22,108] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-02-24 17:25:22,108] 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}} [2024-02-24 17:25:22,109] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-02-24 17:25:22,476] multiqc [WARNING] MultiQC Version v1.20 now available! [2024-02-24 17:25:22,476] multiqc [INFO ] This is MultiQC v1.9 [2024-02-24 17:25:22,476] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-02-24 17:25:22,476] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/64/a2e7b6b3c7f7c9f6a53dcc18747747/1 [2024-02-24 17:25:22,476] multiqc [INFO ] Template : default [2024-02-24 17:25:22,476] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-02-24 17:25:22,476] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/64/a2e7b6b3c7f7c9f6a53dcc18747747/1 [2024-02-24 17:25:22,477] 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 [2024-02-24 17:25:22,477] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-43349782/tmpybhhksw4 [2024-02-24 17:25:22,615] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTG72DMXY_l01_n01_K562_4sU_200_01h_1_240124_fastqc.html [2024-02-24 17:25:22,624] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTG72DMXY_l01_n01_K562_4sU_200_01h_1_240124_fastqc.html [2024-02-24 17:25:22,722] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search 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HTG72DMXY_l01_n02_K562_4sU_200_24h_1_240117_fastqc.html [2024-02-24 17:25:25,928] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTG72DMXY_l01_n02_K562_4sU_200_24h_1_240214_fastqc.html [2024-02-24 17:25:25,940] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTG72DMXY_l01_n02_K562_4sU_200_24h_1_240214_fastqc.html [2024-02-24 17:25:26,014] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTG72DMXY_l01_n02_K562_4sU_200_24h_2_240117_fastqc.html [2024-02-24 17:25:26,023] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTG72DMXY_l01_n02_K562_4sU_200_24h_2_240117_fastqc.html [2024-02-24 17:25:26,093] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTG72DMXY_l01_n02_K562_4sU_200_24h_2_240214_fastqc.html [2024-02-24 17:25:26,101] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTG72DMXY_l01_n02_K562_4sU_200_24h_2_240214_fastqc.html [2024-02-24 17:25:26,171] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTG72DMXY_l01_n02_K562_6sG_200_24h_1_240214_fastqc.html [2024-02-24 17:25:26,177] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTG72DMXY_l01_n02_K562_6sG_200_24h_1_240214_fastqc.html [2024-02-24 17:25:26,247] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTG72DMXY_l01_n02_K562_6sG_200_24h_2_240214_fastqc.html [2024-02-24 17:25:26,254] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTG72DMXY_l01_n02_K562_6sG_200_24h_2_240214_fastqc.html [2024-02-24 17:25:26,322] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTG72DMXY_l01_n02_RS_4sU_1000_15h_2_240124_fastqc.html [2024-02-24 17:25:26,328] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTG72DMXY_l01_n02_RS_4sU_1000_15h_2_240124_fastqc.html [2024-02-24 17:25:26,396] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTG72DMXY_l01_n02_RS_4sU_1000_24h_2_240124_fastqc.html [2024-02-24 17:25:26,402] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTG72DMXY_l01_n02_RS_4sU_1000_24h_2_240124_fastqc.html [2024-02-24 17:25:26,468] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTG72DMXY_l01_n02_undetermined_fastqc.html [2024-02-24 17:25:26,475] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTG72DMXY_l01_n02_undetermined_fastqc.html [2024-02-24 17:25:26,537] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-02-24 17:25:26,543] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-02-24 17:25:26,995] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-02-24 17:25:26,997] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-02-24 17:25:27,025] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 25 samples (table) [2024-02-24 17:25:27,027] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-02-24 17:25:27,037] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-02-24 17:25:27,043] multiqc [DEBUG ] No samples found: conpair [2024-02-24 17:25:27,049] multiqc [DEBUG ] No samples found: peddy [2024-02-24 17:25:27,055] multiqc [DEBUG ] No samples found: somalier [2024-02-24 17:25:27,061] multiqc [DEBUG ] No samples found: methylQA [2024-02-24 