[2022-11-17 01:15:01,849] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-11-17 01:15:01,849] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-11-17 01:15:01,849] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-11-17 01:15:01,850] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-11-17 01:15:01,851] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-11-17 01:15:01,851] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H3TFCBGXN/merged [2022-11-17 01:15:02,429] multiqc [WARNING] MultiQC Version v1.13 now available! [2022-11-17 01:15:02,429] multiqc [INFO ] This is MultiQC v1.9 [2022-11-17 01:15:02,429] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H3TFCBGXN/merged [2022-11-17 01:15:02,429] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H3TFCBGXN/merged [2022-11-17 01:15:02,429] multiqc [INFO ] Template : default [2022-11-17 01:15:02,429] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-11-17 01:15:02,429] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H3TFCBGXN/merged [2022-11-17 01:15:02,430] 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 [2022-11-17 01:15:02,430] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-27067552/tmparax4sed [2022-11-17 01:15:02,556] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-11-17 01:15:02,559] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-11-17 01:15:02,559] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-11-17 01:15:02,559] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-11-17 01:15:02,559] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-11-17 01:15:02,559] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-11-17 01:15:02,559] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-11-17 01:15:02,597] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-11-17 01:15:04,308] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3TFCBGXN_n02_IR64-1_fastqc.html [2022-11-17 01:15:04,310] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3TFCBGXN_n02_IR64-1_fastqc.html [2022-11-17 01:15:04,354] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3TFCBGXN_n01_undetermined_fastqc.html [2022-11-17 01:15:04,356] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3TFCBGXN_n01_undetermined_fastqc.html [2022-11-17 01:15:04,396] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3TFCBGXN_n01_IR64-1_fastqc.html [2022-11-17 01:15:04,398] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3TFCBGXN_n01_IR64-1_fastqc.html [2022-11-17 01:15:04,437] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3TFCBGXN_n02_undetermined_fastqc.html [2022-11-17 01:15:04,439] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3TFCBGXN_n02_undetermined_fastqc.html [2022-11-17 01:15:04,481] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3TFCBGXN_n01_NPB-4_fastqc.html [2022-11-17 01:15:04,483] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3TFCBGXN_n01_NPB-4_fastqc.html [2022-11-17 01:15:04,527] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3TFCBGXN_n02_NPB-4_fastqc.html [2022-11-17 01:15:04,529] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3TFCBGXN_n02_NPB-4_fastqc.html [2022-11-17 01:15:04,948] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-11-17 01:15:04,950] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-11-17 01:15:04,958] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-11-17 01:15:04,967] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-11-17 01:15:04,969] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 3 samples (table) [2022-11-17 