[2023-10-17 21:04:53,166] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-10-17 21:04:53,166] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-10-17 21:04:53,167] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-10-17 21:04:53,169] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2023-10-17 21:04:53,169] 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}} [2023-10-17 21:04:53,169] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2023-10-17 21:04:54,197] multiqc [WARNING] MultiQC Version v1.16 now available! [2023-10-17 21:04:54,197] multiqc [INFO ] This is MultiQC v1.9 [2023-10-17 21:04:54,197] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2023-10-17 21:04:54,197] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/e0/5f1ebe2658d0b45c38a36a4127650f/merged [2023-10-17 21:04:54,197] multiqc [INFO ] Template : default [2023-10-17 21:04:54,197] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-10-17 21:04:54,197] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/e0/5f1ebe2658d0b45c38a36a4127650f/merged [2023-10-17 21:04:54,198] 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 [2023-10-17 21:04:54,198] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-38972618/tmpwp2b3cgf [2023-10-17 21:04:54,330] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFFVKDRX3_n01_Donor2_pre_trogo_fastqc.html [2023-10-17 21:04:54,339] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFFVKDRX3_n01_Donor2_pre_trogo_fastqc.html [2023-10-17 21:04:54,430] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize 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multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFFVKDRX3_n02_Donor4_bot_trogo_fastqc.html [2023-10-17 21:04:56,114] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFFVKDRX3_n02_Donor4_bot_trogo_fastqc.html [2023-10-17 21:04:56,214] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFFVKDRX3_n02_Donor4_pre_TCF1_fastqc.html [2023-10-17 21:04:56,225] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFFVKDRX3_n02_Donor4_pre_TCF1_fastqc.html [2023-10-17 21:04:56,331] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFFVKDRX3_n02_Donor4_pre_trogo_fastqc.html [2023-10-17 21:04:56,339] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFFVKDRX3_n02_Donor4_pre_trogo_fastqc.html [2023-10-17 21:04:56,431] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFFVKDRX3_n02_Donor4_top_TCF1_fastqc.html [2023-10-17 21:04:56,437] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFFVKDRX3_n02_Donor4_top_TCF1_fastqc.html [2023-10-17 21:04:56,534] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFFVKDRX3_n02_Donor4_top_trogo_fastqc.html [2023-10-17 21:04:56,541] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFFVKDRX3_n02_Donor4_top_trogo_fastqc.html [2023-10-17 21:04:56,641] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFFVKDRX3_n02_Donor5_bot_TCF1_fastqc.html [2023-10-17 21:04:56,651] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFFVKDRX3_n02_Donor5_bot_TCF1_fastqc.html [2023-10-17 21:04:56,750] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFFVKDRX3_n02_Donor5_bot_trogo_fastqc.html [2023-10-17 21:04:56,758] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFFVKDRX3_n02_Donor5_bot_trogo_fastqc.html [2023-10-17 21:04:56,860] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFFVKDRX3_n02_Donor5_pre_TCF1_fastqc.html [2023-10-17 21:04:56,869] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFFVKDRX3_n02_Donor5_pre_TCF1_fastqc.html [2023-10-17 21:04:56,966] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFFVKDRX3_n02_Donor5_pre_trogo_fastqc.html [2023-10-17 21:04:56,974] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFFVKDRX3_n02_Donor5_pre_trogo_fastqc.html [2023-10-17 21:04:57,091] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFFVKDRX3_n02_Donor5_top_TCF1_fastqc.html [2023-10-17 21:04:57,107] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFFVKDRX3_n02_Donor5_top_TCF1_fastqc.html [2023-10-17 21:04:57,240] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFFVKDRX3_n02_Donor5_top_trogo_fastqc.html [2023-10-17 21:04:57,248] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFFVKDRX3_n02_Donor5_top_trogo_fastqc.html [2023-10-17 21:04:57,350] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFFVKDRX3_n02_undetermined_fastqc.html [2023-10-17 21:04:57,358] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFFVKDRX3_n02_undetermined_fastqc.html [2023-10-17 21:04:57,434] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-10-17 21:04:57,443] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-10-17 21:04:57,444] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-10-17 21:04:57,444] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-10-17 21:04:57,444] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-10-17 