[2022-05-11 18:03:41,183] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-05-11 18:03:41,183] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-05-11 18:03:41,183] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-05-11 18:03:41,184] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-05-11 18:03:41,184] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-05-11 18:03:41,185] 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-K6GDW/1 [2022-05-11 18:03:41,965] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-05-11 18:03:41,966] multiqc [INFO ] This is MultiQC v1.9 [2022-05-11 18:03:41,966] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/000000000-K6GDW/1 [2022-05-11 18:03:41,966] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/000000000-K6GDW/1 [2022-05-11 18:03:41,966] multiqc [INFO ] Template : default [2022-05-11 18:03:41,966] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-05-11 18:03:41,966] multiqc [INFO ] Searching : /scratch/gencore/logs/html/000000000-K6GDW/1 [2022-05-11 18:03:41,966] 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 [2022-05-11 18:03:41,967] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-19443952/tmpwkeeq0cc [2022-05-11 18:03:42,077] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-05-11 18:03:42,080] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-05-11 18:03:42,080] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-05-11 18:03:42,080] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-05-11 18:03:42,080] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-05-11 18:03:42,080] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-05-11 18:03:42,080] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-05-11 18:03:42,097] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-05-11 18:03:42,838] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-K6GDW_l01_n02_NPB-2_fastqc.html [2022-05-11 18:03:42,840] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-K6GDW_l01_n02_NPB-2_fastqc.html [2022-05-11 18:03:42,883] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-K6GDW_l01_n01_NPB-2_fastqc.html [2022-05-11 18:03:42,885] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-K6GDW_l01_n01_NPB-2_fastqc.html [2022-05-11 18:03:42,928] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-K6GDW_l01_n02_NPB-3_fastqc.html [2022-05-11 18:03:42,930] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-K6GDW_l01_n02_NPB-3_fastqc.html [2022-05-11 18:03:42,972] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-K6GDW_l01_n01_undetermined_fastqc.html [2022-05-11 18:03:42,974] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-K6GDW_l01_n01_undetermined_fastqc.html [2022-05-11 18:03:43,016] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-K6GDW_l01_n02_undetermined_fastqc.html [2022-05-11 18:03:43,018] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-K6GDW_l01_n02_undetermined_fastqc.html [2022-05-11 18:03:43,059] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-K6GDW_l01_n01_NPB-3_fastqc.html [2022-05-11 18:03:43,061] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-K6GDW_l01_n01_NPB-3_fastqc.html [2022-05-11 18:03:43,644] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-05-11 18:03:43,646] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-05-11 18:03:43,656] multiqc.modules.custom_content.custom_content [INFO ] demux_report-1: Found 3 samples (table) [2022-05-11 18:03:43,657] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-05-11 18:03:43,668] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-05-11 18:03:43,674] multiqc [DEBUG ] No samples found: conpair [2022-05-11 18:03:43,682] multiqc [DEBUG ] No samples found: peddy [2022-05-11 18:03:43,688] multiqc [DEBUG ] No samples found: somalier [2022-05-11 18:03:43,693] multiqc [DEBUG ] No samples found: methylQA [2022-05-11 18:03:43,703] multiqc [DEBUG ] No samples found: mosdepth [2022-05-11 18:03:43,709] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-05-11 18:03:43,712] multiqc [DEBUG ] No samples found: qualimap [2022-05-11 18:03:43,719] multiqc [DEBUG ] No samples found: preseq [2022-05-11 18:03:43,724] multiqc [DEBUG ] No samples found: quast [2022-05-11 18:03:43,731] multiqc [DEBUG ] No samples found: qorts [2022-05-11 18:03:43,738] multiqc [DEBUG ] No samples found: rna_seqc [2022-05-11 18:03:43,747] multiqc [DEBUG ] No samples found: rockhopper [2022-05-11 18:03:43,753] multiqc [DEBUG ] No samples found: rsem [2022-05-11 18:03:43,767] multiqc [DEBUG ] No samples found: rseqc [2022-05-11 18:03:43,773] multiqc [DEBUG ] No samples found: busco [2022-05-11 18:03:43,779] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-05-11 18:03:43,784] multiqc [DEBUG ] No samples found: disambiguate [2022-05-11 18:03:43,789] multiqc [DEBUG ] No samples found: supernova [2022-05-11 18:03:43,807] multiqc [DEBUG ] No samples found: deeptools [2022-05-11 18:03:43,813] multiqc [DEBUG ] No samples found: sargasso [2022-05-11 18:03:43,818] multiqc [DEBUG ] No samples found: verifybamid [2022-05-11 18:03:43,822] multiqc [DEBUG ] No samples found: mirtrace [2022-05-11 18:03:43,828] multiqc [DEBUG ] No samples found: happy [2022-05-11 18:03:43,834] multiqc [DEBUG ] No samples found: mirtop [2022-05-11 18:03:43,841] multiqc [DEBUG ] No samples found: homer [2022-05-11 18:03:43,846] multiqc [DEBUG ] No samples found: macs2 [2022-05-11 18:03:43,853] multiqc [DEBUG ] No samples found: theta2 [2022-05-11 18:03:43,860] multiqc [DEBUG ] No samples found: snpeff [2022-05-11 18:03:43,872] multiqc [DEBUG ] No samples found: gatk [2022-05-11 18:03:43,878] multiqc [DEBUG ] No samples found: htseq [2022-05-11 18:03:43,885] multiqc [DEBUG ] No samples found: bcftools [2022-05-11 18:03:43,891] multiqc [DEBUG ] No samples found: featureCounts [2022-05-11 18:03:43,899] multiqc [DEBUG ] No samples found: fgbio [2022-05-11 18:03:43,920] multiqc [DEBUG ] No samples found: dragen [2022-05-11 18:03:43,924] multiqc [DEBUG ] No samples found: dedup [2022-05-11 18:03:43,931] multiqc [DEBUG ] No samples found: damageprofiler [2022-05-11 18:03:43,968] multiqc [DEBUG ] No samples found: biobambam2 [2022-05-11 18:03:43,974] multiqc [DEBUG ] No samples found: mtnucratio [2022-05-11 18:03:43,976] multiqc [DEBUG ] No samples found: picard [2022-05-11 18:03:43,983] multiqc [DEBUG ] No samples found: prokka [2022-05-11 18:03:43,989] multiqc [DEBUG ] No samples found: samblaster [2022-05-11 18:03:44,001] multiqc [DEBUG ] No samples found: samtools [2022-05-11 18:03:44,007] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-05-11 18:03:44,017] multiqc [DEBUG ] No samples found: bamtools [2022-05-11 18:03:44,023] multiqc [DEBUG ] No samples found: jellyfish [2022-05-11 18:03:44,036] multiqc [DEBUG ] No samples found: vcftools [2022-05-11 18:03:44,042] multiqc [DEBUG ] No samples found: longranger [2022-05-11 18:03:44,047] multiqc [DEBUG ] No samples found: stacks [2022-05-11 18:03:44,053] multiqc [DEBUG ] No samples found: varscan2 [2022-05-11 18:03:44,075] multiqc [DEBUG ] No samples found: bbmap [2022-05-11 18:03:44,083] multiqc [DEBUG ] No samples found: bismark [2022-05-11 18:03:44,090] multiqc [DEBUG ] No samples found: