[2023-12-13 22:25:30,878] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-12-13 22:25:30,878] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-12-13 22:25:30,878] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-12-13 22:25:30,881] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2023-12-13 22:25:30,881] 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}} [2023-12-13 22:25:30,881] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2023-12-13 22:25:31,026] multiqc [WARNING] MultiQC Version v1.17 now available! [2023-12-13 22:25:31,026] multiqc [INFO ] This is MultiQC v1.9 [2023-12-13 22:25:31,027] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2023-12-13 22:25:31,027] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/42/a339dcf7f38e240a70328423d0a715/merged [2023-12-13 22:25:31,027] multiqc [INFO ] Template : default [2023-12-13 22:25:31,027] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-12-13 22:25:31,027] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/42/a339dcf7f38e240a70328423d0a715/merged [2023-12-13 22:25:31,027] 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 [2023-12-13 22:25:31,027] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-40830145/tmp0trqap6x [2023-12-13 22:25:31,165] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJWLYBGXV_n01_DO100_fastqc.html [2023-12-13 22:25:31,174] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJWLYBGXV_n01_DO100_fastqc.html [2023-12-13 22:25:31,244] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 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filesize limit: HJWLYBGXV_n01_YZ61_fastqc.html [2023-12-13 22:25:32,877] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJWLYBGXV_n01_YZ61_fastqc.html [2023-12-13 22:25:32,944] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJWLYBGXV_n01_undetermined_fastqc.html [2023-12-13 22:25:32,951] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJWLYBGXV_n01_undetermined_fastqc.html [2023-12-13 22:25:33,013] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-12-13 22:25:33,020] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-12-13 22:25:33,738] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-12-13 22:25:33,740] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-12-13 22:25:33,761] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 25 samples (table) [2023-12-13 22:25:33,763] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-12-13 22:25:33,773] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-12-13 22:25:33,779] multiqc [DEBUG ] No samples found: conpair [2023-12-13 22:25:33,785] multiqc [DEBUG ] No samples found: peddy [2023-12-13 22:25:33,790] multiqc [DEBUG ] No samples found: somalier [2023-12-13 22:25:33,796] multiqc [DEBUG ] No samples found: methylQA [2023-12-13 22:25:33,805] multiqc [DEBUG ] No samples found: mosdepth [2023-12-13 22:25:33,810] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-12-13 22:25:33,814] multiqc [DEBUG ] No samples found: qualimap [2023-12-13 22:25:33,820] multiqc [DEBUG ] No samples found: preseq [2023-12-13 22:25:33,825] multiqc [DEBUG ] No samples found: quast [2023-12-13 22:25:33,831] multiqc [DEBUG ] No samples found: qorts [2023-12-13 22:25:33,836] multiqc [DEBUG ] No samples found: rna_seqc [2023-12-13 22:25:33,842] multiqc [DEBUG ] No samples found: rockhopper [2023-12-13 22:25:33,847] multiqc [DEBUG ] No samples found: rsem [2023-12-13 22:25:33,860] multiqc [DEBUG ] No samples found: rseqc [2023-12-13 22:25:33,865] multiqc [DEBUG ] No samples found: busco [2023-12-13 22:25:33,871] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-12-13 22:25:33,876] multiqc [DEBUG ] No samples found: disambiguate [2023-12-13 22:25:33,882] multiqc [DEBUG ] No samples found: supernova [2023-12-13 22:25:33,906] multiqc [DEBUG ] No samples found: deeptools [2023-12-13 