[2022-11-21 15:19:22,557] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-11-21 15:19:22,557] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-11-21 15:19:22,557] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-11-21 15:19:22,558] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-11-21 15:19:22,558] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-11-21 15:19:22,558] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H3TJ5BGXN/merged [2022-11-21 15:19:23,042] multiqc [WARNING] MultiQC Version v1.13 now available! [2022-11-21 15:19:23,042] multiqc [INFO ] This is MultiQC v1.9 [2022-11-21 15:19:23,042] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H3TJ5BGXN/merged [2022-11-21 15:19:23,042] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H3TJ5BGXN/merged [2022-11-21 15:19:23,042] multiqc [INFO ] Template : default [2022-11-21 15:19:23,042] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-11-21 15:19:23,042] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H3TJ5BGXN/merged [2022-11-21 15:19:23,043] 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 [2022-11-21 15:19:23,043] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-27201809/tmpix4kt_6x [2022-11-21 15:19:23,148] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3TJ5BGXN_n01_R20rc_fastqc.html [2022-11-21 15:19:23,150] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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[2022-11-21 15:19:25,891] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3TJ5BGXN_n01_R16_2_fastqc.html [2022-11-21 15:19:25,952] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3TJ5BGXN_n01_R23rc_fastqc.html [2022-11-21 15:19:25,954] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3TJ5BGXN_n01_R23rc_fastqc.html [2022-11-21 15:19:25,974] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3TJ5BGXN_n01_R08_fastqc.html [2022-11-21 15:19:25,976] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3TJ5BGXN_n01_R08_fastqc.html [2022-11-21 15:19:26,029] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3TJ5BGXN_n01_R07rc_fastqc.html [2022-11-21 15:19:26,031] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3TJ5BGXN_n01_R07rc_fastqc.html [2022-11-21 15:19:26,078] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3TJ5BGXN_n01_R15_2_fastqc.html [2022-11-21 15:19:26,079] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3TJ5BGXN_n01_R15_2_fastqc.html [2022-11-21 15:19:26,441] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-11-21 15:19:26,443] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-11-21 15:19:26,472] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 49 samples (table) [2022-11-21 15:19:26,474] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-11-21 15:19:26,483] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-11-21 15:19:26,490] multiqc [DEBUG ] No samples found: conpair [2022-11-21 15:19:26,500] multiqc [DEBUG ] No samples found: peddy [2022-11-21 15:19:26,509] multiqc [DEBUG ] No samples found: somalier [2022-11-21 15:19:26,515] multiqc [DEBUG ] No samples found: methylQA [2022-11-21 15:19:26,524] multiqc [DEBUG ] No samples found: mosdepth [2022-11-21 15:19:26,528] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-11-21 15:19:26,532] multiqc [DEBUG ] No samples found: qualimap [2022-11-21 15:19:26,537] multiqc [DEBUG ] No samples found: preseq [2022-11-21 15:19:26,542] multiqc [DEBUG ] No samples found: quast [2022-11-21 15:19:26,547] multiqc [DEBUG ] No samples found: qorts [2022-11-21 15:19:26,552] multiqc [DEBUG ] No samples found: rna_seqc [2022-11-21 15:19:26,557] multiqc [DEBUG ] No samples found: rockhopper [2022-11-21 