[2023-09-20 23:53:55,890] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-09-20 23:53:55,890] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-09-20 23:53:55,891] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-09-20 23:53:55,893] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2023-09-20 23:53:55,894] 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}} [2023-09-20 23:53:55,894] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2023-09-20 23:53:56,849] multiqc [WARNING] MultiQC Version v1.15 now available! [2023-09-20 23:53:56,850] multiqc [INFO ] This is MultiQC v1.9 [2023-09-20 23:53:56,850] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2023-09-20 23:53:56,850] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/6b/3570b6bf92aebf6746219ccaae4c4a/merged [2023-09-20 23:53:56,850] multiqc [INFO ] Template : default [2023-09-20 23:53:56,850] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-09-20 23:53:56,850] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/6b/3570b6bf92aebf6746219ccaae4c4a/merged [2023-09-20 23:53:56,850] 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 [2023-09-20 23:53:56,850] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-37936868/tmpz_givwgj [2023-09-20 23:53:57,008] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWLGMBGXT_n01_AtbZIP18_ampCol-B_ae1_fastqc.html [2023-09-20 23:53:57,016] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWLGMBGXT_n01_AtbZIP18_ampCol-B_ae1_fastqc.html [2023-09-20 23:53:57,120] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern 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[DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWLGMBGXT_n01_AtbZIP8_ampCol-B_ae2_fastqc.html [2023-09-20 23:54:05,736] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWLGMBGXT_n01_pIXHALO_ampCol-B_ae1_fastqc.html [2023-09-20 23:54:05,743] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWLGMBGXT_n01_pIXHALO_ampCol-B_ae1_fastqc.html [2023-09-20 23:54:05,807] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWLGMBGXT_n01_pIXHALO_ampCol-B_ae2_fastqc.html [2023-09-20 23:54:05,815] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWLGMBGXT_n01_pIXHALO_ampCol-B_ae2_fastqc.html [2023-09-20 23:54:05,884] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWLGMBGXT_n01_undetermined_fastqc.html [2023-09-20 23:54:05,891] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWLGMBGXT_n01_undetermined_fastqc.html [2023-09-20 23:54:06,585] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-09-20 23:54:06,587] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-09-20 23:54:06,650] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 109 samples (table) [2023-09-20 23:54:06,652] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-09-20 23:54:06,662] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-09-20 23:54:06,668] multiqc [DEBUG ] No samples found: conpair [2023-09-20 23:54:06,674] multiqc [DEBUG ] No samples found: peddy [2023-09-20 23:54:06,681] multiqc [DEBUG ] No samples found: somalier [2023-09-20 23:54:06,687] multiqc [DEBUG ] No samples found: methylQA [2023-09-20 23:54:06,698] multiqc [DEBUG ] No samples found: mosdepth [2023-09-20 23:54:06,703] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-09-20 23:54:06,708] multiqc [DEBUG ] No samples found: qualimap [2023-09-20 23:54:06,714] multiqc [DEBUG ] No samples found: preseq [2023-09-20 23:54:06,720] multiqc [DEBUG ] No samples found: quast [2023-09-20 23:54:06,726] multiqc [DEBUG ] No samples found: qorts [2023-09-20 23:54:06,732] multiqc [DEBUG ] No samples found: rna_seqc [2023-09-20 23:54:06,738] multiqc [DEBUG ] No samples found: rockhopper [2023-09-20 23:54:06,744] multiqc [DEBUG ] No samples found: rsem [2023-09-20 23:54:06,760] multiqc [DEBUG ] No samples found: rseqc [2023-09-20 23:54:06,766] multiqc [DEBUG ] No samples found: busco [2023-09-20 23:54:06,772] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-09-20 