[2024-01-16 20:13:26,532] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-01-16 20:13:26,532] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-01-16 20:13:26,532] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-01-16 20:13:26,535] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2024-01-16 20:13:26,535] 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}} [2024-01-16 20:13:26,535] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HT2VYDRX3/merged [2024-01-16 20:13:26,687] multiqc [WARNING] MultiQC Version v1.19 now available! [2024-01-16 20:13:26,687] multiqc [INFO ] This is MultiQC v1.9 [2024-01-16 20:13:26,687] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HT2VYDRX3/merged [2024-01-16 20:13:26,687] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HT2VYDRX3/merged [2024-01-16 20:13:26,687] multiqc [INFO ] Template : default [2024-01-16 20:13:26,687] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-01-16 20:13:26,687] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HT2VYDRX3/merged [2024-01-16 20:13:26,687] 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 [2024-01-16 20:13:26,687] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-41890471/tmpwm_bb_am [2024-01-16 20:13:26,795] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-01-16 20:13:26,797] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-01-16 20:13:26,797] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-01-16 20:13:26,797] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-01-16 20:13:26,798] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-01-16 20:13:26,798] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-01-16 20:13:26,798] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-01-16 20:13:26,821] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-01-16 20:13:27,753] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HT2VYDRX3_n01_JAY_dialout_fastqc.html [2024-01-16 20:13:27,755] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HT2VYDRX3_n01_JAY_dialout_fastqc.html [2024-01-16 20:13:27,799] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HT2VYDRX3_n01_undetermined_fastqc.html [2024-01-16 20:13:27,800] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HT2VYDRX3_n01_undetermined_fastqc.html [2024-01-16 20:13:27,844] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HT2VYDRX3_n02_JAY_dialout_fastqc.html [2024-01-16 20:13:27,846] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HT2VYDRX3_n02_JAY_dialout_fastqc.html [2024-01-16 20:13:27,920] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HT2VYDRX3_n01_JAY_10X_fastqc.html [2024-01-16 20:13:27,922] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HT2VYDRX3_n01_JAY_10X_fastqc.html [2024-01-16 20:13:27,966] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HT2VYDRX3_n02_undetermined_fastqc.html [2024-01-16 20:13:27,968] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HT2VYDRX3_n02_undetermined_fastqc.html [2024-01-16 20:13:28,011] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HT2VYDRX3_n02_JAY_10X_fastqc.html [2024-01-16 20:13:28,013] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HT2VYDRX3_n02_JAY_10X_fastqc.html [2024-01-16 20:13:28,488] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-01-16 20:13:28,489] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-01-16 20:13:28,497] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-01-16 20:13:28,507] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-01-16 20:13:28,509] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 3 samples (table) [2024-01-16 20:13:28,513] multiqc [DEBUG ] No samples found: conpair [2024-01-16 20:13:28,518] multiqc [DEBUG ] No samples found: peddy [2024-01-16 20:13:28,522] multiqc [DEBUG ] No samples found: somalier [2024-01-16 20:13:28,526] multiqc [DEBUG ] No samples found: methylQA [2024-01-16 20:13:28,533] multiqc [DEBUG ] No samples found: mosdepth [2024-01-16 20:13:28,537] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-01-16 20:13:28,541] multiqc [DEBUG ] No samples found: qualimap [2024-01-16 20:13:28,545] multiqc [DEBUG ] No samples found: preseq [2024-01-16 20:13:28,549] multiqc [DEBUG ] No samples