[2022-09-28 08:50:33,443] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-09-28 08:50:33,443] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-09-28 08:50:33,443] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-09-28 08:50:33,444] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-09-28 08:50:33,445] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-09-28 08:50:33,445] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HKK55DRX2/merged [2022-09-28 08:50:33,941] multiqc [WARNING] MultiQC Version v1.13 now available! [2022-09-28 08:50:33,941] multiqc [INFO ] This is MultiQC v1.9 [2022-09-28 08:50:33,941] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HKK55DRX2/merged [2022-09-28 08:50:33,941] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HKK55DRX2/merged [2022-09-28 08:50:33,941] multiqc [INFO ] Template : default [2022-09-28 08:50:33,941] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-09-28 08:50:33,941] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HKK55DRX2/merged [2022-09-28 08:50:33,942] 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 [2022-09-28 08:50:33,942] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-25495680/tmpy9jni9qw [2022-09-28 08:50:34,090] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKK55DRX2_n01_CisCeD1_fastqc.html [2022-09-28 08:50:34,093] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKK55DRX2_n01_CisCeD1_fastqc.html [2022-09-28 08:50:34,144] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-09-28 08:50:34,146] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-09-28 08:50:34,275] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKK55DRX2_n01_CisCeT5_fastqc.html [2022-09-28 08:50:34,277] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKK55DRX2_n01_CisCeT5_fastqc.html [2022-09-28 08:50:34,371] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKK55DRX2_n01_CisCeC3_fastqc.html [2022-09-28 08:50:34,373] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKK55DRX2_n01_CisCeC3_fastqc.html [2022-09-28 08:50:34,436] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKK55DRX2_n01_CisCeD4_fastqc.html [2022-09-28 08:50:34,438] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKK55DRX2_n01_CisCeD4_fastqc.html [2022-09-28 08:50:34,521] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKK55DRX2_n01_CisCeT4_fastqc.html [2022-09-28 08:50:34,523] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKK55DRX2_n01_CisCeT4_fastqc.html [2022-09-28 08:50:34,584] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKK55DRX2_n01_CisCeC1_fastqc.html [2022-09-28 08:50:34,586] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKK55DRX2_n01_CisCeC1_fastqc.html [2022-09-28 08:50:34,646] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKK55DRX2_n01_CisCeD5_fastqc.html [2022-09-28 08:50:34,648] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKK55DRX2_n01_CisCeD5_fastqc.html [2022-09-28 08:50:34,709] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKK55DRX2_n01_CisCeD3_fastqc.html [2022-09-28 08:50:34,711] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKK55DRX2_n01_CisCeD3_fastqc.html [2022-09-28 08:50:34,794] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKK55DRX2_n01_undetermined_fastqc.html [2022-09-28 08:50:34,796] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKK55DRX2_n01_undetermined_fastqc.html [2022-09-28 08:50:34,859] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKK55DRX2_n01_CisCeT6_fastqc.html [2022-09-28 08:50:34,861] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKK55DRX2_n01_CisCeT6_fastqc.html [2022-09-28 08:50:34,921] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKK55DRX2_n01_CisCeD6_fastqc.html [2022-09-28 08:50:34,924] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKK55DRX2_n01_CisCeD6_fastqc.html [2022-09-28 08:50:34,993] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKK55DRX2_n01_CisCeT1_fastqc.html [2022-09-28 08:50:34,995] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKK55DRX2_n01_CisCeT1_fastqc.html [2022-09-28 08:50:35,056] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKK55DRX2_n01_CisCeT3_fastqc.html [2022-09-28 08:50:35,058] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKK55DRX2_n01_CisCeT3_fastqc.html [2022-09-28 08:50:35,165] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKK55DRX2_n01_CisCeC6_fastqc.html [2022-09-28 08:50:35,167] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKK55DRX2_n01_CisCeC6_fastqc.html [2022-09-28 08:50:35,230] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKK55DRX2_n01_CisCeT2_fastqc.html [2022-09-28 08:50:35,232] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKK55DRX2_n01_CisCeT2_fastqc.html [2022-09-28 08:50:35,295] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKK55DRX2_n01_CisCeC4_fastqc.html [2022-09-28 08:50:35,296] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKK55DRX2_n01_CisCeC4_fastqc.html [2022-09-28 08:50:35,358] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKK55DRX2_n01_CisCeC5_fastqc.html [2022-09-28 08:50:35,360] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKK55DRX2_n01_CisCeC5_fastqc.html [2022-09-28 08:50:35,436] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKK55DRX2_n01_CisCeD2_fastqc.html [2022-09-28 08:50:35,438] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKK55DRX2_n01_CisCeD2_fastqc.html [2022-09-28 08:50:35,499] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKK55DRX2_n01_CisCeC2_fastqc.html [2022-09-28 08:50:35,502] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKK55DRX2_n01_CisCeC2_fastqc.html [2022-09-28 08:50:35,937] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-09-28 08:50:35,939] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-09-28 08:50:35,949] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-09-28 08:50:35,959] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 19 samples (table) [2022-09-28 08:50:35,969] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-09-28 08:50:35,976] multiqc [DEBUG ] No samples found: conpair [2022-09-28 08:50:35,982] multiqc [DEBUG ] No samples found: peddy [2022-09-28 08:50:35,988] multiqc [DEBUG ] No samples found: somalier [2022-09-28 08:50:35,994] multiqc [DEBUG ] No samples found: methylQA [2022-09-28 08:50:36,008] multiqc [DEBUG ] No samples found: mosdepth [2022-09-28 08:50:36,014] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-09-28 08:50:36,018] multiqc [DEBUG ] No samples found: qualimap [2022-09-28 08:50:36,025] multiqc [DEBUG ] No samples found: preseq [2022-09-28 08:50:36,031] multiqc [DEBUG ] No samples found: quast [2022-09-28 08:50:36,037] multiqc [DEBUG ] No samples found: qorts [2022-09-28 08:50:36,043] multiqc [DEBUG ] No samples found: rna_seqc [2022-09-28 08:50:36,049] multiqc [DEBUG ] No samples found: rockhopper [2022-09-28 08:50:36,055] multiqc [DEBUG ] No samples found: rsem [2022-09-28 08:50:36,070] multiqc [DEBUG ] No samples found: rseqc [2022-09-28 08:50:36,076] multiqc [DEBUG ] No samples found: busco [2022-09-28 08:50:36,083] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-09-28 08:50:36,088] multiqc [DEBUG ] No samples found: disambiguate [2022-09-28 08:50:36,095] multiqc [DEBUG ] No samples found: supernova [2022-09-28 08:50:36,114] multiqc [DEBUG ] No samples found: deeptools [2022-09-28 08:50:36,120] multiqc [DEBUG ] No samples found: sargasso [2022-09-28 08:50:36,126] multiqc [DEBUG ] No samples found: verifybamid [2022-09-28 08:50:36,132] multiqc [DEBUG ] No samples found: mirtrace [2022-09-28 08:50:36,138] multiqc [DEBUG ] No samples found: happy [2022-09-28 08:50:36,144] multiqc [DEBUG ] No samples found: mirtop [2022-09-28 08:50:36,152] multiqc [DEBUG ] No samples found: homer [2022-09-28 08:50:36,158] multiqc [DEBUG ] No samples found: macs2 [2022-09-28 08:50:36,164] multiqc [DEBUG ] No samples found: theta2 [2022-09-28 08:50:36,170] multiqc [DEBUG ] No samples found: snpeff [2022-09-28 08:50:36,179] multiqc [DEBUG ] No samples found: gatk [2022-09-28 08:50:36,184] multiqc [DEBUG ] No samples found: htseq [2022-09-28 08:50:36,191] multiqc [DEBUG ] No samples found: bcftools [2022-09-28 08:50:36,197] multiqc [DEBUG ] No samples found: featureCounts [2022-09-28 08:50:36,205] multiqc [DEBUG ] No samples found: fgbio [2022-09-28 08:50:36,224] multiqc [DEBUG ] No samples found: dragen [2022-09-28 08:50:36,229] multiqc [DEBUG ] No samples found: dedup [2022-09-28 08:50:36,234] multiqc [DEBUG ] No samples found: damageprofiler [2022-09-28 08:50:36,260] multiqc [DEBUG ] No samples found: biobambam2 [2022-09-28 08:50:36,266] multiqc [DEBUG ] No samples found: mtnucratio [2022-09-28 08:50:36,268] multiqc [DEBUG ] No samples found: picard [2022-09-28 