[2022-04-29 22:06:04,543] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-04-29 22:06:04,543] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-04-29 22:06:04,543] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-04-29 22:06:04,544] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-04-29 22:06:04,544] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-04-29 22:06:04,544] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HKGTTBGXL/merged [2022-04-29 22:06:05,106] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-04-29 22:06:05,106] multiqc [INFO ] This is MultiQC v1.9 [2022-04-29 22:06:05,106] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HKGTTBGXL/merged [2022-04-29 22:06:05,106] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HKGTTBGXL/merged [2022-04-29 22:06:05,106] multiqc [INFO ] Template : default [2022-04-29 22:06:05,106] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-04-29 22:06:05,106] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HKGTTBGXL/merged [2022-04-29 22:06:05,107] 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 [2022-04-29 22:06:05,107] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-18820033/tmps27hdgqy [2022-04-29 22:06:05,230] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKGTTBGXL_n01_JK110_fastqc.html [2022-04-29 22:06:05,233] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKGTTBGXL_n01_JK110_fastqc.html [2022-04-29 22:06:05,276] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKGTTBGXL_n01_JK104_fastqc.html [2022-04-29 22:06:05,278] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKGTTBGXL_n01_JK104_fastqc.html [2022-04-29 22:06:05,318] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKGTTBGXL_n01_JK113_fastqc.html [2022-04-29 22:06:05,320] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKGTTBGXL_n01_JK113_fastqc.html [2022-04-29 22:06:05,358] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-04-29 22:06:05,360] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-04-29 22:06:05,495] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKGTTBGXL_n01_JK119_fastqc.html [2022-04-29 22:06:05,497] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKGTTBGXL_n01_JK119_fastqc.html [2022-04-29 22:06:05,536] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKGTTBGXL_n01_JK112_fastqc.html [2022-04-29 22:06:05,538] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKGTTBGXL_n01_JK112_fastqc.html [2022-04-29 22:06:05,579] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKGTTBGXL_n01_AKM357_fastqc.html [2022-04-29 22:06:05,581] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKGTTBGXL_n01_AKM357_fastqc.html [2022-04-29 22:06:05,621] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKGTTBGXL_n01_JK116_fastqc.html [2022-04-29 22:06:05,623] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKGTTBGXL_n01_JK116_fastqc.html [2022-04-29 22:06:05,664] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKGTTBGXL_n01_JK106_fastqc.html [2022-04-29 22:06:05,666] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKGTTBGXL_n01_JK106_fastqc.html [2022-04-29 22:06:05,705] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKGTTBGXL_n01_AKM360_fastqc.html [2022-04-29 22:06:05,707] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKGTTBGXL_n01_AKM360_fastqc.html [2022-04-29 22:06:05,746] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKGTTBGXL_n01_JK108_fastqc.html [2022-04-29 22:06:05,748] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKGTTBGXL_n01_JK108_fastqc.html [2022-04-29 22:06:05,788] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKGTTBGXL_n01_JK114_fastqc.html [2022-04-29 22:06:05,790] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKGTTBGXL_n01_JK114_fastqc.html [2022-04-29 22:06:05,831] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKGTTBGXL_n01_JK115_fastqc.html [2022-04-29 22:06:05,833] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKGTTBGXL_n01_JK115_fastqc.html [2022-04-29 22:06:05,872] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKGTTBGXL_n01_JK105_fastqc.html [2022-04-29 22:06:05,874] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKGTTBGXL_n01_JK105_fastqc.html [2022-04-29 22:06:05,916] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKGTTBGXL_n01_JK109_fastqc.html [2022-04-29 22:06:05,918] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKGTTBGXL_n01_JK109_fastqc.html [2022-04-29 22:06:05,957] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKGTTBGXL_n01_AKM361_fastqc.html [2022-04-29 22:06:05,959] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKGTTBGXL_n01_AKM361_fastqc.html [2022-04-29 22:06:05,999] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKGTTBGXL_n01_JK121_fastqc.html [2022-04-29 