found: quast [2024-01-16 20:13:28,554] multiqc [DEBUG ] No samples found: qorts [2024-01-16 20:13:28,558] multiqc [DEBUG ] No samples found: rna_seqc [2024-01-16 20:13:28,562] multiqc [DEBUG ] No samples found: rockhopper [2024-01-16 20:13:28,568] multiqc [DEBUG ] No samples found: rsem [2024-01-16 20:13:28,578] multiqc [DEBUG ] No samples found: rseqc [2024-01-16 20:13:28,582] multiqc [DEBUG ] No samples found: busco [2024-01-16 20:13:28,586] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-01-16 20:13:28,590] multiqc [DEBUG ] No samples found: disambiguate [2024-01-16 20:13:28,594] multiqc [DEBUG ] No samples found: supernova [2024-01-16 20:13:28,606] multiqc [DEBUG ] No samples found: deeptools [2024-01-16 20:13:28,610] multiqc [DEBUG ] No samples found: sargasso [2024-01-16 20:13:28,614] multiqc [DEBUG ] No samples found: verifybamid [2024-01-16 20:13:28,618] multiqc [DEBUG ] No samples found: mirtrace [2024-01-16 20:13:28,622] multiqc [DEBUG ] No samples found: happy [2024-01-16 20:13:28,627] multiqc [DEBUG ] No samples found: mirtop [2024-01-16 20:13:28,633] multiqc [DEBUG ] No samples found: homer [2024-01-16 20:13:28,637] multiqc [DEBUG ] No samples found: macs2 [2024-01-16 20:13:28,641] multiqc [DEBUG ] No samples found: theta2 [2024-01-16 20:13:28,645] multiqc [DEBUG ] No samples found: snpeff [2024-01-16 20:13:28,651] multiqc [DEBUG ] No samples found: gatk [2024-01-16 20:13:28,655] multiqc [DEBUG ] No samples found: htseq [2024-01-16 20:13:28,661] multiqc [DEBUG ] No samples found: bcftools [2024-01-16 20:13:28,665] multiqc [DEBUG ] No samples found: featureCounts [2024-01-16 20:13:28,670] multiqc [DEBUG ] No samples found: fgbio [2024-01-16 20:13:28,680] multiqc [DEBUG ] No samples found: dragen [2024-01-16 20:13:28,685] multiqc [DEBUG ] No samples found: dedup [2024-01-16 20:13:28,689] multiqc [DEBUG ] No samples found: damageprofiler [2024-01-16 20:13:28,708] multiqc [DEBUG ] No samples found: biobambam2 [2024-01-16 20:13:28,712] multiqc [DEBUG ] No samples found: mtnucratio [2024-01-16 20:13:28,714] multiqc [DEBUG ] No samples found: picard [2024-01-16 20:13:28,718] multiqc [DEBUG ] No samples found: prokka [2024-01-16 20:13:28,722] multiqc [DEBUG ] No samples found: samblaster [2024-01-16 20:13:28,729] multiqc [DEBUG ] No samples found: samtools [2024-01-16 20:13:28,734] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-01-16 20:13:28,738] multiqc [DEBUG ] No samples found: bamtools [2024-01-16 20:13:28,743] multiqc [DEBUG ] No samples found: jellyfish [2024-01-16 20:13:28,749] multiqc [DEBUG ] No samples found: vcftools [2024-01-16 20:13:28,753] multiqc [DEBUG ] No samples found: longranger [2024-01-16 20:13:28,757] multiqc [DEBUG ] No samples found: stacks [2024-01-16 20:13:28,761] multiqc [DEBUG ] No samples found: varscan2 [2024-01-16 20:13:28,773] multiqc [DEBUG ] No samples found: bbmap [2024-01-16 20:13:28,779] multiqc [DEBUG ] No samples found: bismark [2024-01-16 20:13:28,783] multiqc [DEBUG ] No samples found: biscuit [2024-01-16 20:13:28,787] multiqc [DEBUG ] No samples found: hicexplorer [2024-01-16 20:13:28,791] multiqc [DEBUG ] No samples found: hicup [2024-01-16 20:13:28,796] multiqc [DEBUG ] No samples found: hicpro [2024-01-16 20:13:28,799] multiqc [DEBUG ] No samples found: salmon [2024-01-16 20:13:28,803] multiqc [DEBUG ] No samples found: kallisto [2024-01-16 20:13:28,808] multiqc [DEBUG ] No samples found: slamdunk [2024-01-16 20:13:28,812] multiqc [DEBUG ] No samples found: star [2024-01-16 20:13:28,816] multiqc [DEBUG ] No samples found: hisat2 [2024-01-16 20:13:28,820] multiqc [DEBUG ] No samples found: tophat [2024-01-16 20:13:28,824] multiqc [DEBUG ] No samples found: bowtie2 [2024-01-16 20:13:28,828] multiqc [DEBUG ] No samples found: bowtie1 [2024-01-16 20:13:28,832] multiqc [DEBUG ] No samples found: snpsplit [2024-01-16 20:13:28,836] multiqc [DEBUG ] No samples found: kat [2024-01-16 20:13:28,840] multiqc [DEBUG ] No samples found: leehom [2024-01-16 20:13:28,844] multiqc [DEBUG ] No samples found: adapterRemoval [2024-01-16 20:13:28,848] multiqc [DEBUG ] No samples found: clipandmerge [2024-01-16 20:13:28,852] multiqc [DEBUG ] No samples found: cutadapt [2024-01-16 20:13:28,856] multiqc [DEBUG ] No samples found: flexbar [2024-01-16 20:13:28,860] multiqc [DEBUG ] No samples found: kaiju [2024-01-16 20:13:28,864] multiqc [DEBUG ] No samples found: kraken [2024-01-16 20:13:28,869] multiqc [DEBUG ] No samples found: malt [2024-01-16 20:13:28,873] multiqc [DEBUG ] No samples found: trimmomatic [2024-01-16 20:13:28,877] multiqc [DEBUG ] No samples found: sickle [2024-01-16 20:13:28,881] multiqc [DEBUG ] No samples found: skewer [2024-01-16 20:13:28,885] multiqc [DEBUG ] No samples found: sortmerna [2024-01-16 20:13:28,889] multiqc [DEBUG ] No samples found: biobloomtools [2024-01-16 20:13:28,893] multiqc [DEBUG ] No samples found: fastq_screen [2024-01-16 20:13:28,897] multiqc [DEBUG ] No samples found: afterqc [2024-01-16 20:13:28,901] multiqc [DEBUG ] No samples found: fastp [2024-01-16 20:13:29,041] multiqc.modules.fastqc.fastqc [INFO ] Found 6 reports [2024-01-16 20:13:29,107] multiqc [DEBUG ] No samples found: pycoqc [2024-01-16 20:13:29,111] multiqc [DEBUG ] No samples found: minionqc [2024-01-16 20:13:29,116] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-01-16 20:13:29,120] multiqc [DEBUG ] No samples found: clusterflow [2024-01-16 20:13:29,124] multiqc [DEBUG ] No samples found: bcl2fastq [2024-01-16 20:13:29,128] multiqc [DEBUG ] No samples found: interop [2024-01-16 20:13:29,132] multiqc [DEBUG ] No samples found: ivar [2024-01-16 20:13:29,137] multiqc [DEBUG ] No samples found: flash [2024-01-16 20:13:29,141] multiqc [DEBUG ] No samples found: seqyclean [2024-01-16 20:13:29,141] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-01-16 20:13:29,141] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-01-16 20:13:29,141] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-01-16 20:13:29,141] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-01-16 20:13:29,141] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-01-16 20:13:29,141] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-01-16 20:13:29,141] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-01-16 20:13:29,141] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-01-16 20:13:29,141] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-01-16 20:13:29,141] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-01-16 20:13:29,141] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-01-16 20:13:29,141] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-01-16 20:13:29,141] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-01-16 20:13:29,141] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-01-16 20:13:29,141] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-01-16 20:13:29,141] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-01-16 20:13:29,141] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-01-16 20:13:29,141] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-01-16 20:13:29,141] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-01-16 20:13:29,141] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-01-16 20:13:29,141] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-01-16 20:13:29,142] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-01-16 20:13:29,142] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-01-16 20:13:29,142] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-01-16 20:13:29,142] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-01-16 20:13:29,142] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-01-16 20:13:29,142] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-01-16 20:13:29,142] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-01-16 20:13:29,142] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-01-16 20:13:29,142] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-01-16 20:13:29,150] multiqc [INFO ] Compressing plot data [2024-01-16 20:13:29,255] multiqc [INFO ] Report : multiqc_report.html [2024-01-16 20:13:29,255] multiqc [INFO ] Data : multiqc_data [2024-01-16 20:13:29,255] multiqc [DEBUG ] Moving data file from '/state/partition1/job-41890471/tmpwm_bb_am/multiqc_data' to '/scratch/gencore/logs/html/HT2VYDRX3/merged/multiqc_data' [2024-01-16 20:14:33,912] multiqc [INFO ] MultiQC complete