[2021-12-21 03:39:54,751] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-12-21 03:39:54,752] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-12-21 03:39:54,752] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-12-21 03:39:54,753] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-12-21 03:39:54,753] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-12-21 03:39:54,753] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/000000000-JVJ4T/1 [2021-12-21 03:39:56,113] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-12-21 03:39:56,113] multiqc [INFO ] This is MultiQC v1.9 [2021-12-21 03:39:56,113] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/000000000-JVJ4T/1 [2021-12-21 03:39:56,113] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/000000000-JVJ4T/1 [2021-12-21 03:39:56,113] multiqc [INFO ] Template : default [2021-12-21 03:39:56,113] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-12-21 03:39:56,113] multiqc [INFO ] Searching : /scratch/gencore/logs/html/000000000-JVJ4T/1 [2021-12-21 03:39:56,113] 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 [2021-12-21 03:39:56,114] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-13227770/tmpzxvzy01z [2021-12-21 03:39:56,237] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JVJ4T_l01_n01_undetermined_fastqc.html [2021-12-21 03:39:56,240] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JVJ4T_l01_n01_undetermined_fastqc.html [2021-12-21 03:39:56,287] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JVJ4T_l01_n01_14B_fastqc.html [2021-12-21 03:39:56,288] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JVJ4T_l01_n01_14B_fastqc.html [2021-12-21 03:39:56,328] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-12-21 03:39:56,329] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-12-21 03:39:56,329] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-12-21 03:39:56,329] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-12-21 03:39:56,329] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-12-21 03:39:56,329] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-12-21 03:39:56,329] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-12-21 03:39:56,589] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JVJ4T_l01_n01_28B_fastqc.html [2021-12-21 03:39:56,591] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JVJ4T_l01_n01_28B_fastqc.html [2021-12-21 03:39:56,632] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JVJ4T_l01_n02_47_fastqc.html [2021-12-21 03:39:56,634] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JVJ4T_l01_n02_47_fastqc.html [2021-12-21 03:39:56,674] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JVJ4T_l01_n01_40_fastqc.html [2021-12-21 03:39:56,676] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JVJ4T_l01_n01_40_fastqc.html [2021-12-21 03:39:56,717] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JVJ4T_l01_n02_undetermined_fastqc.html [2021-12-21 03:39:56,719] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JVJ4T_l01_n02_undetermined_fastqc.html [2021-12-21 03:39:56,762] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JVJ4T_l01_n01_47_fastqc.html [2021-12-21 03:39:56,764] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JVJ4T_l01_n01_47_fastqc.html [2021-12-21 03:39:56,803] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JVJ4T_l01_n02_14B_fastqc.html [2021-12-21 03:39:56,805] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JVJ4T_l01_n02_14B_fastqc.html [2021-12-21 03:39:56,846] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JVJ4T_l01_n02_28B_fastqc.html [2021-12-21 03:39:56,847] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JVJ4T_l01_n02_28B_fastqc.html [2021-12-21 03:39:56,890] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JVJ4T_l01_n02_46_fastqc.html [2021-12-21 03:39:56,891] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JVJ4T_l01_n02_46_fastqc.html [2021-12-21 03:39:56,931] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JVJ4T_l01_n01_39_fastqc.html [2021-12-21 03:39:56,933] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JVJ4T_l01_n01_39_fastqc.html [2021-12-21 03:39:56,974] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JVJ4T_l01_n02_39_fastqc.html [2021-12-21 03:39:56,976] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JVJ4T_l01_n02_39_fastqc.html [2021-12-21 03:39:57,017] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JVJ4T_l01_n01_46_fastqc.html [2021-12-21 03:39:57,018] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JVJ4T_l01_n01_46_fastqc.html [2021-12-21 03:39:57,057] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JVJ4T_l01_n02_40_fastqc.html [2021-12-21 03:39:57,059] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JVJ4T_l01_n02_40_fastqc.html [2021-12-21 03:39:57,429] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-12-21 03:39:57,431] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-12-21 03:39:57,439] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-12-21 03:39:57,443] multiqc.modules.custom_content.custom_content [INFO ] demux_report-1: Found 7 samples (table) [2021-12-21 03:39:57,453] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-12-21 03:39:57,458] multiqc [DEBUG ] No samples found: conpair [2021-12-21 03:39:57,468] multiqc [DEBUG ] No samples found: peddy [2021-12-21 03:39:57,475] multiqc [DEBUG ] No samples found: somalier [2021-12-21 03:39:57,484] multiqc [DEBUG ] No samples found: methylQA [2021-12-21 03:39:57,495] multiqc [DEBUG ] No samples found: mosdepth [2021-12-21 03:39:57,500] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-12-21 03:39:57,504] multiqc [DEBUG ] No samples found: qualimap [2021-12-21 03:39:57,512] multiqc [DEBUG ] No samples found: preseq [2021-12-21 03:39:57,518] multiqc [DEBUG ] No samples found: quast [2021-12-21 03:39:57,524] multiqc [DEBUG ] No samples found: qorts [2021-12-21 03:39:57,530] multiqc [DEBUG ] No samples found: rna_seqc [2021-12-21 03:39:57,535] multiqc [DEBUG ] No samples found: rockhopper [2021-12-21 03:39:57,540] multiqc [DEBUG ] No samples found: rsem [2021-12-21 03:39:57,554] multiqc [DEBUG ] No samples found: rseqc [2021-12-21 03:39:57,560] multiqc [DEBUG ] No samples found: busco [2021-12-21 03:39:57,566] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-12-21 03:39:57,571] multiqc [DEBUG ] No samples found: disambiguate [2021-12-21 03:39:57,578] multiqc [DEBUG ] No samples found: supernova [2021-12-21 03:39:57,591] multiqc [DEBUG ] No samples found: deeptools [2021-12-21 03:39:57,596] multiqc [DEBUG ] No samples found: sargasso [2021-12-21 03:39:57,602] multiqc [DEBUG ] No samples found: verifybamid [2021-12-21 03:39:57,608] multiqc [DEBUG ] No samples found: mirtrace [2021-12-21 03:39:57,615] multiqc [DEBUG ] No samples found: happy [2021-12-21 03:39:57,621] multiqc [DEBUG ] No samples found: mirtop [2021-12-21 03:39:57,628] multiqc [DEBUG ] No samples found: homer [2021-12-21 03:39:57,634] multiqc [DEBUG ] No samples found: macs2 [2021-12-21 03:39:57,640] multiqc [DEBUG ] No samples found: theta2 [2021-12-21 03:39:57,645] multiqc [DEBUG ] No samples found: snpeff [2021-12-21 03:39:57,655] multiqc [DEBUG ] No samples found: gatk [2021-12-21 03:39:57,660] multiqc [DEBUG ] No samples found: htseq [2021-12-21 03:39:57,666] multiqc [DEBUG ] No samples found: bcftools [2021-12-21 03:39:57,674] multiqc [DEBUG ] No samples found: featureCounts [2021-12-21 03:39:57,681] multiqc [DEBUG ] No samples found: fgbio [2021-12-21 03:39:57,695] multiqc [DEBUG ] No samples found: dragen [2021-12-21 03:39:57,701] multiqc [DEBUG ] No samples found: dedup [2021-12-21 03:39:57,710] multiqc [DEBUG ] No samples found: damageprofiler [2021-12-21 03:39:57,745] multiqc [DEBUG ] No samples found: biobambam2 [2021-12-21 03:39:57,750] multiqc [DEBUG ] No samples found: mtnucratio [2021-12-21 03:39:57,753] multiqc [DEBUG ] No samples found: picard [2021-12-21 03:39:57,758] multiqc [DEBUG ] No samples found: prokka [2021-12-21 03:39:57,764] multiqc [DEBUG ] No samples found: samblaster [2021-12-21 03:39:57,777] multiqc [DEBUG ] No samples found: samtools [2021-12-21 03:39:57,783] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-12-21 03:39:57,788] multiqc [DEBUG ] No samples found: bamtools [2021-12-21 03:39:57,793] multiqc [DEBUG ] No samples found: jellyfish [2021-12-21 03:39:57,801] multiqc [DEBUG ] No samples found: vcftools [2021-12-21 03:39:57,807] multiqc [DEBUG ] No samples found: longranger [2021-12-21 03:39:57,813] multiqc [DEBUG ] No samples found: stacks [2021-12-21 03:39:57,818] multiqc [DEBUG ] No samples found: varscan2 [2021-12-21 03:39:57,834] multiqc [DEBUG ] No samples found: bbmap [2021-12-21 03:39:57,845] multiqc [DEBUG ] No samples found: bismark [2021-12-21 03:39:57,851] multiqc [DEBUG ] No samples found: biscuit [2021-12-21 03:39:57,857] multiqc [DEBUG ] No samples found: hicexplorer [2021-12-21 03:39:57,869] multiqc [DEBUG ] No samples found: hicup [2021-12-21 03:39:57,876] multiqc [DEBUG ] No samples found: hicpro [2021-12-21 03:39:57,881] multiqc [DEBUG ] No samples found: salmon [2021-12-21 03:39:57,887] multiqc [DEBUG ] No samples found: kallisto [2021-12-21 03:39:57,893] multiqc [DEBUG ] No samples found: slamdunk [2021-12-21 03:39:57,898] multiqc [DEBUG ] No samples found: star [2021-12-21 03:39:57,904] multiqc [DEBUG ] No samples found: hisat2 [2021-12-21 03:39:57,909] multiqc [DEBUG ] No samples found: tophat [2021-12-21 03:39:57,915] multiqc [DEBUG ] No samples found: bowtie2 [2021-12-21 03:39:57,920] multiqc [DEBUG ] No samples found: bowtie1 [2021-12-21 03:39:57,925] multiqc [DEBUG ] No samples found: snpsplit [2021-12-21 03:39:57,931] multiqc [DEBUG ] No samples found: kat [2021-12-21 03:39:57,936] multiqc [DEBUG ] No samples found: leehom [2021-12-21 03:39:57,941] multiqc [DEBUG ] No samples found: adapterRemoval [2021-12-21 03:39:57,946] multiqc [DEBUG ] No samples found: clipandmerge [2021-12-21 03:39:57,951] multiqc [DEBUG ] No samples found: cutadapt [2021-12-21 03:39:57,956] multiqc [DEBUG ] No samples found: flexbar [2021-12-21 03:39:57,962] multiqc [DEBUG ] No samples found: kaiju [2021-12-21 03:39:57,967] multiqc [DEBUG ] No samples found: kraken [2021-12-21 03:39:57,981] multiqc [DEBUG ] No samples found: malt [2021-12-21 03:39:57,988] multiqc [DEBUG ] No samples found: trimmomatic [2021-12-21 03:39:57,993] multiqc [DEBUG ] No samples found: sickle [2021-12-21 03:39:57,998] multiqc [DEBUG ] No samples found: skewer [2021-12-21 03:39:58,003] multiqc [DEBUG ] No samples found: sortmerna [2021-12-21 03:39:58,009] multiqc [DEBUG ] No samples found: biobloomtools [2021-12-21 03:39:58,016] multiqc [DEBUG ] No samples found: fastq_screen [2021-12-21 03:39:58,022] multiqc [DEBUG ] No samples found: afterqc [2021-12-21 03:39:58,028] multiqc [DEBUG ] No samples found: fastp [2021-12-21 03:39:58,153] multiqc.modules.fastqc.fastqc [INFO ] Found 14 reports [2021-12-21 03:39:58,458] multiqc [DEBUG ] No samples found: pycoqc [2021-12-21 03:39:58,463] multiqc [DEBUG ] No samples found: minionqc [2021-12-21 03:39:58,469] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-12-21 03:39:58,475] multiqc [DEBUG ] No samples found: clusterflow [2021-12-21 03:39:58,483] multiqc [DEBUG ] No samples found: bcl2fastq [2021-12-21 03:39:58,490] multiqc [DEBUG ] No samples found: interop [2021-12-21 03:39:58,498] multiqc [DEBUG ] No samples found: ivar [2021-12-21 03:39:58,503] multiqc [DEBUG ] No samples found: flash [2021-12-21 03:39:58,509] multiqc [DEBUG ] No samples found: seqyclean [2021-12-21 03:39:58,509] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2021-12-21 03:39:58,509] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2021-12-21 03:39:58,509] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 1 Demultiplexing Report'. [2021-12-21 03:39:58,509] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-12-21 03:39:58,509] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-12-21 03:39:58,528] multiqc [INFO ] Compressing plot data [2021-12-21 03:39:58,791] multiqc [INFO ] Report : multiqc_report.html [2021-12-21 03:39:58,792] multiqc [INFO ] Data : multiqc_data [2021-12-21 03:39:58,792] multiqc [DEBUG ] Moving data file from '/state/partition1/job-13227770/tmpzxvzy01z/multiqc_data' to '/scratch/gencore/logs/html/000000000-JVJ4T/1/multiqc_data' [2021-12-21 03:39:58,930] multiqc [INFO ] MultiQC complete