[2024-03-01 02:30:59,012] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-03-01 02:30:59,012] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-03-01 02:30:59,012] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-03-01 02:30:59,015] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-03-01 02:30:59,015] 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}} [2024-03-01 02:30:59,015] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-03-01 02:30:59,396] multiqc [WARNING] MultiQC Version v1.21 now available! [2024-03-01 02:30:59,396] multiqc [INFO ] This is MultiQC v1.9 [2024-03-01 02:30:59,396] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-03-01 02:30:59,396] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/e0/0dc741d99f985db5ecf57ec95e9fb7/merged [2024-03-01 02:30:59,396] multiqc [INFO ] Template : default [2024-03-01 02:30:59,396] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-03-01 02:30:59,396] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/e0/0dc741d99f985db5ecf57ec95e9fb7/merged [2024-03-01 02:30:59,397] 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 [2024-03-01 02:30:59,397] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-43535685/tmptdlqt5en [2024-03-01 02:30:59,533] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HL3KCBGXV_n01_AA82__fastqc.html [2024-03-01 02:30:59,548] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HL3KCBGXV_n01_AA82__fastqc.html [2024-03-01 02:30:59,628] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 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filesize limit: HL3KCBGXV_n01_YZ67__fastqc.html [2024-03-01 02:31:01,260] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HL3KCBGXV_n01_YZ67__fastqc.html [2024-03-01 02:31:01,322] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HL3KCBGXV_n01_undetermined_fastqc.html [2024-03-01 02:31:01,328] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HL3KCBGXV_n01_undetermined_fastqc.html [2024-03-01 02:31:01,391] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-03-01 02:31:01,397] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-03-01 02:31:01,991] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-03-01 02:31:01,993] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-03-01 02:31:02,016] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 25 samples (table) [2024-03-01 02:31:02,018] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-03-01 02:31:02,029] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-03-01 02:31:02,035] multiqc [DEBUG ] No samples found: conpair [2024-03-01 02:31:02,040] multiqc [DEBUG ] No samples found: peddy [2024-03-01 02:31:02,049] multiqc [DEBUG ] No samples found: somalier [2024-03-01 02:31:02,054] multiqc [DEBUG ] No samples found: methylQA [2024-03-01 02:31:02,062] multiqc [DEBUG ] No samples found: mosdepth [2024-03-01 02:31:02,067] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-03-01 02:31:02,071] multiqc [DEBUG ] No samples found: qualimap [2024-03-01 02:31:02,076] multiqc [DEBUG ] No samples found: preseq [2024-03-01 02:31:02,081] multiqc [DEBUG ] No samples found: quast [2024-03-01 02:31:02,086] multiqc [DEBUG ] No samples found: qorts [2024-03-01 02:31:02,091] multiqc [DEBUG ] No samples found: rna_seqc [2024-03-01 02:31:02,096] multiqc [DEBUG ] No samples found: rockhopper [2024-03-01 02:31:02,101] multiqc [DEBUG ] No samples found: rsem [2024-03-01 02:31:02,115] multiqc [DEBUG ] No samples found: rseqc [2024-03-01 02:31:02,120] multiqc [DEBUG ] No samples found: busco [2024-03-01 02:31:02,125] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-03-01 02:31:02,130] multiqc [DEBUG ] No samples found: disambiguate [2024-03-01 02:31:02,135] multiqc [DEBUG ] No samples found: supernova [2024-03-01 02:31:02,150] multiqc [DEBUG ] No samples found: deeptools [2024-03-01 