[2025-01-30 18:57:23,061] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2025-01-30 18:57:23,062] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2025-01-30 18:57:23,062] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2025-01-30 18:57:23,064] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2025-01-30 18:57:23,064] 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}} [2025-01-30 18:57:23,065] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2025-01-30 18:57:23,100] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2025-01-30 18:57:23,100] multiqc [INFO ] This is MultiQC v1.9 [2025-01-30 18:57:23,100] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2025-01-30 18:57:23,100] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/78/28d323a4e1a39aaed58f3e40343b9a/2 [2025-01-30 18:57:23,100] multiqc [INFO ] Template : default [2025-01-30 18:57:23,100] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2025-01-30 18:57:23,100] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/78/28d323a4e1a39aaed58f3e40343b9a/2 [2025-01-30 18:57:23,100] 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 [2025-01-30 18:57:23,101] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-56666202/tmpd1w5i47q [2025-01-30 18:57:23,210] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2MF5DSXF_l02_n02_ECA3046_POOLRET87_fastqc.html [2025-01-30 18:57:23,213] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2MF5DSXF_l02_n02_ECA3046_POOLRET87_fastqc.html [2025-01-30 18:57:23,262] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern 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H2MF5DSXF_l02_n01_ECA3505_POOLRET87_fastqc.html [2025-01-30 18:57:41,807] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2MF5DSXF_l02_n01_ECA3505_POOLRET87_fastqc.html [2025-01-30 18:57:41,852] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2MF5DSXF_l02_n02_ECA3058_POOLRET87_fastqc.html [2025-01-30 18:57:41,854] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2MF5DSXF_l02_n02_ECA3058_POOLRET87_fastqc.html [2025-01-30 18:57:41,900] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2MF5DSXF_l02_n01_ECA3518_POOLRET87_fastqc.html [2025-01-30 18:57:41,902] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2MF5DSXF_l02_n01_ECA3518_POOLRET87_fastqc.html [2025-01-30 18:57:41,964] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2MF5DSXF_l02_n01_ECA3127_POOLRET87_fastqc.html [2025-01-30 18:57:41,966] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2MF5DSXF_l02_n01_ECA3127_POOLRET87_fastqc.html [2025-01-30 18:57:42,033] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2MF5DSXF_l02_n02_ECA3501_POOLRET87_fastqc.html [2025-01-30 18:57:42,035] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2MF5DSXF_l02_n02_ECA3501_POOLRET87_fastqc.html [2025-01-30 18:57:42,081] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2MF5DSXF_l02_n02_ECA2119_287_POOLRET87_fastqc.html [2025-01-30 18:57:42,083] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2MF5DSXF_l02_n02_ECA2119_287_POOLRET87_fastqc.html [2025-01-30 18:57:42,128] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2MF5DSXF_l02_n01_ECA3003_POOLRET87_fastqc.html [2025-01-30 18:57:42,130] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2MF5DSXF_l02_n01_ECA3003_POOLRET87_fastqc.html [2025-01-30 18:57:42,175] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2MF5DSXF_l02_n01_ECA3009_POOLRET87_fastqc.html [2025-01-30 18:57:42,177] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2MF5DSXF_l02_n01_ECA3009_POOLRET87_fastqc.html [2025-01-30 18:57:42,223] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2MF5DSXF_l02_n02_ECA3661_POOLRET87_fastqc.html [2025-01-30 18:57:42,225] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2MF5DSXF_l02_n02_ECA3661_POOLRET87_fastqc.html [2025-01-30 18:57:42,269] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2MF5DSXF_l02_n01_ECA3686_POOLRET87_fastqc.html [2025-01-30 18:57:42,271] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2MF5DSXF_l02_n01_ECA3686_POOLRET87_fastqc.html [2025-01-30 18:57:42,316] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2MF5DSXF_l02_n02_ECA2996_POOLRET87_fastqc.html [2025-01-30 18:57:42,318] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2MF5DSXF_l02_n02_ECA2996_POOLRET87_fastqc.html [2025-01-30 18:57:42,780] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2025-01-30 18:57:42,782] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2025-01-30 18:57:42,792] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2025-01-30 18:57:42,880] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 193 