biscuit [2022-05-11 18:03:44,096] multiqc [DEBUG ] No samples found: hicexplorer [2022-05-11 18:03:44,102] multiqc [DEBUG ] No samples found: hicup [2022-05-11 18:03:44,107] multiqc [DEBUG ] No samples found: hicpro [2022-05-11 18:03:44,113] multiqc [DEBUG ] No samples found: salmon [2022-05-11 18:03:44,117] multiqc [DEBUG ] No samples found: kallisto [2022-05-11 18:03:44,123] multiqc [DEBUG ] No samples found: slamdunk [2022-05-11 18:03:44,129] multiqc [DEBUG ] No samples found: star [2022-05-11 18:03:44,137] multiqc [DEBUG ] No samples found: hisat2 [2022-05-11 18:03:44,142] multiqc [DEBUG ] No samples found: tophat [2022-05-11 18:03:44,148] multiqc [DEBUG ] No samples found: bowtie2 [2022-05-11 18:03:44,156] multiqc [DEBUG ] No samples found: bowtie1 [2022-05-11 18:03:44,161] multiqc [DEBUG ] No samples found: snpsplit [2022-05-11 18:03:44,165] multiqc [DEBUG ] No samples found: kat [2022-05-11 18:03:44,171] multiqc [DEBUG ] No samples found: leehom [2022-05-11 18:03:44,175] multiqc [DEBUG ] No samples found: adapterRemoval [2022-05-11 18:03:44,182] multiqc [DEBUG ] No samples found: clipandmerge [2022-05-11 18:03:44,188] multiqc [DEBUG ] No samples found: cutadapt [2022-05-11 18:03:44,192] multiqc [DEBUG ] No samples found: flexbar [2022-05-11 18:03:44,198] multiqc [DEBUG ] No samples found: kaiju [2022-05-11 18:03:44,204] multiqc [DEBUG ] No samples found: kraken [2022-05-11 18:03:44,211] multiqc [DEBUG ] No samples found: malt [2022-05-11 18:03:44,218] multiqc [DEBUG ] No samples found: trimmomatic [2022-05-11 18:03:44,226] multiqc [DEBUG ] No samples found: sickle [2022-05-11 18:03:44,232] multiqc [DEBUG ] No samples found: skewer [2022-05-11 18:03:44,237] multiqc [DEBUG ] No samples found: sortmerna [2022-05-11 18:03:44,243] multiqc [DEBUG ] No samples found: biobloomtools [2022-05-11 18:03:44,251] multiqc [DEBUG ] No samples found: fastq_screen [2022-05-11 18:03:44,259] multiqc [DEBUG ] No samples found: afterqc [2022-05-11 18:03:44,265] multiqc [DEBUG ] No samples found: fastp [2022-05-11 18:03:44,307] multiqc.modules.fastqc.fastqc [INFO ] Found 6 reports [2022-05-11 18:03:44,381] multiqc [DEBUG ] No samples found: pycoqc [2022-05-11 18:03:44,388] multiqc [DEBUG ] No samples found: minionqc [2022-05-11 18:03:44,394] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-05-11 18:03:44,401] multiqc [DEBUG ] No samples found: clusterflow [2022-05-11 18:03:44,406] multiqc [DEBUG ] No samples found: bcl2fastq [2022-05-11 18:03:44,414] multiqc [DEBUG ] No samples found: interop [2022-05-11 18:03:44,420] multiqc [DEBUG ] No samples found: ivar [2022-05-11 18:03:44,427] multiqc [DEBUG ] No samples found: flash [2022-05-11 18:03:44,433] multiqc [DEBUG ] No samples found: seqyclean [2022-05-11 18:03:44,433] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2022-05-11 18:03:44,433] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 1 Demultiplexing Report'. [2022-05-11 18:03:44,433] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2022-05-11 18:03:44,433] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-05-11 18:03:44,433] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-05-11 18:03:44,442] multiqc [INFO ] Compressing plot data [2022-05-11 18:03:44,542] multiqc [INFO ] Report : multiqc_report.html [2022-05-11 18:03:44,542] multiqc [INFO ] Data : multiqc_data [2022-05-11 18:03:44,542] multiqc [DEBUG ] Moving data file from '/state/partition1/job-19443952/tmpwkeeq0cc/multiqc_data' to '/scratch/gencore/logs/html/000000000-K6GDW/1/multiqc_data' [2022-05-11 18:03:44,668] multiqc [INFO ] MultiQC complete