08:50:36,274] multiqc [DEBUG ] No samples found: prokka [2022-09-28 08:50:36,280] multiqc [DEBUG ] No samples found: samblaster [2022-09-28 08:50:36,290] multiqc [DEBUG ] No samples found: samtools [2022-09-28 08:50:36,295] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-09-28 08:50:36,301] multiqc [DEBUG ] No samples found: bamtools [2022-09-28 08:50:36,306] multiqc [DEBUG ] No samples found: jellyfish [2022-09-28 08:50:36,315] multiqc [DEBUG ] No samples found: vcftools [2022-09-28 08:50:36,321] multiqc [DEBUG ] No samples found: longranger [2022-09-28 08:50:36,326] multiqc [DEBUG ] No samples found: stacks [2022-09-28 08:50:36,331] multiqc [DEBUG ] No samples found: varscan2 [2022-09-28 08:50:36,348] multiqc [DEBUG ] No samples found: bbmap [2022-09-28 08:50:36,354] multiqc [DEBUG ] No samples found: bismark [2022-09-28 08:50:36,361] multiqc [DEBUG ] No samples found: biscuit [2022-09-28 08:50:36,367] multiqc [DEBUG ] No samples found: hicexplorer [2022-09-28 08:50:36,372] multiqc [DEBUG ] No samples found: hicup [2022-09-28 08:50:36,378] multiqc [DEBUG ] No samples found: hicpro [2022-09-28 08:50:36,384] multiqc [DEBUG ] No samples found: salmon [2022-09-28 08:50:36,390] multiqc [DEBUG ] No samples found: kallisto [2022-09-28 08:50:36,396] multiqc [DEBUG ] No samples found: slamdunk [2022-09-28 08:50:36,401] multiqc [DEBUG ] No samples found: star [2022-09-28 08:50:36,406] multiqc [DEBUG ] No samples found: hisat2 [2022-09-28 08:50:36,412] multiqc [DEBUG ] No samples found: tophat [2022-09-28 08:50:36,418] multiqc [DEBUG ] No samples found: bowtie2 [2022-09-28 08:50:36,423] multiqc [DEBUG ] No samples found: bowtie1 [2022-09-28 08:50:36,429] multiqc [DEBUG ] No samples found: snpsplit [2022-09-28 08:50:36,434] multiqc [DEBUG ] No samples found: kat [2022-09-28 08:50:36,438] multiqc [DEBUG ] No samples found: leehom [2022-09-28 08:50:36,444] multiqc [DEBUG ] No samples found: adapterRemoval [2022-09-28 08:50:36,450] multiqc [DEBUG ] No samples found: clipandmerge [2022-09-28 08:50:36,455] multiqc [DEBUG ] No samples found: cutadapt [2022-09-28 08:50:36,461] multiqc [DEBUG ] No samples found: flexbar [2022-09-28 08:50:36,467] multiqc [DEBUG ] No samples found: kaiju [2022-09-28 08:50:36,474] multiqc [DEBUG ] No samples found: kraken [2022-09-28 08:50:36,480] multiqc [DEBUG ] No samples found: malt [2022-09-28 08:50:36,486] multiqc [DEBUG ] No samples found: trimmomatic [2022-09-28 08:50:36,493] multiqc [DEBUG ] No samples found: sickle [2022-09-28 08:50:36,499] multiqc [DEBUG ] No samples found: skewer [2022-09-28 08:50:36,504] multiqc [DEBUG ] No samples found: sortmerna [2022-09-28 08:50:36,509] multiqc [DEBUG ] No samples found: biobloomtools [2022-09-28 08:50:36,515] multiqc [DEBUG ] No samples found: fastq_screen [2022-09-28 08:50:36,520] multiqc [DEBUG ] No samples found: afterqc [2022-09-28 08:50:36,528] multiqc [DEBUG ] No samples found: fastp [2022-09-28 08:50:39,311] multiqc.modules.fastqc.fastqc [INFO ] Found 19 reports [2022-09-28 08:50:39,801] multiqc [DEBUG ] No samples found: pycoqc [2022-09-28 08:50:39,807] multiqc [DEBUG ] No samples found: minionqc [2022-09-28 08:50:39,813] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-09-28 08:50:39,818] multiqc [DEBUG ] No samples found: clusterflow [2022-09-28 08:50:39,825] multiqc [DEBUG ] No samples found: bcl2fastq [2022-09-28 08:50:39,831] multiqc [DEBUG ] No samples found: interop [2022-09-28 08:50:39,837] multiqc [DEBUG ] No samples found: ivar [2022-09-28 08:50:39,843] multiqc [DEBUG ] No samples found: flash [2022-09-28 08:50:39,848] multiqc [DEBUG ] No samples found: seqyclean [2022-09-28 08:50:39,848] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-09-28 08:50:39,848] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-09-28 08:50:39,848] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-09-28 08:50:39,848] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-09-28 08:50:39,872] multiqc [INFO ] Compressing plot data [2022-09-28 08:50:40,292] multiqc [INFO ] Report : multiqc_report.html [2022-09-28 08:50:40,292] multiqc [INFO ] Data : multiqc_data [2022-09-28 08:50:40,292] multiqc [DEBUG ] Moving data file from '/state/partition1/job-25495680/tmpy9jni9qw/multiqc_data' to '/scratch/gencore/logs/html/HKK55DRX2/merged/multiqc_data' [2022-09-28 08:50:40,444] multiqc [INFO ] MultiQC complete