02:31:02,155] multiqc [DEBUG ] No samples found: sargasso [2024-03-01 02:31:02,160] multiqc [DEBUG ] No samples found: verifybamid [2024-03-01 02:31:02,165] multiqc [DEBUG ] No samples found: mirtrace [2024-03-01 02:31:02,170] multiqc [DEBUG ] No samples found: happy [2024-03-01 02:31:02,175] multiqc [DEBUG ] No samples found: mirtop [2024-03-01 02:31:02,182] multiqc [DEBUG ] No samples found: homer [2024-03-01 02:31:02,187] multiqc [DEBUG ] No samples found: macs2 [2024-03-01 02:31:02,193] multiqc [DEBUG ] No samples found: theta2 [2024-03-01 02:31:02,198] multiqc [DEBUG ] No samples found: snpeff [2024-03-01 02:31:02,205] multiqc [DEBUG ] No samples found: gatk [2024-03-01 02:31:02,210] multiqc [DEBUG ] No samples found: htseq [2024-03-01 02:31:02,216] multiqc [DEBUG ] No samples found: bcftools [2024-03-01 02:31:02,221] multiqc [DEBUG ] No samples found: featureCounts [2024-03-01 02:31:02,228] multiqc [DEBUG ] No samples found: fgbio [2024-03-01 02:31:02,244] multiqc [DEBUG ] No samples found: dragen [2024-03-01 02:31:02,249] multiqc [DEBUG ] No samples found: dedup [2024-03-01 02:31:02,254] multiqc [DEBUG ] No samples found: damageprofiler [2024-03-01 02:31:02,279] multiqc [DEBUG ] No samples found: biobambam2 [2024-03-01 02:31:02,285] multiqc [DEBUG ] No samples found: mtnucratio [2024-03-01 02:31:02,288] multiqc [DEBUG ] No samples found: picard [2024-03-01 02:31:02,292] multiqc [DEBUG ] No samples found: prokka [2024-03-01 02:31:02,297] multiqc [DEBUG ] No samples found: samblaster [2024-03-01 02:31:02,309] multiqc [DEBUG ] No samples found: samtools [2024-03-01 02:31:02,315] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-03-01 02:31:02,320] multiqc [DEBUG ] No samples found: bamtools [2024-03-01 02:31:02,325] multiqc [DEBUG ] No samples found: jellyfish [2024-03-01 02:31:02,335] multiqc [DEBUG ] No samples found: vcftools [2024-03-01 02:31:02,340] multiqc [DEBUG ] No samples found: longranger [2024-03-01 02:31:02,345] multiqc [DEBUG ] No samples found: stacks [2024-03-01 02:31:02,350] multiqc [DEBUG ] No samples found: varscan2 [2024-03-01 02:31:02,366] multiqc [DEBUG ] No samples found: bbmap [2024-03-01 02:31:02,372] multiqc [DEBUG ] No samples found: bismark [2024-03-01 02:31:02,378] multiqc [DEBUG ] No samples found: biscuit [2024-03-01 02:31:02,383] multiqc [DEBUG ] No samples found: hicexplorer [2024-03-01 02:31:02,389] multiqc [DEBUG ] No samples found: hicup [2024-03-01 02:31:02,394] multiqc [DEBUG ] No samples found: hicpro [2024-03-01 02:31:02,399] multiqc [DEBUG ] No samples found: salmon [2024-03-01 02:31:02,404] multiqc [DEBUG ] No samples found: kallisto [2024-03-01 02:31:02,409] multiqc [DEBUG ] No samples found: slamdunk [2024-03-01 02:31:02,414] multiqc [DEBUG ] No samples found: star [2024-03-01 02:31:02,419] multiqc [DEBUG ] No samples found: hisat2 [2024-03-01 02:31:02,424] multiqc [DEBUG ] No samples found: tophat [2024-03-01 02:31:02,429] multiqc [DEBUG ] No samples found: bowtie2 [2024-03-01 02:31:02,434] multiqc [DEBUG ] No samples found: bowtie1 [2024-03-01 02:31:02,440] multiqc [DEBUG ] No samples found: snpsplit [2024-03-01 02:31:02,444] multiqc [DEBUG ] No samples found: kat [2024-03-01 02:31:02,449] multiqc [DEBUG ] No samples found: leehom [2024-03-01 02:31:02,455] multiqc [DEBUG ] No samples found: adapterRemoval [2024-03-01 02:31:02,459] multiqc [DEBUG ] No samples found: clipandmerge [2024-03-01 02:31:02,465] multiqc [DEBUG ] No samples found: cutadapt [2024-03-01 02:31:02,469] multiqc [DEBUG ] No samples found: flexbar [2024-03-01 02:31:02,475] multiqc [DEBUG ] No samples found: kaiju [2024-03-01 02:31:02,479] multiqc [DEBUG ] No samples found: kraken [2024-03-01 02:31:02,484] multiqc [DEBUG ] No samples found: malt [2024-03-01 02:31:02,489] multiqc [DEBUG ] No samples found: trimmomatic [2024-03-01 02:31:02,493] multiqc [DEBUG ] No samples found: sickle [2024-03-01 02:31:02,498] multiqc [DEBUG ] No samples found: skewer [2024-03-01 02:31:02,503] multiqc [DEBUG ] No samples found: sortmerna [2024-03-01 02:31:02,508] multiqc [DEBUG ] No samples found: biobloomtools [2024-03-01 02:31:02,513] multiqc [DEBUG ] No samples found: fastq_screen [2024-03-01 02:31:02,517] multiqc [DEBUG ] No samples found: afterqc [2024-03-01 02:31:02,522] multiqc [DEBUG ] No samples found: fastp [2024-03-01 02:31:04,399] multiqc.modules.fastqc.fastqc [INFO ] Found 25 reports [2024-03-01 02:31:05,043] multiqc [DEBUG ] No samples found: pycoqc [2024-03-01 02:31:05,049] multiqc [DEBUG ] No samples found: minionqc [2024-03-01 02:31:05,054] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-03-01 02:31:05,059] multiqc [DEBUG ] No samples found: clusterflow [2024-03-01 02:31:05,065] multiqc [DEBUG ] No samples found: bcl2fastq [2024-03-01 02:31:05,070] multiqc [DEBUG ] No samples found: interop [2024-03-01 02:31:05,075] multiqc [DEBUG ] No samples found: ivar [2024-03-01 02:31:05,080] multiqc [DEBUG ] No samples found: flash [2024-03-01 02:31:05,085] multiqc [DEBUG ] No samples found: seqyclean [2024-03-01 02:31:05,085] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-03-01 02:31:05,085] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-03-01 02:31:05,085] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-03-01 02:31:05,085] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-03-01 02:31:05,085] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-03-01 02:31:05,085] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-03-01 02:31:05,085] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-03-01 02:31:05,085] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-03-01 02:31:05,085] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-03-01 02:31:05,085] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-03-01 02:31:05,085] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-03-01 02:31:05,086] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-03-01 02:31:05,086] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-03-01 02:31:05,086] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-03-01 02:31:05,086] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-03-01 02:31:05,086] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-03-01 02:31:05,086] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-03-01 02:31:05,086] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-03-01 02:31:05,086] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-03-01 02:31:05,086] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-03-01 02:31:05,086] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-03-01 02:31:05,086] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-03-01 02:31:05,086] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-03-01 02:31:05,086] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-03-01 02:31:05,086] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-03-01 02:31:05,086] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-03-01 02:31:05,086] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-03-01 02:31:05,086] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-03-01 02:31:05,086] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-03-01 02:31:05,086] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-03-01 02:31:05,118] multiqc [INFO ] Compressing plot data [2024-03-01 02:31:05,626] multiqc [INFO ] Report : multiqc_report.html [2024-03-01 02:31:05,626] multiqc [INFO ] Data : multiqc_data [2024-03-01 02:31:05,626] multiqc [DEBUG ] Moving data file from '/state/partition1/job-43535685/tmptdlqt5en/multiqc_data' to '/vast/gencore/GENEFLOW/work/e0/0dc741d99f985db5ecf57ec95e9fb7/merged/multiqc_data' [2024-03-01 02:31:05,815] multiqc [INFO ] MultiQC complete