[2024-11-16 02:29:00,154] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-11-16 02:29:00,155] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-11-16 02:29:00,155] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-11-16 02:29:00,157] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-11-16 02:29:00,157] 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}} [2024-11-16 02:29:00,157] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-11-16 02:29:00,187] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-11-16 02:29:00,187] multiqc [INFO ] This is MultiQC v1.9 [2024-11-16 02:29:00,187] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-11-16 02:29:00,187] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/21/436322fb7dc5dc4f7b4d04c66c9d57/merged [2024-11-16 02:29:00,187] multiqc [INFO ] Template : default [2024-11-16 02:29:00,187] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-11-16 02:29:00,187] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/21/436322fb7dc5dc4f7b4d04c66c9d57/merged [2024-11-16 02:29:00,188] 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 [2024-11-16 02:29:00,188] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-53633117/tmpq55769dt [2024-11-16 02:29:00,293] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5LN2BGYW_2_fastqc.html [2024-11-16 02:29:00,296] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5LN2BGYW_2_fastqc.html [2024-11-16 02:29:00,346] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5LN2BGYW_1_fastqc.html [2024-11-16 02:29:00,347] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5LN2BGYW_1_fastqc.html [2024-11-16 02:29:00,874] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-11-16 02:29:00,876] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-11-16 02:29:00,880] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-11-16 02:29:00,886] multiqc [DEBUG ] No samples found: conpair [2024-11-16 02:29:00,892] multiqc [DEBUG ] No samples found: peddy [2024-11-16 02:29:00,900] multiqc [DEBUG ] No samples found: somalier [2024-11-16 02:29:00,906] multiqc [DEBUG ] No samples found: methylQA [2024-11-16 02:29:00,916] multiqc [DEBUG ] No samples found: mosdepth [2024-11-16 02:29:00,921] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-11-16 02:29:00,924] multiqc [DEBUG ] No samples found: qualimap [2024-11-16 02:29:00,930] multiqc [DEBUG ] No samples found: preseq [2024-11-16 02:29:00,935] multiqc [DEBUG ] No samples found: quast [2024-11-16 02:29:00,941] multiqc [DEBUG ] No samples found: qorts [2024-11-16 02:29:00,946] multiqc [DEBUG ] No samples found: rna_seqc [2024-11-16 02:29:00,951] multiqc [DEBUG ] No samples found: rockhopper [2024-11-16 02:29:00,957] multiqc [DEBUG ] No samples found: rsem [2024-11-16 02:29:00,970] multiqc [DEBUG ] No samples found: rseqc [2024-11-16 02:29:00,975] multiqc [DEBUG ] No samples found: busco [2024-11-16 02:29:00,981] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-11-16 02:29:00,986] multiqc [DEBUG ] No samples found: disambiguate [2024-11-16 02:29:00,991] multiqc [DEBUG ] No samples found: supernova [2024-11-16 02:29:01,006] multiqc [DEBUG ] No samples found: deeptools [2024-11-16 02:29:01,012] multiqc [DEBUG ] No samples found: sargasso [2024-11-16 02:29:01,017] multiqc [DEBUG ] No samples found: verifybamid [2024-11-16 02:29:01,022] multiqc [DEBUG ] No samples found: mirtrace [2024-11-16 02:29:01,027] multiqc [DEBUG ] No samples found: happy [2024-11-16 02:29:01,032] multiqc [DEBUG ] No samples found: mirtop [2024-11-16 02:29:01,039] multiqc [DEBUG ] No samples found: homer [2024-11-16 02:29:01,044] multiqc [DEBUG ] No samples found: macs2 [2024-11-16 02:29:01,049] multiqc [DEBUG ] No samples found: theta2 [2024-11-16 02:29:01,054] multiqc [DEBUG ] No samples found: snpeff [2024-11-16 02:29:01,062] multiqc [DEBUG ] No samples found: gatk [2024-11-16 02:29:01,067] multiqc [DEBUG ] No samples found: htseq [2024-11-16 02:29:01,073] multiqc [DEBUG ] No samples found: bcftools [2024-11-16 02:29:01,079] multiqc [DEBUG ] No samples found: featureCounts [2024-11-16 02:29:01,086] multiqc [DEBUG ] No samples found: fgbio [2024-11-16 02:29:01,101] multiqc [DEBUG ] No samples found: dragen [2024-11-16 02:29:01,106] multiqc [DEBUG ] No samples found: dedup [2024-11-16 02:29:01,111] multiqc [DEBUG ] No samples found: damageprofiler [2024-11-16 02:29:01,135] multiqc [DEBUG ] No samples found: biobambam2 [2024-11-16 02:29:01,140] multiqc [DEBUG ] No samples found: mtnucratio [2024-11-16 02:29:01,142] multiqc [DEBUG ] No samples found: picard [2024-11-16 02:29:01,147] multiqc [DEBUG ] No samples found: prokka [2024-11-16 02:29:01,152] multiqc [DEBUG ] No samples found: samblaster [2024-11-16 02:29:01,163] multiqc [DEBUG ] No samples found: samtools [2024-11-16 02:29:01,168] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-11-16 02:29:01,174] multiqc [DEBUG ] No samples found: bamtools [2024-11-16 02:29:01,179] multiqc [DEBUG ] No samples found: jellyfish [2024-11-16 02:29:01,189] multiqc [DEBUG ] No samples found: vcftools [2024-11-16 02:29:01,194] multiqc [DEBUG ] No samples found: longranger [2024-11-16 02:29:01,199] multiqc [DEBUG ] No samples found: stacks [2024-11-16 02:29:01,204] multiqc [DEBUG ] No samples found: varscan2 [2024-11-16 02:29:01,220] multiqc [DEBUG ] No samples found: bbmap [2024-11-16 02:29:01,226] multiqc [DEBUG ] No samples found: bismark [2024-11-16 02:29:01,231] multiqc [DEBUG ] No samples found: biscuit [2024-11-16 02:29:01,236] multiqc [DEBUG ] No samples found: hicexplorer [2024-11-16 02:29:01,242] multiqc [DEBUG ] No samples found: hicup [2024-11-16 02:29:01,247] multiqc [DEBUG ] No samples found: hicpro [2024-11-16 02:29:01,251] multiqc [DEBUG ] No samples found: salmon [2024-11-16 02:29:01,256] multiqc [DEBUG ] No samples found: kallisto [2024-11-16 02:29:01,261] multiqc [DEBUG ] No samples found: slamdunk [2024-11-16 02:29:01,266] multiqc [DEBUG ] No samples found: star [2024-11-16 02:29:01,271] multiqc [DEBUG ] No samples found: hisat2 [2024-11-16 02:29:01,276] multiqc [DEBUG ] No samples found: tophat [2024-11-16 02:29:01,282] multiqc [DEBUG ] No samples found: bowtie2 [2024-11-16 02:29:01,287] multiqc [DEBUG ] No samples found: bowtie1 [2024-11-16 02:29:01,293] multiqc [DEBUG ] No samples found: snpsplit [2024-11-16 02:29:01,298] multiqc [DEBUG ] No samples found: kat [2024-11-16 02:29:01,304] multiqc [DEBUG ] No samples found: leehom [2024-11-16 02:29:01,309] multiqc [DEBUG ] No samples found: adapterRemoval [2024-11-16 02:29:01,315] multiqc [DEBUG ] No samples found: clipandmerge [2024-11-16 02:29:01,319] multiqc [DEBUG ] No samples found: cutadapt [2024-11-16 02:29:01,324] multiqc [DEBUG ] No samples found: flexbar [2024-11-16 02:29:01,329] multiqc [DEBUG ] No samples found: kaiju [2024-11-16 02:29:01,334] multiqc [DEBUG ] No samples found: kraken [2024-11-16 02:29:01,339] multiqc [DEBUG ] No samples found: malt [2024-11-16 02:29:01,344] multiqc [DEBUG ] No samples found: trimmomatic [2024-11-16 02:29:01,349] multiqc [DEBUG ] No samples found: sickle [2024-11-16 02:29:01,354] multiqc [DEBUG ] No samples found: skewer [2024-11-16 02:29:01,358] multiqc [DEBUG ] No samples found: sortmerna [2024-11-16 02:29:01,363] multiqc [DEBUG ] No samples found: biobloomtools [2024-11-16 02:29:01,369] multiqc [DEBUG ] No samples found: fastq_screen [2024-11-16 02:29:01,373] multiqc [DEBUG ] No samples found: afterqc [2024-11-16 02:29:01,378] multiqc [DEBUG ] No samples found: fastp [2024-11-16 02:29:01,463] multiqc.modules.fastqc.fastqc [INFO ] Found 2 reports [2024-11-16 02:29:01,515] multiqc [DEBUG ] No samples found: pycoqc [2024-11-16 02:29:01,519] multiqc [DEBUG ] No samples found: minionqc [2024-11-16 02:29:01,524] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-11-16 02:29:01,529] multiqc [DEBUG ] No samples found: clusterflow [2024-11-16 02:29:01,534] multiqc [DEBUG ] No samples found: bcl2fastq [2024-11-16 02:29:01,540] multiqc [DEBUG ] No samples found: interop [2024-11-16 02:29:01,544] multiqc [DEBUG ] No samples found: ivar [2024-11-16 02:29:01,549] multiqc [DEBUG ] No samples found: flash [2024-11-16 02:29:01,554] multiqc [DEBUG ] No samples found: seqyclean [2024-11-16 02:29:01,554] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-11-16 02:29:01,554] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2024-11-16 02:29:01,554] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-11-16 02:29:01,554] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-11-16 02:29:01,554] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found. [2024-11-16 02:29:01,554] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-11-16 02:29:01,554] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-11-16 02:29:01,554] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-11-16 02:29:01,554] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-11-16 02:29:01,554] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-11-16 02:29:01,555] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-11-16 02:29:01,555] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-11-16 02:29:01,555] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-11-16 02:29:01,555] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-11-16 02:29:01,555] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-11-16 02:29:01,555] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-11-16 02:29:01,555] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-11-16 02:29:01,555] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-11-16 02:29:01,555] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-11-16 02:29:01,558] multiqc [INFO ] Compressing plot data [2024-11-16 02:29:01,597] multiqc [INFO ] Report : multiqc_report.html [2024-11-16 02:29:01,597] multiqc [INFO ] Data : multiqc_data [2024-11-16 02:29:01,597] multiqc [DEBUG ] Moving data file from '/state/partition1/job-53633117/tmpq55769dt/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/21/436322fb7dc5dc4f7b4d04c66c9d57/merged/multiqc_data' [2024-11-16 02:29:01,726] multiqc [INFO ] MultiQC complete