[2024-12-24 02:36:26,484] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-12-24 02:36:26,485] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-12-24 02:36:26,485] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-12-24 02:36:26,487] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-12-24 02:36:26,487] 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}} [2024-12-24 02:36:26,487] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-12-24 02:36:26,518] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-12-24 02:36:26,519] multiqc [INFO ] This is MultiQC v1.9 [2024-12-24 02:36:26,519] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-12-24 02:36:26,519] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/ba/4ac90ab256bd3ebd22e636b549d281/merged [2024-12-24 02:36:26,519] multiqc [INFO ] Template : default [2024-12-24 02:36:26,519] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-12-24 02:36:26,519] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/ba/4ac90ab256bd3ebd22e636b549d281/merged [2024-12-24 02:36:26,519] 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 [2024-12-24 02:36:26,519] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-55341764/tmpffyxypcf [2024-12-24 02:36:26,624] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLLT2AFX7_n01_Donor1_GECKO_fastqc.html [2024-12-24 02:36:26,627] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLLT2AFX7_n01_Donor1_GECKO_fastqc.html [2024-12-24 02:36:26,690] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-12-24 02:36:26,692] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-12-24 02:36:26,922] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLLT2AFX7_n01_Donor1_ETP_fastqc.html [2024-12-24 02:36:26,924] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLLT2AFX7_n01_Donor1_ETP_fastqc.html [2024-12-24 02:36:26,990] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLLT2AFX7_n01_Donor1_ky9_fastqc.html [2024-12-24 02:36:26,992] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLLT2AFX7_n01_Donor1_ky9_fastqc.html [2024-12-24 02:36:27,054] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLLT2AFX7_n01_Donor1_kk10_fastqc.html [2024-12-24 02:36:27,056] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLLT2AFX7_n01_Donor1_kk10_fastqc.html [2024-12-24 02:36:27,117] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLLT2AFX7_n01_undetermined_fastqc.html [2024-12-24 02:36:27,119] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLLT2AFX7_n01_undetermined_fastqc.html [2024-12-24 02:36:27,518] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-12-24 02:36:27,520] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-12-24 02:36:27,527] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-12-24 02:36:27,530] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 5 samples (table) [2024-12-24 02:36:27,540] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-12-24 02:36:27,545] multiqc [DEBUG ] No samples found: conpair [2024-12-24 02:36:27,549] multiqc [DEBUG ] No samples found: peddy [2024-12-24 02:36:27,554] multiqc [DEBUG ] No samples found: somalier [2024-12-24 02:36:27,559] multiqc [DEBUG ] No samples found: methylQA [2024-12-24 02:36:27,567] multiqc [DEBUG ] No samples found: mosdepth [2024-12-24 02:36:27,571] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-12-24 02:36:27,575] multiqc [DEBUG ] No samples found: qualimap [2024-12-24 02:36:27,580] multiqc [DEBUG ] No samples found: preseq [2024-12-24 02:36:27,584] multiqc [DEBUG ] No samples found: quast [2024-12-24 02:36:27,589] multiqc [DEBUG ] No samples found: qorts [2024-12-24 02:36:27,594] multiqc [DEBUG ] No samples found: rna_seqc [2024-12-24 02:36:27,599] multiqc [DEBUG ] No samples found: rockhopper [2024-12-24 02:36:27,604] multiqc [DEBUG ] No samples found: rsem [2024-12-24 02:36:27,615] multiqc [DEBUG ] No samples found: rseqc [2024-12-24 02:36:27,619] multiqc [DEBUG ] No samples found: busco [2024-12-24 