[2023-03-16 17:44:04,613] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-03-16 17:44:04,613] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-03-16 17:44:04,613] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-03-16 17:44:04,615] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-03-16 17:44:04,616] 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}} [2023-03-16 17:44:04,616] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HMKJKDRX2/merged [2023-03-16 17:44:05,148] multiqc [WARNING] MultiQC Version v1.14 now available! [2023-03-16 17:44:05,149] multiqc [INFO ] This is MultiQC v1.9 [2023-03-16 17:44:05,149] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HMKJKDRX2/merged [2023-03-16 17:44:05,149] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HMKJKDRX2/merged [2023-03-16 17:44:05,149] multiqc [INFO ] Template : default [2023-03-16 17:44:05,149] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-03-16 17:44:05,149] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HMKJKDRX2/merged [2023-03-16 17:44:05,149] 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 [2023-03-16 17:44:05,149] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-31062550/tmpudyxbxwb [2023-03-16 17:44:05,407] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMKJKDRX2_n01_DO64_A_fastqc.html [2023-03-16 17:44:05,410] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMKJKDRX2_n01_DO64_A_fastqc.html [2023-03-16 17:44:05,453] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMKJKDRX2_n02_JK180_A_fastqc.html [2023-03-16 17:44:05,455] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMKJKDRX2_n02_JK180_A_fastqc.html [2023-03-16 17:44:05,493] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-03-16 17:44:05,495] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-03-16 17:44:05,495] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-03-16 17:44:05,495] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-03-16 17:44:05,495] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-03-16 17:44:05,495] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-03-16 17:44:05,495] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-03-16 17:44:05,567] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-03-16 17:44:08,496] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMKJKDRX2_n01_JK181_A_fastqc.html [2023-03-16 17:44:08,498] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMKJKDRX2_n01_JK181_A_fastqc.html [2023-03-16 17:44:08,537] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMKJKDRX2_n02_JK181_A_fastqc.html [2023-03-16 17:44:08,539] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMKJKDRX2_n02_JK181_A_fastqc.html [2023-03-16 17:44:08,596] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMKJKDRX2_n02_DO64_A_fastqc.html [2023-03-16 17:44:08,598] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMKJKDRX2_n02_DO64_A_fastqc.html [2023-03-16 17:44:08,638] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMKJKDRX2_n01_DO63_A_fastqc.html [2023-03-16 17:44:08,640] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMKJKDRX2_n01_DO63_A_fastqc.html [2023-03-16 17:44:08,681] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMKJKDRX2_n02_DO63_A_fastqc.html [2023-03-16 17:44:08,683] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMKJKDRX2_n02_DO63_A_fastqc.html [2023-03-16 17:44:08,722] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMKJKDRX2_n01_JK180_A_fastqc.html [2023-03-16 17:44:08,724] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMKJKDRX2_n01_JK180_A_fastqc.html [2023-03-16 17:44:08,796] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMKJKDRX2_n01_undetermined_fastqc.html [2023-03-16 17:44:08,797] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMKJKDRX2_n01_undetermined_fastqc.html [2023-03-16 17:44:08,857] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMKJKDRX2_n02_undetermined_fastqc.html [2023-03-16 17:44:08,859] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMKJKDRX2_n02_undetermined_fastqc.html [2023-03-16 17:44:09,746] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-03-16 17:44:09,747] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-03-16 17:44:09,778] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-03-16 17:44:09,781] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 5 samples (table) [2023-03-16 17:44:09,791] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-03-16 17:44:09,860] multiqc [DEBUG ] No samples