samples (table) [2025-01-30 18:57:42,889] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2025-01-30 18:57:42,894] multiqc [DEBUG ] No samples found: conpair [2025-01-30 18:57:42,899] multiqc [DEBUG ] No samples found: peddy [2025-01-30 18:57:42,904] multiqc [DEBUG ] No samples found: somalier [2025-01-30 18:57:42,908] multiqc [DEBUG ] No samples found: methylQA [2025-01-30 18:57:42,915] multiqc [DEBUG ] No samples found: mosdepth [2025-01-30 18:57:42,919] multiqc [DEBUG ] No samples found: phantompeakqualtools [2025-01-30 18:57:42,922] multiqc [DEBUG ] No samples found: qualimap [2025-01-30 18:57:42,927] multiqc [DEBUG ] No samples found: preseq [2025-01-30 18:57:42,931] multiqc [DEBUG ] No samples found: quast [2025-01-30 18:57:42,936] multiqc [DEBUG ] No samples found: qorts [2025-01-30 18:57:42,940] multiqc [DEBUG ] No samples found: rna_seqc [2025-01-30 18:57:42,944] multiqc [DEBUG ] No samples found: rockhopper [2025-01-30 18:57:42,949] multiqc [DEBUG ] No samples found: rsem [2025-01-30 18:57:42,959] multiqc [DEBUG ] No samples found: rseqc [2025-01-30 18:57:42,963] multiqc [DEBUG ] No samples found: busco [2025-01-30 18:57:42,967] multiqc [DEBUG ] No samples found: goleft_indexcov [2025-01-30 18:57:42,971] multiqc [DEBUG ] No samples found: disambiguate [2025-01-30 18:57:42,975] multiqc [DEBUG ] No samples found: supernova [2025-01-30 18:57:42,986] multiqc [DEBUG ] No samples found: deeptools [2025-01-30 18:57:42,991] multiqc [DEBUG ] No samples found: sargasso [2025-01-30 18:57:42,995] multiqc [DEBUG ] No samples found: verifybamid [2025-01-30 18:57:42,999] multiqc [DEBUG ] No samples found: mirtrace [2025-01-30 18:57:43,004] multiqc [DEBUG ] No samples found: happy [2025-01-30 18:57:43,008] multiqc [DEBUG ] No samples found: mirtop [2025-01-30 18:57:43,013] multiqc [DEBUG ] No samples found: homer [2025-01-30 18:57:43,018] multiqc [DEBUG ] No samples found: macs2 [2025-01-30 18:57:43,022] multiqc [DEBUG ] No samples found: theta2 [2025-01-30 18:57:43,026] multiqc [DEBUG ] No samples found: snpeff [2025-01-30 18:57:43,032] multiqc [DEBUG ] No samples found: gatk [2025-01-30 18:57:43,036] multiqc [DEBUG ] No samples found: htseq [2025-01-30 18:57:43,041] multiqc [DEBUG ] No samples found: bcftools [2025-01-30 18:57:43,046] multiqc [DEBUG ] No samples found: featureCounts [2025-01-30 18:57:43,051] multiqc [DEBUG ] No samples found: fgbio [2025-01-30 18:57:43,062] multiqc [DEBUG ] No samples found: dragen [2025-01-30 18:57:43,067] multiqc [DEBUG ] No samples found: dedup [2025-01-30 18:57:43,071] multiqc [DEBUG ] No samples found: damageprofiler [2025-01-30 18:57:43,091] multiqc [DEBUG ] No samples found: biobambam2 [2025-01-30 18:57:43,095] multiqc [DEBUG ] No samples found: mtnucratio [2025-01-30 18:57:43,098] multiqc [DEBUG ] No samples found: picard [2025-01-30 18:57:43,102] multiqc [DEBUG ] No samples found: prokka [2025-01-30 18:57:43,106] multiqc [DEBUG ] No samples found: samblaster [2025-01-30 18:57:43,113] multiqc [DEBUG ] No samples found: samtools [2025-01-30 18:57:43,118] multiqc [DEBUG ] No samples found: sexdeterrmine [2025-01-30 18:57:43,122] multiqc [DEBUG ] No samples found: bamtools [2025-01-30 18:57:43,126] multiqc [DEBUG ] No samples found: jellyfish [2025-01-30 18:57:43,134] multiqc [DEBUG ] No samples found: vcftools [2025-01-30 18:57:43,138] multiqc [DEBUG ] No samples found: longranger [2025-01-30 18:57:43,143] multiqc [DEBUG ] No samples found: stacks [2025-01-30 18:57:43,147] multiqc [DEBUG ] No samples found: varscan2 [2025-01-30 18:57:43,159] multiqc [DEBUG ] No samples found: bbmap [2025-01-30 18:57:43,163] multiqc [DEBUG ] No samples found: bismark [2025-01-30 18:57:43,168] multiqc [DEBUG ] No samples found: biscuit [2025-01-30 18:57:43,172] multiqc [DEBUG ] No samples found: hicexplorer [2025-01-30 18:57:43,177] multiqc [DEBUG ] No samples found: hicup [2025-01-30 18:57:43,181] multiqc [DEBUG ] No samples found: hicpro [2025-01-30 18:57:43,185] multiqc [DEBUG ] No samples found: salmon [2025-01-30 18:57:43,190] multiqc [DEBUG ] No samples found: kallisto [2025-01-30 18:57:43,194] multiqc [DEBUG ] No samples found: slamdunk [2025-01-30 18:57:43,199] multiqc [DEBUG ] No samples found: star [2025-01-30 18:57:43,203] multiqc [DEBUG ] No samples found: hisat2 [2025-01-30 18:57:43,207] multiqc [DEBUG ] No samples found: tophat [2025-01-30 18:57:43,212] multiqc [DEBUG ] No samples found: bowtie2 [2025-01-30 18:57:43,216] multiqc [DEBUG ] No samples found: bowtie1 [2025-01-30 18:57:43,220] multiqc [DEBUG ] No samples found: snpsplit [2025-01-30 18:57:43,224] multiqc [DEBUG ] No samples found: kat [2025-01-30 18:57:43,228] multiqc [DEBUG ] No samples found: leehom [2025-01-30 18:57:43,232] multiqc [DEBUG ] No samples found: adapterRemoval [2025-01-30 18:57:43,237] multiqc [DEBUG ] No samples found: clipandmerge [2025-01-30 18:57:43,241] multiqc [DEBUG ] No samples found: cutadapt [2025-01-30 18:57:43,245] multiqc [DEBUG ] No samples found: flexbar [2025-01-30 18:57:43,249] multiqc [DEBUG ] No samples found: kaiju [2025-01-30 18:57:43,253] multiqc [DEBUG ] No samples found: kraken [2025-01-30 18:57:43,258] multiqc [DEBUG ] No samples found: malt [2025-01-30 18:57:43,262] multiqc [DEBUG ] No samples found: trimmomatic [2025-01-30 18:57:43,266] multiqc [DEBUG ] No samples found: sickle [2025-01-30 18:57:43,270] multiqc [DEBUG ] No samples found: skewer [2025-01-30 18:57:43,274] multiqc [DEBUG ] No samples found: sortmerna [2025-01-30 18:57:43,278] multiqc [DEBUG ] No samples found: biobloomtools [2025-01-30 18:57:43,283] multiqc [DEBUG ] No samples found: fastq_screen [2025-01-30 18:57:43,287] multiqc [DEBUG ] No samples found: afterqc [2025-01-30 18:57:43,291] multiqc [DEBUG ] No samples found: fastp [2025-01-30 18:58:42,743] multiqc.modules.fastqc.fastqc [INFO ] Found 386 reports [2025-01-30 18:59:10,955] multiqc [DEBUG ] No samples found: pycoqc [2025-01-30 18:59:10,960] multiqc [DEBUG ] No samples found: minionqc [2025-01-30 18:59:10,965] multiqc [DEBUG ] No samples found: multivcfanalyzer [2025-01-30 18:59:10,970] multiqc [DEBUG ] No samples found: clusterflow [2025-01-30 18:59:10,975] multiqc [DEBUG ] No samples found: bcl2fastq [2025-01-30 18:59:10,980] multiqc [DEBUG ] No samples found: interop [2025-01-30 18:59:10,984] multiqc [DEBUG ] No samples found: ivar [2025-01-30 18:59:10,989] multiqc [DEBUG ] No samples found: flash [2025-01-30 18:59:10,993] multiqc [DEBUG ] No samples found: seqyclean [2025-01-30 18:59:10,993] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2025-01-30 18:59:10,993] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2025-01-30 18:59:10,993] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2025-01-30 18:59:10,993] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2025-01-30 18:59:10,993] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2025-01-30 18:59:10,993] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2025-01-30 18:59:10,993] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2025-01-30 18:59:10,993] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2025-01-30 18:59:10,993] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2025-01-30 18:59:10,993] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2025-01-30 18:59:10,993] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2025-01-30 18:59:10,994] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2025-01-30 18:59:10,994] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2025-01-30 18:59:10,994] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2025-01-30 18:59:10,994] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2025-01-30 18:59:10,994] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2025-01-30 18:59:10,994] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2025-01-30 18:59:10,994] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2025-01-30 18:59:10,994] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2025-01-30 18:59:10,994] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2025-01-30 18:59:10,994] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2025-01-30 18:59:10,994] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2025-01-30 18:59:10,994] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2025-01-30 18:59:10,994] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2025-01-30 18:59:10,994] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2025-01-30 18:59:10,994] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2025-01-30 18:59:10,994] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2025-01-30 18:59:10,994] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2025-01-30 18:59:10,994] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2025-01-30 18:59:10,994] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2025-01-30 18:59:11,436] multiqc [INFO ] Compressing plot data [2025-01-30 18:59:11,572] multiqc [INFO ] Report : multiqc_report.html [2025-01-30 18:59:11,572] multiqc [INFO ] Data : multiqc_data [2025-01-30 18:59:11,572] multiqc [DEBUG ] Moving data file from '/state/partition1/job-56666202/tmpd1w5i47q/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/78/28d323a4e1a39aaed58f3e40343b9a/2/multiqc_data' [2025-01-30 18:59:12,107] multiqc [INFO ] MultiQC complete