02:36:27,624] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-12-24 02:36:27,629] multiqc [DEBUG ] No samples found: disambiguate [2024-12-24 02:36:27,634] multiqc [DEBUG ] No samples found: supernova [2024-12-24 02:36:27,646] multiqc [DEBUG ] No samples found: deeptools [2024-12-24 02:36:27,651] multiqc [DEBUG ] No samples found: sargasso [2024-12-24 02:36:27,656] multiqc [DEBUG ] No samples found: verifybamid [2024-12-24 02:36:27,661] multiqc [DEBUG ] No samples found: mirtrace [2024-12-24 02:36:27,665] multiqc [DEBUG ] No samples found: happy [2024-12-24 02:36:27,670] multiqc [DEBUG ] No samples found: mirtop [2024-12-24 02:36:27,677] multiqc [DEBUG ] No samples found: homer [2024-12-24 02:36:27,681] multiqc [DEBUG ] No samples found: macs2 [2024-12-24 02:36:27,685] multiqc [DEBUG ] No samples found: theta2 [2024-12-24 02:36:27,690] multiqc [DEBUG ] No samples found: snpeff [2024-12-24 02:36:27,697] multiqc [DEBUG ] No samples found: gatk [2024-12-24 02:36:27,701] multiqc [DEBUG ] No samples found: htseq [2024-12-24 02:36:27,707] multiqc [DEBUG ] No samples found: bcftools [2024-12-24 02:36:27,711] multiqc [DEBUG ] No samples found: featureCounts [2024-12-24 02:36:27,718] multiqc [DEBUG ] No samples found: fgbio [2024-12-24 02:36:27,731] multiqc [DEBUG ] No samples found: dragen [2024-12-24 02:36:27,736] multiqc [DEBUG ] No samples found: dedup [2024-12-24 02:36:27,740] multiqc [DEBUG ] No samples found: damageprofiler [2024-12-24 02:36:27,763] multiqc [DEBUG ] No samples found: biobambam2 [2024-12-24 02:36:27,767] multiqc [DEBUG ] No samples found: mtnucratio [2024-12-24 02:36:27,770] multiqc [DEBUG ] No samples found: picard [2024-12-24 02:36:27,774] multiqc [DEBUG ] No samples found: prokka [2024-12-24 02:36:27,779] multiqc [DEBUG ] No samples found: samblaster [2024-12-24 02:36:27,788] multiqc [DEBUG ] No samples found: samtools [2024-12-24 02:36:27,793] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-12-24 02:36:27,798] multiqc [DEBUG ] No samples found: bamtools [2024-12-24 02:36:27,803] multiqc [DEBUG ] No samples found: jellyfish [2024-12-24 02:36:27,811] multiqc [DEBUG ] No samples found: vcftools [2024-12-24 02:36:27,815] multiqc [DEBUG ] No samples found: longranger [2024-12-24 02:36:27,820] multiqc [DEBUG ] No samples found: stacks [2024-12-24 02:36:27,825] multiqc [DEBUG ] No samples found: varscan2 [2024-12-24 02:36:27,838] multiqc [DEBUG ] No samples found: bbmap [2024-12-24 02:36:27,843] multiqc [DEBUG ] No samples found: bismark [2024-12-24 02:36:27,848] multiqc [DEBUG ] No samples found: biscuit [2024-12-24 02:36:27,853] multiqc [DEBUG ] No samples found: hicexplorer [2024-12-24 02:36:27,858] multiqc [DEBUG ] No samples found: hicup [2024-12-24 02:36:27,862] multiqc [DEBUG ] No samples found: hicpro [2024-12-24 02:36:27,867] multiqc [DEBUG ] No samples found: salmon [2024-12-24 02:36:27,871] multiqc [DEBUG ] No samples found: kallisto [2024-12-24 02:36:27,876] multiqc [DEBUG ] No samples found: slamdunk [2024-12-24 02:36:27,881] multiqc [DEBUG ] No samples found: star [2024-12-24 02:36:27,886] multiqc [DEBUG ] No samples found: hisat2 [2024-12-24 02:36:27,891] multiqc [DEBUG ] No samples found: tophat [2024-12-24 02:36:27,895] multiqc [DEBUG ] No samples found: bowtie2 [2024-12-24 02:36:27,900] multiqc [DEBUG ] No samples found: bowtie1 [2024-12-24 02:36:27,905] multiqc [DEBUG ] No samples found: snpsplit [2024-12-24 02:36:27,909] multiqc [DEBUG ] No samples found: kat [2024-12-24 02:36:27,914] multiqc [DEBUG ] No samples found: leehom [2024-12-24 02:36:27,918] multiqc [DEBUG ] No samples found: adapterRemoval [2024-12-24 02:36:27,923] multiqc [DEBUG ] No samples found: clipandmerge [2024-12-24 02:36:27,927] multiqc [DEBUG ] No samples found: cutadapt [2024-12-24 02:36:27,932] multiqc [DEBUG ] No samples found: flexbar [2024-12-24 02:36:27,937] multiqc [DEBUG ] No samples found: kaiju [2024-12-24 02:36:27,941] multiqc [DEBUG ] No samples found: kraken [2024-12-24 02:36:27,946] multiqc [DEBUG ] No samples found: malt [2024-12-24 02:36:27,950] multiqc [DEBUG ] No samples found: trimmomatic [2024-12-24 02:36:27,955] multiqc [DEBUG ] No samples found: sickle [2024-12-24 02:36:27,959] multiqc [DEBUG ] No samples found: skewer [2024-12-24 02:36:27,964] multiqc [DEBUG ] No samples found: sortmerna [2024-12-24 02:36:27,968] multiqc [DEBUG ] No samples found: biobloomtools [2024-12-24 02:36:27,973] multiqc [DEBUG ] No samples found: fastq_screen [2024-12-24 02:36:27,977] multiqc [DEBUG ] No samples found: afterqc [2024-12-24 02:36:27,982] multiqc [DEBUG ] No samples found: fastp [2024-12-24 02:36:28,102] multiqc.modules.fastqc.fastqc [INFO ] Found 5 reports [2024-12-24 02:36:28,168] multiqc [DEBUG ] No samples found: pycoqc [2024-12-24 02:36:28,173] multiqc [DEBUG ] No samples found: minionqc [2024-12-24 02:36:28,177] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-12-24 02:36:28,182] multiqc [DEBUG ] No samples found: clusterflow [2024-12-24 02:36:28,187] multiqc [DEBUG ] No samples found: bcl2fastq [2024-12-24 02:36:28,192] multiqc [DEBUG ] No samples found: interop [2024-12-24 02:36:28,196] multiqc [DEBUG ] No samples found: ivar [2024-12-24 02:36:28,201] multiqc [DEBUG ] No samples found: flash [2024-12-24 02:36:28,205] multiqc [DEBUG ] No samples found: seqyclean [2024-12-24 02:36:28,205] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-12-24 02:36:28,205] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-12-24 02:36:28,205] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-12-24 02:36:28,205] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-12-24 02:36:28,205] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-12-24 02:36:28,205] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-12-24 02:36:28,205] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-12-24 02:36:28,205] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-12-24 02:36:28,205] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-12-24 02:36:28,205] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-12-24 02:36:28,205] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-12-24 02:36:28,206] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-12-24 02:36:28,206] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-12-24 02:36:28,206] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-12-24 02:36:28,206] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-12-24 02:36:28,206] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-12-24 02:36:28,206] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-12-24 02:36:28,206] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-12-24 02:36:28,206] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-12-24 02:36:28,206] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-12-24 02:36:28,206] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-12-24 02:36:28,206] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-12-24 02:36:28,206] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-12-24 02:36:28,206] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-12-24 02:36:28,206] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-12-24 02:36:28,206] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-12-24 02:36:28,206] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-12-24 02:36:28,206] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-12-24 02:36:28,206] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-12-24 02:36:28,206] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-12-24 02:36:28,213] multiqc [INFO ] Compressing plot data [2024-12-24 02:36:28,308] multiqc [INFO ] Report : multiqc_report.html [2024-12-24 02:36:28,308] multiqc [INFO ] Data : multiqc_data [2024-12-24 02:36:28,308] multiqc [DEBUG ] Moving data file from '/state/partition1/job-55341764/tmpffyxypcf/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/ba/4ac90ab256bd3ebd22e636b549d281/merged/multiqc_data' [2024-12-24 02:36:28,425] multiqc [INFO ] MultiQC complete