found: conpair [2023-03-16 17:44:09,926] multiqc [DEBUG ] No samples found: peddy [2023-03-16 17:44:09,981] multiqc [DEBUG ] No samples found: somalier [2023-03-16 17:44:10,045] multiqc [DEBUG ] No samples found: methylQA [2023-03-16 17:44:10,184] multiqc [DEBUG ] No samples found: mosdepth [2023-03-16 17:44:10,233] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-03-16 17:44:10,265] multiqc [DEBUG ] No samples found: qualimap [2023-03-16 17:44:10,298] multiqc [DEBUG ] No samples found: preseq [2023-03-16 17:44:10,348] multiqc [DEBUG ] No samples found: quast [2023-03-16 17:44:10,429] multiqc [DEBUG ] No samples found: qorts [2023-03-16 17:44:10,489] multiqc [DEBUG ] No samples found: rna_seqc [2023-03-16 17:44:10,566] multiqc [DEBUG ] No samples found: rockhopper [2023-03-16 17:44:10,657] multiqc [DEBUG ] No samples found: rsem [2023-03-16 17:44:10,856] multiqc [DEBUG ] No samples found: rseqc [2023-03-16 17:44:10,943] multiqc [DEBUG ] No samples found: busco [2023-03-16 17:44:11,010] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-03-16 17:44:11,028] multiqc [DEBUG ] No samples found: disambiguate [2023-03-16 17:44:11,108] multiqc [DEBUG ] No samples found: supernova [2023-03-16 17:44:11,396] multiqc [DEBUG ] No samples found: deeptools [2023-03-16 17:44:11,475] multiqc [DEBUG ] No samples found: sargasso [2023-03-16 17:44:11,564] multiqc [DEBUG ] No samples found: verifybamid [2023-03-16 17:44:11,636] multiqc [DEBUG ] No samples found: mirtrace [2023-03-16 17:44:11,670] multiqc [DEBUG ] No samples found: happy [2023-03-16 17:44:11,758] multiqc [DEBUG ] No samples found: mirtop [2023-03-16 17:44:11,803] multiqc [DEBUG ] No samples found: homer [2023-03-16 17:44:11,870] multiqc [DEBUG ] No samples found: macs2 [2023-03-16 17:44:11,944] multiqc [DEBUG ] No samples found: theta2 [2023-03-16 17:44:11,993] multiqc [DEBUG ] No samples found: snpeff [2023-03-16 17:44:12,070] multiqc [DEBUG ] No samples found: gatk [2023-03-16 17:44:12,158] multiqc [DEBUG ] No samples found: htseq [2023-03-16 17:44:12,257] multiqc [DEBUG ] No samples found: bcftools [2023-03-16 17:44:12,285] multiqc [DEBUG ] No samples found: featureCounts [2023-03-16 17:44:12,349] multiqc [DEBUG ] No samples found: fgbio [2023-03-16 17:44:12,620] multiqc [DEBUG ] No samples found: dragen [2023-03-16 17:44:12,685] multiqc [DEBUG ] No samples found: dedup [2023-03-16 17:44:12,765] multiqc [DEBUG ] No samples found: damageprofiler [2023-03-16 17:44:13,137] multiqc [DEBUG ] No samples found: biobambam2 [2023-03-16 17:44:13,192] multiqc [DEBUG ] No samples found: mtnucratio [2023-03-16 17:44:13,194] multiqc [DEBUG ] No samples found: picard [2023-03-16 17:44:13,294] multiqc [DEBUG ] No samples found: prokka [2023-03-16 17:44:13,365] multiqc [DEBUG ] No samples found: samblaster [2023-03-16 17:44:13,474] multiqc [DEBUG ] No samples found: samtools [2023-03-16 17:44:13,501] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-03-16 17:44:13,578] multiqc [DEBUG ] No samples found: bamtools [2023-03-16 17:44:13,652] multiqc [DEBUG ] No samples found: jellyfish [2023-03-16 17:44:13,779] multiqc [DEBUG ] No samples found: vcftools [2023-03-16 17:44:13,837] multiqc [DEBUG ] No samples found: longranger [2023-03-16 17:44:13,915] multiqc [DEBUG ] No samples found: stacks [2023-03-16 17:44:13,955] multiqc [DEBUG ] No samples found: varscan2 [2023-03-16 17:44:14,234] multiqc [DEBUG ] No samples found: bbmap [2023-03-16 17:44:14,254] multiqc [DEBUG ] No samples found: bismark [2023-03-16 17:44:14,337] multiqc [DEBUG ] No samples found: biscuit [2023-03-16 17:44:14,400] multiqc [DEBUG ] No samples found: hicexplorer [2023-03-16 17:44:14,421] multiqc [DEBUG ] No samples found: hicup [2023-03-16 17:44:14,445] multiqc [DEBUG ] No samples found: hicpro [2023-03-16 17:44:14,499] multiqc [DEBUG ] No samples found: salmon [2023-03-16 17:44:14,527] multiqc [DEBUG ] No samples found: kallisto [2023-03-16 17:44:14,560] multiqc [DEBUG ] No samples found: slamdunk [2023-03-16 17:44:14,611] multiqc [DEBUG ] No samples found: star [2023-03-16 17:44:14,636] multiqc [DEBUG ] No samples found: hisat2 [2023-03-16 17:44:14,725] multiqc [DEBUG ] No samples found: tophat [2023-03-16 17:44:14,803] multiqc [DEBUG ] No samples found: bowtie2 [2023-03-16 17:44:14,848] multiqc [DEBUG ] No samples found: bowtie1 [2023-03-16 17:44:14,906] multiqc [DEBUG ] No samples found: snpsplit [2023-03-16 17:44:14,939] multiqc [DEBUG ] No samples found: kat [2023-03-16 