22:06:06,001] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKGTTBGXL_n01_JK121_fastqc.html [2022-04-29 22:06:06,040] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKGTTBGXL_n01_JK111_fastqc.html [2022-04-29 22:06:06,042] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKGTTBGXL_n01_JK111_fastqc.html [2022-04-29 22:06:06,082] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKGTTBGXL_n01_AKM358_fastqc.html [2022-04-29 22:06:06,084] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKGTTBGXL_n01_AKM358_fastqc.html [2022-04-29 22:06:06,124] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKGTTBGXL_n01_undetermined_fastqc.html [2022-04-29 22:06:06,126] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKGTTBGXL_n01_undetermined_fastqc.html [2022-04-29 22:06:06,166] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKGTTBGXL_n01_JK117_fastqc.html [2022-04-29 22:06:06,168] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKGTTBGXL_n01_JK117_fastqc.html [2022-04-29 22:06:06,209] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKGTTBGXL_n01_AKM359_fastqc.html [2022-04-29 22:06:06,211] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKGTTBGXL_n01_AKM359_fastqc.html [2022-04-29 22:06:06,250] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKGTTBGXL_n01_JK118_fastqc.html [2022-04-29 22:06:06,252] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKGTTBGXL_n01_JK118_fastqc.html [2022-04-29 22:06:06,292] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKGTTBGXL_n01_AKM356_fastqc.html [2022-04-29 22:06:06,294] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKGTTBGXL_n01_AKM356_fastqc.html [2022-04-29 22:06:06,333] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKGTTBGXL_n01_JK107_fastqc.html [2022-04-29 22:06:06,335] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKGTTBGXL_n01_JK107_fastqc.html [2022-04-29 22:06:06,374] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKGTTBGXL_n01_JK120_fastqc.html [2022-04-29 22:06:06,376] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKGTTBGXL_n01_JK120_fastqc.html [2022-04-29 22:06:06,996] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-04-29 22:06:06,998] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-04-29 22:06:07,018] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 25 samples (table) [2022-04-29 22:06:07,020] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-04-29 22:06:07,030] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-04-29 22:06:07,036] multiqc [DEBUG ] No samples found: conpair [2022-04-29 22:06:07,041] multiqc [DEBUG ] No samples found: peddy [2022-04-29 22:06:07,047] multiqc [DEBUG ] No samples found: somalier [2022-04-29 22:06:07,053] multiqc [DEBUG ] No samples found: methylQA [2022-04-29 22:06:07,064] multiqc [DEBUG ] No samples found: mosdepth [2022-04-29 22:06:07,069] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-04-29 22:06:07,073] multiqc [DEBUG ] No samples found: qualimap [2022-04-29 22:06:07,079] multiqc [DEBUG ] No samples found: preseq [2022-04-29 22:06:07,084] multiqc [DEBUG ] No samples found: quast [2022-04-29 22:06:07,090] multiqc [DEBUG ] No samples found: qorts [2022-04-29 22:06:07,096] multiqc [DEBUG ] No samples found: rna_seqc [2022-04-29 22:06:07,101] multiqc [DEBUG ] No samples found: rockhopper [2022-04-29 22:06:07,108] multiqc [DEBUG ] No samples found: rsem [2022-04-29 22:06:07,122] multiqc [DEBUG ] No samples found: rseqc [2022-04-29 22:06:07,128] multiqc [DEBUG ] No samples found: busco [2022-04-29 22:06:07,135] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-04-29 22:06:07,141] multiqc [DEBUG ] No samples found: disambiguate [2022-04-29 22:06:07,147] multiqc [DEBUG ] No samples found: supernova [2022-04-29 22:06:07,163] multiqc [DEBUG ] No samples found: deeptools [2022-04-29 22:06:07,168] multiqc [DEBUG ] No samples found: sargasso [2022-04-29 22:06:07,174] multiqc [DEBUG ] No samples found: verifybamid [2022-04-29 22:06:07,180] multiqc [DEBUG ] No samples found: mirtrace [2022-04-29 22:06:07,185] multiqc [DEBUG ] No samples found: happy [2022-04-29 22:06:07,191] multiqc [DEBUG ] No samples found: mirtop [2022-04-29 22:06:07,198] multiqc [DEBUG ] No samples found: homer [2022-04-29 22:06:07,204] multiqc [DEBUG ] No samples found: macs2 [2022-04-29 22:06:07,209] multiqc [DEBUG ] No samples found: theta2 [2022-04-29 22:06:07,215] multiqc [DEBUG ] No samples found: snpeff [2022-04-29 22:06:07,224] multiqc [DEBUG ] No samples found: gatk [2022-04-29 22:06:07,229] multiqc [DEBUG ] No samples found: htseq [2022-04-29 22:06:07,235] multiqc [DEBUG ] No samples found: bcftools [2022-04-29 22:06:07,240] multiqc [DEBUG ] No samples found: featureCounts [2022-04-29 22:06:07,248] multiqc [DEBUG ] No samples found: fgbio [2022-04-29 22:06:07,264] multiqc [DEBUG ] No samples found: dragen [2022-04-29 22:06:07,270] multiqc [DEBUG ] No samples found: dedup [2022-04-29 22:06:07,275] multiqc [DEBUG ] No samples found: damageprofiler [2022-04-29 22:06:07,300] multiqc [DEBUG ] No samples found: biobambam2 [2022-04-29 22:06:07,305] multiqc [DEBUG ] No samples found: mtnucratio [2022-04-29 22:06:07,308] multiqc [DEBUG ] No samples found: picard [2022-04-29 22:06:07,313] multiqc [DEBUG ] No samples found: prokka [2022-04-29 22:06:07,318] multiqc [DEBUG ] No samples found: samblaster [2022-04-29 22:06:07,329] multiqc [DEBUG ] No samples found: samtools [2022-04-29 22:06:07,335] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-04-29 22:06:07,342] multiqc [DEBUG ] No samples found: bamtools [2022-04-29 22:06:07,347] multiqc [DEBUG ] No samples found: jellyfish [2022-04-29 22:06:07,357] multiqc [DEBUG ] No samples found: vcftools [2022-04-29 22:06:07,363] multiqc [DEBUG ] No samples found: longranger [2022-04-29 22:06:07,369] multiqc [DEBUG ] No samples found: stacks [2022-04-29 22:06:07,374] multiqc [DEBUG ] No samples found: varscan2 [2022-04-29 22:06:07,391] multiqc [DEBUG ] No samples found: bbmap [2022-04-29 22:06:07,397] multiqc [DEBUG ] No samples found: bismark [2022-04-29 22:06:07,402] multiqc [DEBUG ] No samples found: biscuit [2022-04-29 22:06:07,408] multiqc [DEBUG ] No samples found: hicexplorer [2022-04-29 22:06:07,413] multiqc [DEBUG ] No samples found: hicup [2022-04-29 22:06:07,419] multiqc [DEBUG ] No samples found: hicpro [2022-04-29 22:06:07,424] multiqc [DEBUG ] No samples found: salmon [2022-04-29 22:06:07,429] multiqc [DEBUG ] No samples found: kallisto [2022-04-29 22:06:07,435] multiqc [DEBUG ] No samples found: slamdunk [2022-04-29 22:06:07,440] multiqc [DEBUG ] No samples found: star [2022-04-29 22:06:07,445] multiqc [DEBUG ] No samples found: hisat2 [2022-04-29 22:06:07,450] multiqc [DEBUG ] No samples found: tophat [2022-04-29 22:06:07,456] multiqc [DEBUG ] No samples found: bowtie2 [2022-04-29 22:06:07,461] multiqc [DEBUG ] No samples found: bowtie1 [2022-04-29 22:06:07,466] multiqc [DEBUG ] No samples found: snpsplit [2022-04-29 22:06:07,472] multiqc [DEBUG ] No samples found: kat [2022-04-29 22:06:07,477] multiqc [DEBUG ] No samples found: leehom [2022-04-29 22:06:07,483] multiqc [DEBUG ] No samples found: adapterRemoval [2022-04-29 22:06:07,488] multiqc [DEBUG ] No samples found: clipandmerge [2022-04-29 22:06:07,493] multiqc [DEBUG ] No samples found: cutadapt [2022-04-29 22:06:07,498] multiqc [DEBUG ] No samples found: flexbar [2022-04-29 22:06:07,504] multiqc [DEBUG ] No samples found: kaiju [2022-04-29 22:06:07,509] multiqc [DEBUG ] No samples found: kraken [2022-04-29 22:06:07,515] multiqc [DEBUG ] No samples found: malt [2022-04-29 22:06:07,520] multiqc [DEBUG ] No samples found: trimmomatic [2022-04-29 22:06:07,525] multiqc [DEBUG ] No samples found: sickle [2022-04-29 22:06:07,530] multiqc [DEBUG ] No samples found: skewer [2022-04-29 22:06:07,535] multiqc [DEBUG ] No samples found: sortmerna [2022-04-29 22:06:07,541] multiqc [DEBUG ] No samples found: biobloomtools [2022-04-29 22:06:07,546] multiqc [DEBUG ] No samples found: fastq_screen [2022-04-29 22:06:07,551] multiqc [DEBUG ] No samples found: afterqc [2022-04-29 22:06:07,557] multiqc [DEBUG ] No samples found: fastp [2022-04-29 22:06:09,310] multiqc.modules.fastqc.fastqc [INFO ] Found 25 reports [2022-04-29 22:06:09,862] multiqc [DEBUG ] No samples found: pycoqc [2022-04-29 22:06:09,868] multiqc [DEBUG ] No samples found: minionqc [2022-04-29 22:06:09,874] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-04-29 22:06:09,879] multiqc [DEBUG ] No samples found: clusterflow [2022-04-29 22:06:09,885] multiqc [DEBUG ] No samples found: bcl2fastq [2022-04-29 22:06:09,890] multiqc [DEBUG ] No samples found: interop [2022-04-29 22:06:09,896] multiqc [DEBUG ] No samples found: ivar [2022-04-29 22:06:09,902] multiqc [DEBUG ] No samples found: flash [2022-04-29 22:06:09,907] multiqc [DEBUG ] No samples found: seqyclean [2022-04-29 22:06:09,908] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-04-29 22:06:09,908] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-04-29 22:06:09,908] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-04-29 22:06:09,908] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-04-29 22:06:09,938] multiqc [INFO ] Compressing plot data [2022-04-29 22:06:10,422] multiqc [INFO ] Report : multiqc_report.html [2022-04-29 22:06:10,422] multiqc [INFO ] Data : multiqc_data [2022-04-29 22:06:10,422] multiqc [DEBUG ] Moving data file from '/state/partition1/job-18820033/tmps27hdgqy/multiqc_data' to '/scratch/gencore/logs/html/HKGTTBGXL/merged/multiqc_data' [2022-04-29 22:06:10,575] multiqc [INFO ] MultiQC complete