17:25:27,072] multiqc [DEBUG ] No samples found: mosdepth [2024-02-24 17:25:27,077] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-02-24 17:25:27,081] multiqc [DEBUG ] No samples found: qualimap [2024-02-24 17:25:27,087] multiqc [DEBUG ] No samples found: preseq [2024-02-24 17:25:27,093] multiqc [DEBUG ] No samples found: quast [2024-02-24 17:25:27,098] multiqc [DEBUG ] No samples found: qorts [2024-02-24 17:25:27,104] multiqc [DEBUG ] No samples found: rna_seqc [2024-02-24 17:25:27,109] multiqc [DEBUG ] No samples found: rockhopper [2024-02-24 17:25:27,115] multiqc [DEBUG ] No samples found: rsem [2024-02-24 17:25:27,129] multiqc [DEBUG ] No samples found: rseqc [2024-02-24 17:25:27,134] multiqc [DEBUG ] No samples found: busco [2024-02-24 17:25:27,140] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-02-24 17:25:27,146] multiqc [DEBUG ] No samples found: disambiguate [2024-02-24 17:25:27,152] multiqc [DEBUG ] No samples found: supernova [2024-02-24 17:25:27,168] multiqc [DEBUG ] No samples found: deeptools [2024-02-24 17:25:27,174] multiqc [DEBUG ] No samples found: sargasso [2024-02-24 17:25:27,180] multiqc [DEBUG ] No samples found: verifybamid [2024-02-24 17:25:27,185] multiqc [DEBUG ] No samples found: mirtrace [2024-02-24 17:25:27,191] multiqc [DEBUG ] No samples found: happy [2024-02-24 17:25:27,196] multiqc [DEBUG ] No samples found: mirtop [2024-02-24 17:25:27,204] multiqc [DEBUG ] No samples found: homer [2024-02-24 17:25:27,210] multiqc [DEBUG ] No samples found: macs2 [2024-02-24 17:25:27,215] multiqc [DEBUG ] No samples found: theta2 [2024-02-24 17:25:27,222] multiqc [DEBUG ] No samples found: snpeff [2024-02-24 17:25:27,230] multiqc [DEBUG ] No samples found: gatk [2024-02-24 17:25:27,236] multiqc [DEBUG ] No samples found: htseq [2024-02-24 17:25:27,242] multiqc [DEBUG ] No samples found: bcftools [2024-02-24 17:25:27,247] multiqc [DEBUG ] No samples found: featureCounts [2024-02-24 17:25:27,254] multiqc [DEBUG ] No samples found: fgbio [2024-02-24 17:25:27,269] multiqc [DEBUG ] No samples found: dragen [2024-02-24 17:25:27,275] multiqc [DEBUG ] No samples found: dedup [2024-02-24 17:25:27,280] multiqc [DEBUG ] No samples found: damageprofiler [2024-02-24 17:25:27,306] multiqc [DEBUG ] No samples found: biobambam2 [2024-02-24 17:25:27,312] multiqc [DEBUG ] No samples found: mtnucratio [2024-02-24 17:25:27,315] multiqc [DEBUG ] No samples found: picard [2024-02-24 17:25:27,320] multiqc [DEBUG ] No samples found: prokka [2024-02-24 17:25:27,325] multiqc [DEBUG ] No samples found: samblaster [2024-02-24 17:25:27,335] multiqc [DEBUG ] No samples found: samtools [2024-02-24 17:25:27,341] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-02-24 17:25:27,347] multiqc [DEBUG ] No samples found: bamtools [2024-02-24 17:25:27,352] multiqc [DEBUG ] No samples found: jellyfish [2024-02-24 17:25:27,361] multiqc [DEBUG ] No samples found: vcftools [2024-02-24 17:25:27,367] multiqc [DEBUG ] No samples found: longranger [2024-02-24 17:25:27,372] multiqc [DEBUG ] No samples found: stacks [2024-02-24 17:25:27,378] multiqc [DEBUG ] No samples found: varscan2 [2024-02-24 17:25:27,395] multiqc [DEBUG ] No samples found: bbmap [2024-02-24 17:25:27,401] multiqc [DEBUG ] No samples found: bismark [2024-02-24 17:25:27,406] multiqc [DEBUG ] No samples found: biscuit [2024-02-24 17:25:27,412] multiqc [DEBUG ] No samples found: hicexplorer [2024-02-24 17:25:27,418] multiqc [DEBUG ] No samples found: hicup [2024-02-24 17:25:27,423] multiqc [DEBUG ] No samples found: hicpro [2024-02-24 17:25:27,428] multiqc [DEBUG ] No samples found: salmon [2024-02-24 17:25:27,434] multiqc [DEBUG ] No samples found: kallisto [2024-02-24 17:25:27,439] multiqc [DEBUG ] No samples found: slamdunk [2024-02-24 17:25:27,445] multiqc [DEBUG ] No samples found: star [2024-02-24 17:25:27,450] multiqc [DEBUG ] No samples found: hisat2 [2024-02-24 17:25:27,456] multiqc [DEBUG ] No samples found: tophat [2024-02-24 17:25:27,461] multiqc [DEBUG ] No samples found: bowtie2 [2024-02-24 17:25:27,467] multiqc [DEBUG ] No samples found: bowtie1 [2024-02-24 17:25:27,473] multiqc [DEBUG ] No samples found: snpsplit [2024-02-24 17:25:27,478] multiqc [DEBUG ] No samples found: kat [2024-02-24 17:25:27,483] multiqc [DEBUG ] No samples found: leehom [2024-02-24 17:25:27,488] multiqc [DEBUG ] No samples found: adapterRemoval [2024-02-24 17:25:27,494] multiqc [DEBUG ] No samples found: clipandmerge [2024-02-24 17:25:27,499] multiqc [DEBUG ] No samples found: cutadapt [2024-02-24 17:25:27,504] multiqc [DEBUG ] No samples found: flexbar [2024-02-24 17:25:27,510] multiqc [DEBUG ] No samples found: kaiju [2024-02-24 17:25:27,515] multiqc [DEBUG ] No samples found: kraken [2024-02-24 17:25:27,521] multiqc [DEBUG ] No samples found: malt [2024-02-24 17:25:27,527] multiqc [DEBUG ] No samples found: trimmomatic [2024-02-24 17:25:27,532] multiqc [DEBUG ] No samples found: sickle [2024-02-24 17:25:27,538] multiqc [DEBUG ] No samples found: skewer [2024-02-24 17:25:27,543] multiqc [DEBUG ] No samples found: sortmerna [2024-02-24 17:25:27,548] multiqc [DEBUG ] No samples found: biobloomtools [2024-02-24 17:25:27,553] multiqc [DEBUG ] No samples found: fastq_screen [2024-02-24 17:25:27,558] multiqc [DEBUG ] No samples found: afterqc [2024-02-24 17:25:27,564] multiqc [DEBUG ] No samples found: fastp [2024-02-24 17:25:32,870] multiqc.modules.fastqc.fastqc [INFO ] Found 50 reports [2024-02-24 17:25:33,256] multiqc [DEBUG ] No samples found: pycoqc [2024-02-24 17:25:33,261] multiqc [DEBUG ] No samples found: minionqc [2024-02-24 17:25:33,267] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-02-24 17:25:33,273] multiqc [DEBUG ] No samples found: clusterflow [2024-02-24 17:25:33,279] multiqc [DEBUG ] No samples found: bcl2fastq [2024-02-24 17:25:33,285] multiqc [DEBUG ] No samples found: interop [2024-02-24 17:25:33,290] multiqc [DEBUG ] No samples found: ivar [2024-02-24 17:25:33,297] multiqc [DEBUG ] No samples found: flash [2024-02-24 17:25:33,302] multiqc [DEBUG ] No samples found: seqyclean [2024-02-24 17:25:33,302] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-02-24 17:25:33,303] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-02-24 17:25:33,303] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-02-24 17:25:33,303] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-02-24 17:25:33,303] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-02-24 17:25:33,303] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-02-24 17:25:33,303] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-02-24 17:25:33,303] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-02-24 17:25:33,303] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-02-24 17:25:33,303] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-02-24 17:25:33,303] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-02-24 17:25:33,303] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-02-24 17:25:33,303] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-02-24 17:25:33,303] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-02-24 17:25:33,303] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-02-24 17:25:33,303] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-02-24 17:25:33,303] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-02-24 17:25:33,303] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-02-24 17:25:33,303] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-02-24 17:25:33,303] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-02-24 17:25:33,303] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-02-24 17:25:33,303] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-02-24 17:25:33,303] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-02-24 17:25:33,303] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-02-24 17:25:33,303] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-02-24 17:25:33,303] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-02-24 17:25:33,303] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-02-24 17:25:33,303] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-02-24 17:25:33,303] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-02-24 17:25:33,303] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-02-24 17:25:33,363] multiqc [INFO ] Compressing plot data [2024-02-24 17:25:34,266] multiqc [INFO ] Report : multiqc_report.html [2024-02-24 17:25:34,266] multiqc [INFO ] Data : multiqc_data [2024-02-24 17:25:34,266] multiqc [DEBUG ] Moving data file from '/state/partition1/job-43349782/tmpybhhksw4/multiqc_data' to '/vast/gencore/GENEFLOW/work/64/a2e7b6b3c7f7c9f6a53dcc18747747/1/multiqc_data' [2024-02-24 17:25:34,445] multiqc [INFO ] MultiQC complete