17:44:15,016] multiqc [DEBUG ] No samples found: leehom [2023-03-16 17:44:15,077] multiqc [DEBUG ] No samples found: adapterRemoval [2023-03-16 17:44:15,145] multiqc [DEBUG ] No samples found: clipandmerge [2023-03-16 17:44:15,216] multiqc [DEBUG ] No samples found: cutadapt [2023-03-16 17:44:15,283] multiqc [DEBUG ] No samples found: flexbar [2023-03-16 17:44:15,360] multiqc [DEBUG ] No samples found: kaiju [2023-03-16 17:44:15,416] multiqc [DEBUG ] No samples found: kraken [2023-03-16 17:44:15,459] multiqc [DEBUG ] No samples found: malt [2023-03-16 17:44:15,537] multiqc [DEBUG ] No samples found: trimmomatic [2023-03-16 17:44:15,625] multiqc [DEBUG ] No samples found: sickle [2023-03-16 17:44:15,702] multiqc [DEBUG ] No samples found: skewer [2023-03-16 17:44:15,779] multiqc [DEBUG ] No samples found: sortmerna [2023-03-16 17:44:15,856] multiqc [DEBUG ] No samples found: biobloomtools [2023-03-16 17:44:15,922] multiqc [DEBUG ] No samples found: fastq_screen [2023-03-16 17:44:15,989] multiqc [DEBUG ] No samples found: afterqc [2023-03-16 17:44:16,102] multiqc [DEBUG ] No samples found: fastp [2023-03-16 17:44:16,636] multiqc.modules.fastqc.fastqc [INFO ] Found 10 reports [2023-03-16 17:44:16,892] multiqc [DEBUG ] No samples found: pycoqc [2023-03-16 17:44:16,969] multiqc [DEBUG ] No samples found: minionqc [2023-03-16 17:44:17,072] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-03-16 17:44:17,131] multiqc [DEBUG ] No samples found: clusterflow [2023-03-16 17:44:17,217] multiqc [DEBUG ] No samples found: bcl2fastq [2023-03-16 17:44:17,295] multiqc [DEBUG ] No samples found: interop [2023-03-16 17:44:17,362] multiqc [DEBUG ] No samples found: ivar [2023-03-16 17:44:17,372] multiqc [DEBUG ] No samples found: flash [2023-03-16 17:44:17,472] multiqc [DEBUG ] No samples found: seqyclean [2023-03-16 17:44:17,472] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-03-16 17:44:17,472] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-03-16 17:44:17,472] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-03-16 17:44:17,472] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2023-03-16 17:44:17,472] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2023-03-16 17:44:17,472] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2023-03-16 17:44:17,472] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2023-03-16 17:44:17,472] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2023-03-16 17:44:17,472] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2023-03-16 17:44:17,472] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-03-16 17:44:17,472] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-03-16 17:44:17,472] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-03-16 17:44:17,472] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-03-16 17:44:17,472] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-03-16 17:44:17,472] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-03-16 17:44:17,472] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-03-16 17:44:17,473] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-03-16 17:44:17,473] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-03-16 17:44:17,473] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-03-16 17:44:17,473] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-03-16 17:44:17,473] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-03-16 17:44:17,473] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-03-16 17:44:17,473] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-03-16 17:44:17,473] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-03-16 17:44:17,473] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-03-16 17:44:17,473] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-03-16 17:44:17,473] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-03-16 17:44:17,473] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-03-16 17:44:17,473] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-03-16 17:44:17,473] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-03-16 17:44:17,485] multiqc [INFO ] Compressing plot data [2023-03-16 17:44:17,666] multiqc [INFO ] Report : multiqc_report.html [2023-03-16 17:44:17,666] multiqc [INFO ] Data : multiqc_data [2023-03-16 17:44:17,666] multiqc [DEBUG ] Moving data file from '/state/partition1/job-31062550/tmpudyxbxwb/multiqc_data' to '/scratch/gencore/logs/html/HMKJKDRX2/merged/multiqc_data' [2023-03-16 17:44:18,411] multiqc [INFO ] MultiQC complete