[2022-12-21 06:43:32,200] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-12-21 06:43:32,201] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-12-21 06:43:32,201] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-12-21 06:43:32,202] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-12-21 06:43:32,202] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-12-21 06:43:32,202] 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-KDH3G/1 [2022-12-21 06:43:32,710] multiqc [WARNING] MultiQC Version v1.13 now available! [2022-12-21 06:43:32,710] multiqc [INFO ] This is MultiQC v1.9 [2022-12-21 06:43:32,710] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/000000000-KDH3G/1 [2022-12-21 06:43:32,710] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/000000000-KDH3G/1 [2022-12-21 06:43:32,710] multiqc [INFO ] Template : default [2022-12-21 06:43:32,710] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-12-21 06:43:32,710] multiqc [INFO ] Searching : /scratch/gencore/logs/html/000000000-KDH3G/1 [2022-12-21 06:43:32,711] 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 [2022-12-21 06:43:32,711] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-28504449/tmp8hq21l7b [2022-12-21 06:43:32,849] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-12-21 06:43:32,851] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-12-21 06:43:32,851] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-12-21 06:43:32,851] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-12-21 06:43:32,851] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-12-21 06:43:32,851] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-12-21 06:43:32,851] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-12-21 06:43:32,881] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-12-21 06:43:34,247] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KDH3G_l01_n01_undetermined_fastqc.html [2022-12-21 06:43:34,249] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KDH3G_l01_n01_undetermined_fastqc.html [2022-12-21 06:43:34,300] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KDH3G_l01_n01_Presort_fastqc.html [2022-12-21 06:43:34,302] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KDH3G_l01_n01_Presort_fastqc.html [2022-12-21 06:43:34,355] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KDH3G_l01_n01_Bot10_fastqc.html [2022-12-21 06:43:34,357] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KDH3G_l01_n01_Bot10_fastqc.html [2022-12-21 06:43:34,409] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KDH3G_l01_n01_Top10_fastqc.html [2022-12-21 06:43:34,411] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KDH3G_l01_n01_Top10_fastqc.html [2022-12-21 06:43:34,792] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-12-21 06:43:34,796] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-12-21 06:43:34,806] multiqc.modules.custom_content.custom_content [INFO ] demux_report-1: Found 4 samples (table) [2022-12-21 06:43:34,808] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-12-21 06:43:34,817] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-12-21 06:43:34,829] multiqc [DEBUG ] No samples found: conpair [2022-12-21 06:43:34,840] multiqc [DEBUG ] No samples found: peddy [2022-12-21 06:43:34,853] multiqc [DEBUG ] No samples found: somalier [2022-12-21 06:43:34,862] multiqc [DEBUG ] No samples found: methylQA [2022-12-21 06:43:34,886] multiqc [DEBUG ] No samples found: mosdepth [2022-12-21 06:43:34,897] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-12-21 06:43:34,903] multiqc [DEBUG ] No samples found: qualimap [2022-12-21 06:43:34,915] multiqc [DEBUG ] No samples found: preseq [2022-12-21 06:43:34,925] multiqc [DEBUG ] No samples found: quast [2022-12-21 06:43:34,941] multiqc [DEBUG ] No samples found: qorts [2022-12-21 06:43:34,955] multiqc [DEBUG ] No samples found: rna_seqc [2022-12-21 06:43:34,970] multiqc [DEBUG ] No samples found: rockhopper [2022-12-21 06:43:34,981] multiqc [DEBUG ] No samples found: rsem [2022-12-21 06:43:35,021] multiqc [DEBUG ] No samples found: rseqc [2022-12-21 06:43:35,029] multiqc [DEBUG ] No samples found: busco [2022-12-21 06:43:35,040] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-12-21 06:43:35,052] multiqc [DEBUG ] No samples found: disambiguate [2022-12-21 06:43:35,069] multiqc [DEBUG ] No samples found: supernova [2022-12-21 06:43:35,110] multiqc [DEBUG ] No samples found: deeptools [2022-12-21 06:43:35,122] multiqc [DEBUG ] No samples found: sargasso [2022-12-21 06:43:35,135] multiqc [DEBUG ] No samples found: verifybamid [2022-12-21 06:43:35,147] multiqc [DEBUG ] No samples found: mirtrace [2022-12-21 06:43:35,155] multiqc [DEBUG ] No samples found: happy [2022-12-21 06:43:35,168] multiqc [DEBUG ] No samples found: mirtop [2022-12-21 06:43:35,185] multiqc [DEBUG ] No samples found: homer [2022-12-21 06:43:35,196] multiqc [DEBUG ] No samples found: macs2 [2022-12-21 06:43:35,208] multiqc [DEBUG ] No samples found: theta2 [2022-12-21 06:43:35,222] multiqc [DEBUG ] No samples found: snpeff [2022-12-21 06:43:35,247] multiqc [DEBUG ] No samples found: gatk [2022-12-21 06:43:35,260] multiqc [DEBUG ] No samples found: htseq [2022-12-21 06:43:35,270] multiqc [DEBUG ] No samples found: bcftools [2022-12-21 06:43:35,285] multiqc [DEBUG ] No samples found: featureCounts [2022-12-21 06:43:35,304] multiqc [DEBUG ] No samples found: fgbio [2022-12-21 06:43:35,343] multiqc [DEBUG ] No samples found: dragen [2022-12-21 06:43:35,358] multiqc [DEBUG ] No samples found: dedup [2022-12-21 06:43:35,371] multiqc [DEBUG ] No samples found: damageprofiler [2022-12-21 06:43:35,445] multiqc [DEBUG ] No samples found: biobambam2 [2022-12-21 06:43:35,458] multiqc [DEBUG ] No samples found: mtnucratio [2022-12-21 06:43:35,460] multiqc [DEBUG ] No samples found: picard [2022-12-21 06:43:35,476] multiqc [DEBUG ] No samples found: prokka [2022-12-21 06:43:35,490] multiqc [DEBUG ] No samples found: samblaster [2022-12-21 06:43:35,506] multiqc [DEBUG ] No samples found: samtools [2022-12-21 06:43:35,517] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-12-21 06:43:35,530] multiqc [DEBUG ] No samples found: bamtools [2022-12-21 06:43:35,542] multiqc [DEBUG ] No samples found: jellyfish [2022-12-21 06:43:35,562] multiqc [DEBUG ] No samples found: vcftools [2022-12-21 06:43:35,574] multiqc [DEBUG ] No samples found: longranger [2022-12-21 06:43:35,586] multiqc [DEBUG ] No samples found: stacks [2022-12-21 06:43:35,599] multiqc [DEBUG ] No samples found: varscan2 [2022-12-21 06:43:35,634] multiqc [DEBUG ] No samples found: bbmap [2022-12-21 06:43:35,645] multiqc [DEBUG ] No samples found: bismark [2022-12-21 06:43:35,654] multiqc [DEBUG ] No samples found: biscuit [2022-12-21 06:43:35,669] multiqc [DEBUG ] No samples found: hicexplorer [2022-12-21 06:43:35,677] multiqc [DEBUG ] No samples found: hicup [2022-12-21 06:43:35,686] multiqc [DEBUG ] No samples found: hicpro [2022-12-21 06:43:35,698] multiqc [DEBUG ] No samples found: salmon [2022-12-21 06:43:35,713] multiqc [DEBUG ] No samples found: kallisto [2022-12-21 06:43:35,730] multiqc [DEBUG ] No samples found: slamdunk [2022-12-21 06:43:35,739] multiqc [DEBUG ] No samples found: star [2022-12-21 06:43:35,751] multiqc [DEBUG ] No samples found: hisat2 [2022-12-21 06:43:35,765] multiqc [DEBUG ] No samples found: tophat [2022-12-21 06:43:35,777] multiqc [DEBUG ] No samples found: bowtie2 [2022-12-21 06:43:35,788] multiqc [DEBUG ] No samples found: bowtie1 [2022-12-21 06:43:35,796] multiqc [DEBUG ] No samples found: snpsplit [2022-12-21 06:43:35,808] multiqc [DEBUG ] No samples found: kat [2022-12-21 06:43:35,818] multiqc [DEBUG ] No samples found: leehom [2022-12-21 06:43:35,833] multiqc [DEBUG ] No samples found: adapterRemoval [2022-12-21 06:43:35,843] multiqc [DEBUG ] No samples found: clipandmerge [2022-12-21 06:43:35,847] multiqc [DEBUG ] No samples found: cutadapt [2022-12-21 06:43:35,857] multiqc [DEBUG ] No samples found: flexbar [2022-12-21 06:43:35,869] multiqc [DEBUG ] No samples found: kaiju [2022-12-21 06:43:35,883] multiqc [DEBUG ] No samples found: kraken [2022-12-21 06:43:35,899] multiqc [DEBUG ] No samples found: malt [2022-12-21 06:43:35,908] multiqc [DEBUG ] No samples found: trimmomatic [2022-12-21 06:43:35,914] multiqc [DEBUG ] No samples found: sickle [2022-12-21 06:43:35,925] multiqc [DEBUG ] No samples found: skewer [2022-12-21 06:43:35,937] multiqc [DEBUG ] No samples found: sortmerna [2022-12-21 06:43:35,948] multiqc [DEBUG ] No samples found: biobloomtools [2022-12-21 06:43:35,957] multiqc [DEBUG ] No samples found: fastq_screen [2022-12-21 06:43:35,968] multiqc [DEBUG ] No samples found: afterqc [2022-12-21 06:43:35,981] multiqc [DEBUG ] No samples found: fastp [2022-12-21 06:43:36,022] multiqc.modules.fastqc.fastqc [INFO ] Found 4 reports [2022-12-21 06:43:36,092] multiqc [DEBUG ] No samples found: pycoqc [2022-12-21 06:43:36,104] multiqc [DEBUG ] No samples found: minionqc [2022-12-21 06:43:36,117] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-12-21 06:43:36,130] multiqc [DEBUG ] No samples found: clusterflow [2022-12-21 06:43:36,144] multiqc [DEBUG ] No samples found: bcl2fastq [2022-12-21 06:43:36,151] multiqc [DEBUG ] No samples found: interop [2022-12-21 06:43:36,161] multiqc [DEBUG ] No samples found: ivar [2022-12-21 06:43:36,175] multiqc [DEBUG ] No samples found: flash [2022-12-21 06:43:36,187] multiqc [DEBUG ] No samples found: seqyclean [2022-12-21 06:43:36,187] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2022-12-21 06:43:36,187] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 1 Demultiplexing Report'. [2022-12-21 06:43:36,187] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2022-12-21 06:43:36,187] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-12-21 06:43:36,187] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-12-21 06:43:36,193] multiqc [INFO ] Compressing plot data [2022-12-21 06:43:36,261] multiqc [INFO ] Report : multiqc_report.html [2022-12-21 06:43:36,261] multiqc [INFO ] Data : multiqc_data [2022-12-21 06:43:36,262] multiqc [DEBUG ] Moving data file from '/state/partition1/job-28504449/tmp8hq21l7b/multiqc_data' to '/scratch/gencore/logs/html/000000000-KDH3G/1/multiqc_data' [2022-12-21 06:43:36,472] multiqc [INFO ] MultiQC complete