21:04:57,444] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-10-17 21:04:57,444] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-10-17 21:04:58,544] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-10-17 21:04:58,547] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-10-17 21:04:58,567] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 14 samples (table) [2023-10-17 21:04:58,569] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-10-17 21:04:58,579] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-10-17 21:04:58,585] multiqc [DEBUG ] No samples found: conpair [2023-10-17 21:04:58,591] multiqc [DEBUG ] No samples found: peddy [2023-10-17 21:04:58,598] multiqc [DEBUG ] No samples found: somalier [2023-10-17 21:04:58,603] multiqc [DEBUG ] No samples found: methylQA [2023-10-17 21:04:58,613] multiqc [DEBUG ] No samples found: mosdepth [2023-10-17 21:04:58,618] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-10-17 21:04:58,622] multiqc [DEBUG ] No samples found: qualimap [2023-10-17 21:04:58,628] multiqc [DEBUG ] No samples found: preseq [2023-10-17 21:04:58,633] multiqc [DEBUG ] No samples found: quast [2023-10-17 21:04:58,639] multiqc [DEBUG ] No samples found: qorts [2023-10-17 21:04:58,644] multiqc [DEBUG ] No samples found: rna_seqc [2023-10-17 21:04:58,650] multiqc [DEBUG ] No samples found: rockhopper [2023-10-17 21:04:58,656] multiqc [DEBUG ] No samples found: rsem [2023-10-17 21:04:58,670] multiqc [DEBUG ] No samples found: rseqc [2023-10-17 21:04:58,675] multiqc [DEBUG ] No samples found: busco [2023-10-17 21:04:58,681] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-10-17 21:04:58,687] multiqc [DEBUG ] No samples found: disambiguate [2023-10-17 21:04:58,692] multiqc [DEBUG ] No samples found: supernova [2023-10-17 21:04:58,709] multiqc [DEBUG ] No samples found: deeptools [2023-10-17 21:04:58,715] multiqc [DEBUG ] No samples found: sargasso [2023-10-17 21:04:58,720] multiqc [DEBUG ] No samples found: verifybamid [2023-10-17 21:04:58,726] multiqc [DEBUG ] No samples found: mirtrace [2023-10-17 21:04:58,732] multiqc [DEBUG ] No samples found: happy [2023-10-17 21:04:58,738] multiqc [DEBUG ] No samples found: mirtop [2023-10-17 21:04:58,747] multiqc [DEBUG ] No samples found: homer [2023-10-17 21:04:58,753] multiqc [DEBUG ] No samples found: macs2 [2023-10-17 21:04:58,758] multiqc [DEBUG ] No samples found: theta2 [2023-10-17 21:04:58,764] multiqc [DEBUG ] No samples found: snpeff [2023-10-17 21:04:58,772] multiqc [DEBUG ] No samples found: gatk [2023-10-17 21:04:58,777] multiqc [DEBUG ] No samples found: htseq [2023-10-17 21:04:58,783] multiqc [DEBUG ] No samples found: bcftools [2023-10-17 21:04:58,788] multiqc [DEBUG ] No samples found: featureCounts [2023-10-17 21:04:58,796] multiqc [DEBUG ] No samples found: fgbio [2023-10-17 21:04:58,812] multiqc [DEBUG ] No samples found: dragen [2023-10-17 21:04:58,819] multiqc [DEBUG ] No samples found: dedup [2023-10-17 21:04:58,825] multiqc [DEBUG ] No samples found: damageprofiler [2023-10-17 21:04:58,859] multiqc [DEBUG ] No samples found: biobambam2 [2023-10-17 21:04:58,866] multiqc [DEBUG ] No samples found: mtnucratio [2023-10-17 21:04:58,868] multiqc [DEBUG ] No samples found: picard [2023-10-17 21:04:58,875] multiqc [DEBUG ] No samples found: prokka [2023-10-17 21:04:58,882] multiqc [DEBUG ] No samples found: samblaster [2023-10-17 21:04:58,896] multiqc [DEBUG ] No samples found: samtools [2023-10-17 21:04:58,902] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-10-17 21:04:58,909] multiqc [DEBUG ] No samples found: bamtools [2023-10-17 21:04:58,916] multiqc [DEBUG ] No samples found: jellyfish [2023-10-17 21:04:58,928] multiqc [DEBUG ] No samples found: vcftools [2023-10-17 21:04:58,935] multiqc [DEBUG ] No samples found: longranger [2023-10-17 21:04:58,941] multiqc [DEBUG ] No samples found: stacks [2023-10-17 21:04:58,948] multiqc [DEBUG ] No samples found: varscan2 [2023-10-17 21:04:58,973] multiqc [DEBUG ] No samples found: bbmap [2023-10-17 21:04:58,980] multiqc [DEBUG ] No samples found: bismark [2023-10-17 21:04:58,987] multiqc [DEBUG ] No samples found: biscuit [2023-10-17 21:04:58,995] multiqc [DEBUG ] No samples found: hicexplorer [2023-10-17 21:04:59,001] multiqc [DEBUG ] No samples found: hicup [2023-10-17 21:04:59,007] multiqc [DEBUG ] No samples found: hicpro [2023-10-17 21:04:59,013] multiqc [DEBUG ] No samples found: salmon [2023-10-17 21:04:59,019] multiqc [DEBUG ] No samples found: kallisto [2023-10-17 21:04:59,026] multiqc [DEBUG ] No samples found: slamdunk [2023-10-17 21:04:59,033] multiqc [DEBUG ] No samples found: star [2023-10-17 21:04:59,038] multiqc [DEBUG ] No samples found: hisat2 [2023-10-17 21:04:59,045] multiqc [DEBUG ] No samples found: tophat [2023-10-17 21:04:59,051] multiqc [DEBUG ] No samples found: bowtie2 [2023-10-17 21:04:59,057] multiqc [DEBUG ] No samples found: bowtie1 [2023-10-17 21:04:59,064] multiqc [DEBUG ] No samples found: snpsplit [2023-10-17 21:04:59,070] multiqc [DEBUG ] No samples found: kat [2023-10-17 21:04:59,076] multiqc [DEBUG ] No samples found: leehom [2023-10-17 21:04:59,082] multiqc [DEBUG ] No samples found: adapterRemoval [2023-10-17 21:04:59,088] multiqc [DEBUG ] No samples found: clipandmerge [2023-10-17 21:04:59,095] multiqc [DEBUG ] No samples found: cutadapt [2023-10-17 21:04:59,101] multiqc [DEBUG ] No samples found: flexbar [2023-10-17 21:04:59,107] multiqc [DEBUG ] No samples found: kaiju [2023-10-17 21:04:59,113] multiqc [DEBUG ] No samples found: kraken [2023-10-17 21:04:59,120] multiqc [DEBUG ] No samples found: malt [2023-10-17 21:04:59,127] multiqc [DEBUG ] No samples found: trimmomatic [2023-10-17 21:04:59,134] multiqc [DEBUG ] No samples found: sickle [2023-10-17 21:04:59,141] multiqc [DEBUG ] No samples found: skewer [2023-10-17 21:04:59,147] multiqc [DEBUG ] No samples found: sortmerna [2023-10-17 21:04:59,153] multiqc [DEBUG ] No samples found: biobloomtools [2023-10-17 21:04:59,160] multiqc [DEBUG ] No samples found: fastq_screen [2023-10-17 21:04:59,176] multiqc [DEBUG ] No samples found: afterqc [2023-10-17 21:04:59,195] multiqc [DEBUG ] No samples found: fastp [2023-10-17 21:05:00,025] multiqc.modules.fastqc.fastqc [INFO ] Found 28 reports [2023-10-17 21:05:00,319] multiqc [DEBUG ] No samples found: pycoqc [2023-10-17 21:05:00,326] multiqc [DEBUG ] No samples found: minionqc [2023-10-17 21:05:00,333] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-10-17 21:05:00,341] multiqc [DEBUG ] No samples found: clusterflow [2023-10-17 21:05:00,351] multiqc [DEBUG ] No samples found: bcl2fastq [2023-10-17 21:05:00,358] multiqc [DEBUG ] No samples found: interop [2023-10-17 21:05:00,365] multiqc [DEBUG ] No samples found: ivar [2023-10-17 21:05:00,371] multiqc [DEBUG ] No samples found: flash [2023-10-17 21:05:00,378] multiqc [DEBUG ] No samples found: seqyclean [2023-10-17 21:05:00,379] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-10-17 21:05:00,379] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-10-17 21:05:00,379] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-10-17 21:05:00,379] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2023-10-17 21:05:00,379] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2023-10-17 21:05:00,379] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2023-10-17 21:05:00,379] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2023-10-17 21:05:00,379] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2023-10-17 21:05:00,379] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2023-10-17 21:05:00,379] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-10-17 21:05:00,379] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-10-17 21:05:00,379] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-10-17 21:05:00,379] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-10-17 21:05:00,379] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-10-17 21:05:00,379] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-10-17 21:05:00,379] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-10-17 21:05:00,379] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-10-17 21:05:00,379] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-10-17 21:05:00,379] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-10-17 21:05:00,379] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-10-17 21:05:00,379] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-10-17 21:05:00,379] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-10-17 21:05:00,379] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-10-17 21:05:00,379] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-10-17 21:05:00,379] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-10-17 21:05:00,379] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-10-17 21:05:00,379] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-10-17 21:05:00,379] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-10-17 21:05:00,380] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-10-17 21:05:00,380] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-10-17 21:05:00,414] multiqc [INFO ] Compressing plot data [2023-10-17 21:05:00,912] multiqc [INFO ] Report : multiqc_report.html [2023-10-17 21:05:00,912] multiqc [INFO ] Data : multiqc_data [2023-10-17 21:05:00,912] multiqc [DEBUG ] Moving data file from '/state/partition1/job-38972618/tmpwp2b3cgf/multiqc_data' to '/vast/gencore/GENEFLOW/work/e0/5f1ebe2658d0b45c38a36a4127650f/merged/multiqc_data' [2023-10-17 21:05:01,144] multiqc [INFO ] MultiQC complete