15:19:26,562] multiqc [DEBUG ] No samples found: rsem [2022-11-21 15:19:26,581] multiqc [DEBUG ] No samples found: rseqc [2022-11-21 15:19:26,588] multiqc [DEBUG ] No samples found: busco [2022-11-21 15:19:26,596] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-11-21 15:19:26,602] multiqc [DEBUG ] No samples found: disambiguate [2022-11-21 15:19:26,608] multiqc [DEBUG ] No samples found: supernova [2022-11-21 15:19:26,626] multiqc [DEBUG ] No samples found: deeptools [2022-11-21 15:19:26,631] multiqc [DEBUG ] No samples found: sargasso [2022-11-21 15:19:26,636] multiqc [DEBUG ] No samples found: verifybamid [2022-11-21 15:19:26,641] multiqc [DEBUG ] No samples found: mirtrace [2022-11-21 15:19:26,646] multiqc [DEBUG ] No samples found: happy [2022-11-21 15:19:26,651] multiqc [DEBUG ] No samples found: mirtop [2022-11-21 15:19:26,660] multiqc [DEBUG ] No samples found: homer [2022-11-21 15:19:26,666] multiqc [DEBUG ] No samples found: macs2 [2022-11-21 15:19:26,672] multiqc [DEBUG ] No samples found: theta2 [2022-11-21 15:19:26,677] multiqc [DEBUG ] No samples found: snpeff [2022-11-21 15:19:26,684] multiqc [DEBUG ] No samples found: gatk [2022-11-21 15:19:26,689] multiqc [DEBUG ] No samples found: htseq [2022-11-21 15:19:26,696] multiqc [DEBUG ] No samples found: bcftools [2022-11-21 15:19:26,702] multiqc [DEBUG ] No samples found: featureCounts [2022-11-21 15:19:26,710] multiqc [DEBUG ] No samples found: fgbio [2022-11-21 15:19:26,725] multiqc [DEBUG ] No samples found: dragen [2022-11-21 15:19:26,730] multiqc [DEBUG ] No samples found: dedup [2022-11-21 15:19:26,736] multiqc [DEBUG ] No samples found: damageprofiler [2022-11-21 15:19:26,761] multiqc [DEBUG ] No samples found: biobambam2 [2022-11-21 15:19:26,765] multiqc [DEBUG ] No samples found: mtnucratio [2022-11-21 15:19:26,768] multiqc [DEBUG ] No samples found: picard [2022-11-21 15:19:26,774] multiqc [DEBUG ] No samples found: prokka [2022-11-21 15:19:26,779] multiqc [DEBUG ] No samples found: samblaster [2022-11-21 15:19:26,792] multiqc [DEBUG ] No samples found: samtools [2022-11-21 15:19:26,797] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-11-21 15:19:26,802] multiqc [DEBUG ] No samples found: bamtools [2022-11-21 15:19:26,807] multiqc [DEBUG ] No samples found: jellyfish [2022-11-21 15:19:26,817] multiqc [DEBUG ] No samples found: vcftools [2022-11-21 15:19:26,821] multiqc [DEBUG ] No samples found: longranger [2022-11-21 15:19:26,826] multiqc [DEBUG ] No samples found: stacks [2022-11-21 15:19:26,831] multiqc [DEBUG ] No samples found: varscan2 [2022-11-21 15:19:26,847] multiqc [DEBUG ] No samples found: bbmap [2022-11-21 15:19:26,852] multiqc [DEBUG ] No samples found: bismark [2022-11-21 15:19:26,857] multiqc [DEBUG ] No samples found: biscuit [2022-11-21 15:19:26,862] multiqc [DEBUG ] No samples found: hicexplorer [2022-11-21 15:19:26,867] multiqc [DEBUG ] No samples found: hicup [2022-11-21 15:19:26,872] multiqc [DEBUG ] No samples found: hicpro [2022-11-21 15:19:26,876] multiqc [DEBUG ] No samples found: salmon [2022-11-21 15:19:26,881] multiqc [DEBUG ] No samples found: kallisto [2022-11-21 15:19:26,886] multiqc [DEBUG ] No samples found: slamdunk [2022-11-21 15:19:26,892] multiqc [DEBUG ] No samples found: star [2022-11-21 15:19:26,898] multiqc [DEBUG ] No samples found: hisat2 [2022-11-21 15:19:26,903] multiqc [DEBUG ] No samples found: tophat [2022-11-21 15:19:26,907] multiqc [DEBUG ] No samples found: bowtie2 [2022-11-21 15:19:26,912] multiqc [DEBUG ] No samples found: bowtie1 [2022-11-21 15:19:26,917] multiqc [DEBUG ] No samples found: snpsplit [2022-11-21 15:19:26,921] multiqc [DEBUG ] No samples found: kat [2022-11-21 15:19:26,926] multiqc [DEBUG ] No samples found: leehom [2022-11-21 15:19:26,931] multiqc [DEBUG ] No samples found: adapterRemoval [2022-11-21 15:19:26,935] multiqc [DEBUG ] No samples found: clipandmerge [2022-11-21 15:19:26,940] multiqc [DEBUG ] No samples found: cutadapt [2022-11-21 15:19:26,944] multiqc [DEBUG ] No samples found: flexbar [2022-11-21 15:19:26,949] multiqc [DEBUG ] No samples found: kaiju [2022-11-21 15:19:26,953] multiqc [DEBUG ] No samples found: kraken [2022-11-21 15:19:26,959] multiqc [DEBUG ] No samples found: malt [2022-11-21 15:19:26,963] multiqc [DEBUG ] No samples found: trimmomatic [2022-11-21 15:19:26,967] multiqc [DEBUG ] No samples found: sickle [2022-11-21 15:19:26,972] multiqc [DEBUG ] No samples found: skewer [2022-11-21 15:19:26,976] multiqc [DEBUG ] No samples found: sortmerna [2022-11-21 15:19:26,980] multiqc [DEBUG ] No samples found: biobloomtools [2022-11-21 15:19:26,985] multiqc [DEBUG ] No samples found: fastq_screen [2022-11-21 15:19:26,989] multiqc [DEBUG ] No samples found: afterqc [2022-11-21 15:19:26,994] multiqc [DEBUG ] No samples found: fastp [2022-11-21 15:19:27,700] multiqc.modules.fastqc.fastqc [INFO ] Found 49 reports [2022-11-21 15:19:27,702] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'H3TJ5BGXN_n01_R10rc' [2022-11-21 15:19:27,702] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'H3TJ5BGXN_n01_R01rc' [2022-11-21 15:19:27,702] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'H3TJ5BGXN_n01_R24rc' [2022-11-21 15:19:27,702] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'H3TJ5BGXN_n01_R22rc' [2022-11-21 15:19:27,702] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'H3TJ5BGXN_n01_R23rc' [2022-11-21 15:19:27,702] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'H3TJ5BGXN_n01_R14rc' [2022-11-21 15:19:27,702] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'H3TJ5BGXN_n01_R20rc' [2022-11-21 15:19:27,702] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'H3TJ5BGXN_n01_R17rc' [2022-11-21 15:19:27,702] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'H3TJ5BGXN_n01_R12rc' [2022-11-21 15:19:27,702] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'H3TJ5BGXN_n01_R21rc' [2022-11-21 15:19:27,702] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'H3TJ5BGXN_n01_R06rc' [2022-11-21 15:19:28,017] multiqc [DEBUG ] No samples found: pycoqc [2022-11-21 15:19:28,024] multiqc [DEBUG ] No samples found: minionqc [2022-11-21 15:19:28,030] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-11-21 15:19:28,036] multiqc [DEBUG ] No samples found: clusterflow [2022-11-21 15:19:28,042] multiqc [DEBUG ] No samples found: bcl2fastq [2022-11-21 15:19:28,049] multiqc [DEBUG ] No samples found: interop [2022-11-21 15:19:28,054] multiqc [DEBUG ] No samples found: ivar [2022-11-21 15:19:28,059] multiqc [DEBUG ] No samples found: flash [2022-11-21 15:19:28,065] multiqc [DEBUG ] No samples found: seqyclean [2022-11-21 15:19:28,065] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-11-21 15:19:28,065] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-11-21 15:19:28,065] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-11-21 15:19:28,065] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-11-21 15:19:28,122] multiqc [INFO ] Compressing plot data [2022-11-21 15:19:28,536] multiqc [INFO ] Report : multiqc_report.html [2022-11-21 15:19:28,537] multiqc [INFO ] Data : multiqc_data [2022-11-21 15:19:28,537] multiqc [DEBUG ] Moving data file from '/state/partition1/job-27201809/tmpix4kt_6x/multiqc_data' to '/scratch/gencore/logs/html/H3TJ5BGXN/merged/multiqc_data' [2022-11-21 15:21:23,269] multiqc [INFO ] MultiQC complete