23:54:06,778] multiqc [DEBUG ] No samples found: disambiguate [2023-09-20 23:54:06,784] multiqc [DEBUG ] No samples found: supernova [2023-09-20 23:54:06,802] multiqc [DEBUG ] No samples found: deeptools [2023-09-20 23:54:06,808] multiqc [DEBUG ] No samples found: sargasso [2023-09-20 23:54:06,815] multiqc [DEBUG ] No samples found: verifybamid [2023-09-20 23:54:06,821] multiqc [DEBUG ] No samples found: mirtrace [2023-09-20 23:54:06,828] multiqc [DEBUG ] No samples found: happy [2023-09-20 23:54:06,834] multiqc [DEBUG ] No samples found: mirtop [2023-09-20 23:54:06,843] multiqc [DEBUG ] No samples found: homer [2023-09-20 23:54:06,849] multiqc [DEBUG ] No samples found: macs2 [2023-09-20 23:54:06,855] multiqc [DEBUG ] No samples found: theta2 [2023-09-20 23:54:06,862] multiqc [DEBUG ] No samples found: snpeff [2023-09-20 23:54:06,871] multiqc [DEBUG ] No samples found: gatk [2023-09-20 23:54:06,877] multiqc [DEBUG ] No samples found: htseq [2023-09-20 23:54:06,884] multiqc [DEBUG ] No samples found: bcftools [2023-09-20 23:54:06,890] multiqc [DEBUG ] No samples found: featureCounts [2023-09-20 23:54:06,898] multiqc [DEBUG ] No samples found: fgbio [2023-09-20 23:54:06,916] multiqc [DEBUG ] No samples found: dragen [2023-09-20 23:54:06,922] multiqc [DEBUG ] No samples found: dedup [2023-09-20 23:54:06,928] multiqc [DEBUG ] No samples found: damageprofiler [2023-09-20 23:54:06,961] multiqc [DEBUG ] No samples found: biobambam2 [2023-09-20 23:54:06,967] multiqc [DEBUG ] No samples found: mtnucratio [2023-09-20 23:54:06,970] multiqc [DEBUG ] No samples found: picard [2023-09-20 23:54:06,976] multiqc [DEBUG ] No samples found: prokka [2023-09-20 23:54:06,982] multiqc [DEBUG ] No samples found: samblaster [2023-09-20 23:54:06,994] multiqc [DEBUG ] No samples found: samtools [2023-09-20 23:54:07,000] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-09-20 23:54:07,007] multiqc [DEBUG ] No samples found: bamtools [2023-09-20 23:54:07,013] multiqc [DEBUG ] No samples found: jellyfish [2023-09-20 23:54:07,023] multiqc [DEBUG ] No samples found: vcftools [2023-09-20 23:54:07,030] multiqc [DEBUG ] No samples found: longranger [2023-09-20 23:54:07,036] multiqc [DEBUG ] No samples found: stacks [2023-09-20 23:54:07,043] multiqc [DEBUG ] No samples found: varscan2 [2023-09-20 23:54:07,063] multiqc [DEBUG ] No samples found: bbmap [2023-09-20 23:54:07,069] multiqc [DEBUG ] No samples found: bismark [2023-09-20 23:54:07,076] multiqc [DEBUG ] No samples found: biscuit [2023-09-20 23:54:07,083] multiqc [DEBUG ] No samples found: hicexplorer [2023-09-20 23:54:07,089] multiqc [DEBUG ] No samples found: hicup [2023-09-20 23:54:07,095] multiqc [DEBUG ] No samples found: hicpro [2023-09-20 23:54:07,101] multiqc [DEBUG ] No samples found: salmon [2023-09-20 23:54:07,107] multiqc [DEBUG ] No samples found: kallisto [2023-09-20 23:54:07,113] multiqc [DEBUG ] No samples found: slamdunk [2023-09-20 23:54:07,119] multiqc [DEBUG ] No samples found: star [2023-09-20 23:54:07,125] multiqc [DEBUG ] No samples found: hisat2 [2023-09-20 23:54:07,131] multiqc [DEBUG ] No samples found: tophat [2023-09-20 23:54:07,136] multiqc [DEBUG ] No samples found: bowtie2 [2023-09-20 23:54:07,142] multiqc [DEBUG ] No samples found: bowtie1 [2023-09-20 23:54:07,148] multiqc [DEBUG ] No samples found: snpsplit [2023-09-20 23:54:07,154] multiqc [DEBUG ] No samples found: kat [2023-09-20 23:54:07,159] multiqc [DEBUG ] No samples found: leehom [2023-09-20 23:54:07,165] multiqc [DEBUG ] No samples found: adapterRemoval [2023-09-20 23:54:07,171] multiqc [DEBUG ] No samples found: clipandmerge [2023-09-20 23:54:07,176] multiqc [DEBUG ] No samples found: cutadapt [2023-09-20 23:54:07,182] multiqc [DEBUG ] No samples found: flexbar [2023-09-20 23:54:07,187] multiqc [DEBUG ] No samples found: kaiju [2023-09-20 23:54:07,193] multiqc [DEBUG ] No samples found: kraken [2023-09-20 23:54:07,199] multiqc [DEBUG ] No samples found: malt [2023-09-20 23:54:07,206] multiqc [DEBUG ] No samples found: trimmomatic [2023-09-20 23:54:07,212] multiqc [DEBUG ] No samples found: sickle [2023-09-20 23:54:07,218] multiqc [DEBUG ] No samples found: skewer [2023-09-20 23:54:07,223] multiqc [DEBUG ] No samples found: sortmerna [2023-09-20 23:54:07,229] multiqc [DEBUG ] No samples found: biobloomtools [2023-09-20 23:54:07,235] multiqc [DEBUG ] No samples found: fastq_screen [2023-09-20 23:54:07,241] multiqc [DEBUG ] No samples found: afterqc [2023-09-20 23:54:07,248] multiqc [DEBUG ] No samples found: fastp [2023-09-20 23:54:15,228] multiqc.modules.fastqc.fastqc [INFO ] Found 109 reports [2023-09-20 23:54:39,923] multiqc [DEBUG ] No samples found: pycoqc [2023-09-20 23:54:39,929] multiqc [DEBUG ] No samples found: minionqc [2023-09-20 23:54:39,935] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-09-20 23:54:39,941] multiqc [DEBUG ] No samples found: clusterflow [2023-09-20 23:54:39,948] multiqc [DEBUG ] No samples found: bcl2fastq [2023-09-20 23:54:39,954] multiqc [DEBUG ] No samples found: interop [2023-09-20 23:54:39,960] multiqc [DEBUG ] No samples found: ivar [2023-09-20 23:54:39,966] multiqc [DEBUG ] No samples found: flash [2023-09-20 23:54:39,971] multiqc [DEBUG ] No samples found: seqyclean [2023-09-20 23:54:39,971] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-09-20 23:54:39,971] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-09-20 23:54:39,971] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-09-20 23:54:39,971] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2023-09-20 23:54:39,972] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2023-09-20 23:54:39,972] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2023-09-20 23:54:39,972] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2023-09-20 23:54:39,972] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2023-09-20 23:54:39,972] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2023-09-20 23:54:39,972] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-09-20 23:54:39,972] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-09-20 23:54:39,972] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-09-20 23:54:39,972] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-09-20 23:54:39,972] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-09-20 23:54:39,972] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-09-20 23:54:39,972] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-09-20 23:54:39,972] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-09-20 23:54:39,972] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-09-20 23:54:39,972] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-09-20 23:54:39,972] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-09-20 23:54:39,972] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-09-20 23:54:39,972] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-09-20 23:54:39,972] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-09-20 23:54:39,972] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-09-20 23:54:39,972] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-09-20 23:54:39,972] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-09-20 23:54:39,972] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-09-20 23:54:39,972] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-09-20 23:54:39,972] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-09-20 23:54:39,972] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-09-20 23:54:40,097] multiqc [INFO ] Compressing plot data [2023-09-20 23:54:40,159] multiqc [INFO ] Report : multiqc_report.html [2023-09-20 23:54:40,159] multiqc [INFO ] Data : multiqc_data [2023-09-20 23:54:40,159] multiqc [DEBUG ] Moving data file from '/state/partition1/job-37936868/tmpz_givwgj/multiqc_data' to '/vast/gencore/GENEFLOW/work/6b/3570b6bf92aebf6746219ccaae4c4a/merged/multiqc_data' [2023-09-20 23:54:40,456] multiqc [INFO ] MultiQC complete