01:15:04,974] multiqc [DEBUG ] No samples found: conpair [2022-11-17 01:15:04,979] multiqc [DEBUG ] No samples found: peddy [2022-11-17 01:15:04,986] multiqc [DEBUG ] No samples found: somalier [2022-11-17 01:15:04,990] multiqc [DEBUG ] No samples found: methylQA [2022-11-17 01:15:04,999] multiqc [DEBUG ] No samples found: mosdepth [2022-11-17 01:15:05,004] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-11-17 01:15:05,007] multiqc [DEBUG ] No samples found: qualimap [2022-11-17 01:15:05,012] multiqc [DEBUG ] No samples found: preseq [2022-11-17 01:15:05,016] multiqc [DEBUG ] No samples found: quast [2022-11-17 01:15:05,021] multiqc [DEBUG ] No samples found: qorts [2022-11-17 01:15:05,026] multiqc [DEBUG ] No samples found: rna_seqc [2022-11-17 01:15:05,030] multiqc [DEBUG ] No samples found: rockhopper [2022-11-17 01:15:05,035] multiqc [DEBUG ] No samples found: rsem [2022-11-17 01:15:05,046] multiqc [DEBUG ] No samples found: rseqc [2022-11-17 01:15:05,050] multiqc [DEBUG ] No samples found: busco [2022-11-17 01:15:05,056] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-11-17 01:15:05,060] multiqc [DEBUG ] No samples found: disambiguate [2022-11-17 01:15:05,066] multiqc [DEBUG ] No samples found: supernova [2022-11-17 01:15:05,082] multiqc [DEBUG ] No samples found: deeptools [2022-11-17 01:15:05,088] multiqc [DEBUG ] No samples found: sargasso [2022-11-17 01:15:05,093] multiqc [DEBUG ] No samples found: verifybamid [2022-11-17 01:15:05,099] multiqc [DEBUG ] No samples found: mirtrace [2022-11-17 01:15:05,104] multiqc [DEBUG ] No samples found: happy [2022-11-17 01:15:05,110] multiqc [DEBUG ] No samples found: mirtop [2022-11-17 01:15:05,117] multiqc [DEBUG ] No samples found: homer [2022-11-17 01:15:05,122] multiqc [DEBUG ] No samples found: macs2 [2022-11-17 01:15:05,127] multiqc [DEBUG ] No samples found: theta2 [2022-11-17 01:15:05,133] multiqc [DEBUG ] No samples found: snpeff [2022-11-17 01:15:05,141] multiqc [DEBUG ] No samples found: gatk [2022-11-17 01:15:05,146] multiqc [DEBUG ] No samples found: htseq [2022-11-17 01:15:05,153] multiqc [DEBUG ] No samples found: bcftools [2022-11-17 01:15:05,158] multiqc [DEBUG ] No samples found: featureCounts [2022-11-17 01:15:05,166] multiqc [DEBUG ] No samples found: fgbio [2022-11-17 01:15:05,184] multiqc [DEBUG ] No samples found: dragen [2022-11-17 01:15:05,189] multiqc [DEBUG ] No samples found: dedup [2022-11-17 01:15:05,195] multiqc [DEBUG ] No samples found: damageprofiler [2022-11-17 01:15:05,223] multiqc [DEBUG ] No samples found: biobambam2 [2022-11-17 01:15:05,228] multiqc [DEBUG ] No samples found: mtnucratio [2022-11-17 01:15:05,231] multiqc [DEBUG ] No samples found: picard [2022-11-17 01:15:05,236] multiqc [DEBUG ] No samples found: prokka [2022-11-17 01:15:05,241] multiqc [DEBUG ] No samples found: samblaster [2022-11-17 01:15:05,252] multiqc [DEBUG ] No samples found: samtools [2022-11-17 01:15:05,258] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-11-17 01:15:05,264] multiqc [DEBUG ] No samples found: bamtools [2022-11-17 01:15:05,269] multiqc [DEBUG ] No samples found: jellyfish [2022-11-17 01:15:05,279] multiqc [DEBUG ] No samples found: vcftools [2022-11-17 01:15:05,284] multiqc [DEBUG ] No samples found: longranger [2022-11-17 01:15:05,290] multiqc [DEBUG ] No samples found: stacks [2022-11-17 01:15:05,295] multiqc [DEBUG ] No samples found: varscan2 [2022-11-17 01:15:05,311] multiqc [DEBUG ] No samples found: bbmap [2022-11-17 01:15:05,317] multiqc [DEBUG ] No samples found: bismark [2022-11-17 01:15:05,323] multiqc [DEBUG ] No samples found: biscuit [2022-11-17 01:15:05,329] multiqc [DEBUG ] No samples found: hicexplorer [2022-11-17 01:15:05,334] multiqc [DEBUG ] No samples found: hicup [2022-11-17 01:15:05,339] multiqc [DEBUG ] No samples found: hicpro [2022-11-17 01:15:05,343] multiqc [DEBUG ] No samples found: salmon [2022-11-17 01:15:05,347] multiqc [DEBUG ] No samples found: kallisto [2022-11-17 01:15:05,352] multiqc [DEBUG ] No samples found: slamdunk [2022-11-17 01:15:05,357] multiqc [DEBUG ] No samples found: star [2022-11-17 01:15:05,361] multiqc [DEBUG ] No samples found: hisat2 [2022-11-17 01:15:05,366] multiqc [DEBUG ] No samples found: tophat [2022-11-17 01:15:05,371] multiqc [DEBUG ] No samples found: bowtie2 [2022-11-17 01:15:05,375] multiqc [DEBUG ] No samples found: bowtie1 [2022-11-17 01:15:05,380] multiqc [DEBUG ] No samples found: snpsplit [2022-11-17 01:15:05,384] multiqc [DEBUG ] No samples found: kat [2022-11-17 01:15:05,388] multiqc [DEBUG ] No samples found: leehom [2022-11-17 01:15:05,393] multiqc [DEBUG ] No samples found: adapterRemoval [2022-11-17 01:15:05,397] multiqc [DEBUG ] No samples found: clipandmerge [2022-11-17 01:15:05,401] multiqc [DEBUG ] No samples found: cutadapt [2022-11-17 01:15:05,405] multiqc [DEBUG ] No samples found: flexbar [2022-11-17 01:15:05,410] multiqc [DEBUG ] No samples found: kaiju [2022-11-17 01:15:05,415] multiqc [DEBUG ] No samples found: kraken [2022-11-17 01:15:05,419] multiqc [DEBUG ] No samples found: malt [2022-11-17 01:15:05,423] multiqc [DEBUG ] No samples found: trimmomatic [2022-11-17 01:15:05,428] multiqc [DEBUG ] No samples found: sickle [2022-11-17 01:15:05,432] multiqc [DEBUG ] No samples found: skewer [2022-11-17 01:15:05,437] multiqc [DEBUG ] No samples found: sortmerna [2022-11-17 01:15:05,441] multiqc [DEBUG ] No samples found: biobloomtools [2022-11-17 01:15:05,445] multiqc [DEBUG ] No samples found: fastq_screen [2022-11-17 01:15:05,450] multiqc [DEBUG ] No samples found: afterqc [2022-11-17 01:15:05,454] multiqc [DEBUG ] No samples found: fastp [2022-11-17 01:15:05,823] multiqc.modules.fastqc.fastqc [INFO ] Found 6 reports [2022-11-17 01:15:05,898] multiqc [DEBUG ] No samples found: pycoqc [2022-11-17 01:15:05,902] multiqc [DEBUG ] No samples found: minionqc [2022-11-17 01:15:05,907] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-11-17 01:15:05,912] multiqc [DEBUG ] No samples found: clusterflow [2022-11-17 01:15:05,917] multiqc [DEBUG ] No samples found: bcl2fastq [2022-11-17 01:15:05,922] multiqc [DEBUG ] No samples found: interop [2022-11-17 01:15:05,926] multiqc [DEBUG ] No samples found: ivar [2022-11-17 01:15:05,931] multiqc [DEBUG ] No samples found: flash [2022-11-17 01:15:05,935] multiqc [DEBUG ] No samples found: seqyclean [2022-11-17 01:15:05,935] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-11-17 01:15:05,935] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-11-17 01:15:05,935] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-11-17 01:15:05,935] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-11-17 01:15:05,943] multiqc [INFO ] Compressing plot data [2022-11-17 01:15:06,056] multiqc [INFO ] Report : multiqc_report.html [2022-11-17 01:15:06,056] multiqc [INFO ] Data : multiqc_data [2022-11-17 01:15:06,056] multiqc [DEBUG ] Moving data file from '/state/partition1/job-27067552/tmparax4sed/multiqc_data' to '/scratch/gencore/logs/html/H3TFCBGXN/merged/multiqc_data' [2022-11-17 01:15:38,168] multiqc [INFO ] MultiQC complete