22:25:33,912] multiqc [DEBUG ] No samples found: sargasso [2023-12-13 22:25:33,923] multiqc [DEBUG ] No samples found: verifybamid [2023-12-13 22:25:33,930] multiqc [DEBUG ] No samples found: mirtrace [2023-12-13 22:25:33,936] multiqc [DEBUG ] No samples found: happy [2023-12-13 22:25:33,945] multiqc [DEBUG ] No samples found: mirtop [2023-12-13 22:25:33,958] multiqc [DEBUG ] No samples found: homer [2023-12-13 22:25:33,964] multiqc [DEBUG ] No samples found: macs2 [2023-12-13 22:25:33,969] multiqc [DEBUG ] No samples found: theta2 [2023-12-13 22:25:33,975] multiqc [DEBUG ] No samples found: snpeff [2023-12-13 22:25:33,983] multiqc [DEBUG ] No samples found: gatk [2023-12-13 22:25:33,988] multiqc [DEBUG ] No samples found: htseq [2023-12-13 22:25:33,995] multiqc [DEBUG ] No samples found: bcftools [2023-12-13 22:25:34,001] multiqc [DEBUG ] No samples found: featureCounts [2023-12-13 22:25:34,013] multiqc [DEBUG ] No samples found: fgbio [2023-12-13 22:25:34,028] multiqc [DEBUG ] No samples found: dragen [2023-12-13 22:25:34,033] multiqc [DEBUG ] No samples found: dedup [2023-12-13 22:25:34,039] multiqc [DEBUG ] No samples found: damageprofiler [2023-12-13 22:25:34,066] multiqc [DEBUG ] No samples found: biobambam2 [2023-12-13 22:25:34,072] multiqc [DEBUG ] No samples found: mtnucratio [2023-12-13 22:25:34,075] multiqc [DEBUG ] No samples found: picard [2023-12-13 22:25:34,080] multiqc [DEBUG ] No samples found: prokka [2023-12-13 22:25:34,085] multiqc [DEBUG ] No samples found: samblaster [2023-12-13 22:25:34,095] multiqc [DEBUG ] No samples found: samtools [2023-12-13 22:25:34,101] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-12-13 22:25:34,107] multiqc [DEBUG ] No samples found: bamtools [2023-12-13 22:25:34,112] multiqc [DEBUG ] No samples found: jellyfish [2023-12-13 22:25:34,120] multiqc [DEBUG ] No samples found: vcftools [2023-12-13 22:25:34,126] multiqc [DEBUG ] No samples found: longranger [2023-12-13 22:25:34,131] multiqc [DEBUG ] No samples found: stacks [2023-12-13 22:25:34,137] multiqc [DEBUG ] No samples found: varscan2 [2023-12-13 22:25:34,153] multiqc [DEBUG ] No samples found: bbmap [2023-12-13 22:25:34,158] multiqc [DEBUG ] No samples found: bismark [2023-12-13 22:25:34,165] multiqc [DEBUG ] No samples found: biscuit [2023-12-13 22:25:34,171] multiqc [DEBUG ] No samples found: hicexplorer [2023-12-13 22:25:34,176] multiqc [DEBUG ] No samples found: hicup [2023-12-13 22:25:34,181] multiqc [DEBUG ] No samples found: hicpro [2023-12-13 22:25:34,187] multiqc [DEBUG ] No samples found: salmon [2023-12-13 22:25:34,193] multiqc [DEBUG ] No samples found: kallisto [2023-12-13 22:25:34,198] multiqc [DEBUG ] No samples found: slamdunk [2023-12-13 22:25:34,204] multiqc [DEBUG ] No samples found: star [2023-12-13 22:25:34,210] multiqc [DEBUG ] No samples found: hisat2 [2023-12-13 22:25:34,215] multiqc [DEBUG ] No samples found: tophat [2023-12-13 22:25:34,220] multiqc [DEBUG ] No samples found: bowtie2 [2023-12-13 22:25:34,226] multiqc [DEBUG ] No samples found: bowtie1 [2023-12-13 22:25:34,231] multiqc [DEBUG ] No samples found: snpsplit [2023-12-13 22:25:34,236] multiqc [DEBUG ] No samples found: kat [2023-12-13 22:25:34,241] multiqc [DEBUG ] No samples found: leehom [2023-12-13 22:25:34,247] multiqc [DEBUG ] No samples found: adapterRemoval [2023-12-13 22:25:34,252] multiqc [DEBUG ] No samples found: clipandmerge [2023-12-13 22:25:34,258] multiqc [DEBUG ] No samples found: cutadapt [2023-12-13 22:25:34,263] multiqc [DEBUG ] No samples found: flexbar [2023-12-13 22:25:34,268] multiqc [DEBUG ] No samples found: kaiju [2023-12-13 22:25:34,274] multiqc [DEBUG ] No samples found: kraken [2023-12-13 22:25:34,279] multiqc [DEBUG ] No samples found: malt [2023-12-13 22:25:34,285] multiqc [DEBUG ] No samples found: trimmomatic [2023-12-13 22:25:34,291] multiqc [DEBUG ] No samples found: sickle [2023-12-13 22:25:34,296] multiqc [DEBUG ] No samples found: skewer [2023-12-13 22:25:34,301] multiqc [DEBUG ] No samples found: sortmerna [2023-12-13 22:25:34,306] multiqc [DEBUG ] No samples found: biobloomtools [2023-12-13 22:25:34,312] multiqc [DEBUG ] No samples found: fastq_screen [2023-12-13 22:25:34,317] multiqc [DEBUG ] No samples found: afterqc [2023-12-13 22:25:34,323] multiqc [DEBUG ] No samples found: fastp [2023-12-13 22:25:36,158] multiqc.modules.fastqc.fastqc [INFO ] Found 25 reports [2023-12-13 22:25:36,735] multiqc [DEBUG ] No samples found: pycoqc [2023-12-13 22:25:36,741] multiqc [DEBUG ] No samples found: minionqc [2023-12-13 22:25:36,748] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-12-13 22:25:36,754] multiqc [DEBUG ] No samples found: clusterflow [2023-12-13 22:25:36,760] multiqc [DEBUG ] No samples found: bcl2fastq [2023-12-13 22:25:36,765] multiqc [DEBUG ] No samples found: interop [2023-12-13 22:25:36,771] multiqc [DEBUG ] No samples found: ivar [2023-12-13 22:25:36,776] multiqc [DEBUG ] No samples found: flash [2023-12-13 22:25:36,782] multiqc [DEBUG ] No samples found: seqyclean [2023-12-13 22:25:36,782] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-12-13 22:25:36,782] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-12-13 22:25:36,782] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-12-13 22:25:36,782] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2023-12-13 22:25:36,782] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2023-12-13 22:25:36,782] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2023-12-13 22:25:36,782] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2023-12-13 22:25:36,782] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2023-12-13 22:25:36,782] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2023-12-13 22:25:36,782] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-12-13 22:25:36,782] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-12-13 22:25:36,782] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-12-13 22:25:36,782] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-12-13 22:25:36,782] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-12-13 22:25:36,782] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-12-13 22:25:36,782] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-12-13 22:25:36,782] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-12-13 22:25:36,782] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-12-13 22:25:36,782] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-12-13 22:25:36,782] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-12-13 22:25:36,782] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-12-13 22:25:36,782] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-12-13 22:25:36,782] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-12-13 22:25:36,782] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-12-13 22:25:36,782] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-12-13 22:25:36,782] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-12-13 22:25:36,783] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-12-13 22:25:36,783] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-12-13 22:25:36,783] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-12-13 22:25:36,783] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-12-13 22:25:36,813] multiqc [INFO ] Compressing plot data [2023-12-13 22:25:37,312] multiqc [INFO ] Report : multiqc_report.html [2023-12-13 22:25:37,312] multiqc [INFO ] Data : multiqc_data [2023-12-13 22:25:37,312] multiqc [DEBUG ] Moving data file from '/state/partition1/job-40830145/tmp0trqap6x/multiqc_data' to '/vast/gencore/GENEFLOW/work/42/a339dcf7f38e240a70328423d0a715/merged/multiqc_data' [2023-12-13 22:25:37,501] multiqc [INFO ] MultiQC complete