[2021-12-18 06:27:19,744] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-12-18 06:27:19,744] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-12-18 06:27:19,745] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-12-18 06:27:19,745] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-12-18 06:27:19,745] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-12-18 06:27:19,746] 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-G992J/1 [2021-12-18 06:27:21,096] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-12-18 06:27:21,096] multiqc [INFO ] This is MultiQC v1.9 [2021-12-18 06:27:21,096] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/000000000-G992J/1 [2021-12-18 06:27:21,097] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/000000000-G992J/1 [2021-12-18 06:27:21,097] multiqc [INFO ] Template : default [2021-12-18 06:27:21,097] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-12-18 06:27:21,097] multiqc [INFO ] Searching : /scratch/gencore/logs/html/000000000-G992J/1 [2021-12-18 06:27:21,097] 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 [2021-12-18 06:27:21,097] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-13144100/tmpetx5617g [2021-12-18 06:27:21,206] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G992J_l01_n02_WGS21-6_fastqc.html [2021-12-18 06:27:21,209] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G992J_l01_n02_WGS21-6_fastqc.html [2021-12-18 06:27:21,271] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G992J_l01_n02_WGS21-4_fastqc.html [2021-12-18 06:27:21,272] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G992J_l01_n02_WGS21-4_fastqc.html [2021-12-18 06:27:21,332] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-12-18 06:27:21,333] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-12-18 06:27:21,333] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-12-18 06:27:21,334] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-12-18 06:27:21,334] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-12-18 06:27:21,334] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-12-18 06:27:21,334] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-12-18 06:27:22,161] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G992J_l01_n01_undetermined_fastqc.html [2021-12-18 06:27:22,162] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G992J_l01_n01_undetermined_fastqc.html [2021-12-18 06:27:22,203] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G992J_l01_n02_WGS21-8_fastqc.html [2021-12-18 06:27:22,205] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G992J_l01_n02_WGS21-8_fastqc.html [2021-12-18 06:27:22,305] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G992J_l01_n02_WGS21-1_fastqc.html [2021-12-18 06:27:22,307] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G992J_l01_n02_WGS21-1_fastqc.html [2021-12-18 06:27:22,366] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G992J_l01_n01_WGS21-5_fastqc.html [2021-12-18 06:27:22,368] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G992J_l01_n01_WGS21-5_fastqc.html [2021-12-18 06:27:22,422] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G992J_l01_n01_WGS21-4_fastqc.html [2021-12-18 06:27:22,423] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G992J_l01_n01_WGS21-4_fastqc.html [2021-12-18 06:27:22,477] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G992J_l01_n02_WGS21-2_fastqc.html [2021-12-18 06:27:22,479] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G992J_l01_n02_WGS21-2_fastqc.html [2021-12-18 06:27:22,538] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G992J_l01_n02_undetermined_fastqc.html [2021-12-18 06:27:22,540] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G992J_l01_n02_undetermined_fastqc.html [2021-12-18 06:27:22,581] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G992J_l01_n01_WGS21-6_fastqc.html [2021-12-18 06:27:22,583] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G992J_l01_n01_WGS21-6_fastqc.html [2021-12-18 06:27:22,640] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G992J_l01_n01_WGS21-7_fastqc.html [2021-12-18 06:27:22,642] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G992J_l01_n01_WGS21-7_fastqc.html [2021-12-18 06:27:22,696] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G992J_l01_n01_WGS21-3_fastqc.html [2021-12-18 06:27:22,698] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G992J_l01_n01_WGS21-3_fastqc.html [2021-12-18 06:27:22,752] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G992J_l01_n01_WGS21-1_fastqc.html [2021-12-18 06:27:22,753] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G992J_l01_n01_WGS21-1_fastqc.html [2021-12-18 06:27:22,810] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G992J_l01_n02_WGS21-3_fastqc.html [2021-12-18 06:27:22,812] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G992J_l01_n02_WGS21-3_fastqc.html [2021-12-18 06:27:22,868] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G992J_l01_n01_WGS21-8_fastqc.html [2021-12-18 06:27:22,870] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G992J_l01_n01_WGS21-8_fastqc.html [2021-12-18 06:27:22,926] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G992J_l01_n02_WGS21-5_fastqc.html [2021-12-18 06:27:22,928] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G992J_l01_n02_WGS21-5_fastqc.html [2021-12-18 06:27:22,980] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G992J_l01_n01_WGS21-2_fastqc.html [2021-12-18 06:27:22,982] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G992J_l01_n01_WGS21-2_fastqc.html [2021-12-18 06:27:23,036] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G992J_l01_n02_WGS21-7_fastqc.html [2021-12-18 06:27:23,038] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G992J_l01_n02_WGS21-7_fastqc.html [2021-12-18 06:27:23,557] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-12-18 06:27:23,559] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-12-18 06:27:23,569] multiqc.modules.custom_content.custom_content [INFO ] demux_report-1: Found 9 samples (table) [2021-12-18 06:27:23,571] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-12-18 06:27:23,581] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-12-18 06:27:23,586] multiqc [DEBUG ] No samples found: conpair [2021-12-18 06:27:23,592] multiqc [DEBUG ] No samples found: peddy [2021-12-18 06:27:23,596] multiqc [DEBUG ] No samples found: somalier [2021-12-18 06:27:23,601] multiqc [DEBUG ] No samples found: methylQA [2021-12-18 06:27:23,612] multiqc [DEBUG ] No samples found: mosdepth [2021-12-18 06:27:23,616] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-12-18 06:27:23,619] multiqc [DEBUG ] No samples found: qualimap [2021-12-18 06:27:23,624] multiqc [DEBUG ] No samples found: preseq [2021-12-18 06:27:23,630] multiqc [DEBUG ] No samples found: quast [2021-12-18 06:27:23,634] multiqc [DEBUG ] No samples found: qorts [2021-12-18 06:27:23,639] multiqc [DEBUG ] No samples found: rna_seqc [2021-12-18 06:27:23,643] multiqc [DEBUG ] No samples found: rockhopper [2021-12-18 06:27:23,648] multiqc [DEBUG ] No samples found: rsem [2021-12-18 06:27:23,665] multiqc [DEBUG ] No samples found: rseqc [2021-12-18 06:27:23,670] multiqc [DEBUG ] No samples found: busco [2021-12-18 06:27:23,674] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-12-18 06:27:23,679] multiqc [DEBUG ] No samples found: disambiguate [2021-12-18 06:27:23,684] multiqc [DEBUG ] No samples found: supernova [2021-12-18 06:27:23,697] multiqc [DEBUG ] No samples found: deeptools [2021-12-18 06:27:23,701] multiqc [DEBUG ] No samples found: sargasso [2021-12-18 06:27:23,706] multiqc [DEBUG ] No samples found: verifybamid [2021-12-18 06:27:23,710] multiqc [DEBUG ] No samples found: mirtrace [2021-12-18 06:27:23,714] multiqc [DEBUG ] No samples found: happy [2021-12-18 06:27:23,718] multiqc [DEBUG ] No samples found: mirtop [2021-12-18 06:27:23,724] multiqc [DEBUG ] No samples found: homer [2021-12-18 06:27:23,729] multiqc [DEBUG ] No samples found: macs2 [2021-12-18 06:27:23,733] multiqc [DEBUG ] No samples found: theta2 [2021-12-18 06:27:23,738] multiqc [DEBUG ] No samples found: snpeff [2021-12-18 06:27:23,745] multiqc [DEBUG ] No samples found: gatk [2021-12-18 06:27:23,749] multiqc [DEBUG ] No samples found: htseq [2021-12-18 06:27:23,754] multiqc [DEBUG ] No samples found: bcftools [2021-12-18 06:27:23,760] multiqc [DEBUG ] No samples found: featureCounts [2021-12-18 06:27:23,766] multiqc [DEBUG ] No samples found: fgbio [2021-12-18 06:27:23,778] multiqc [DEBUG ] No samples found: dragen [2021-12-18 06:27:23,783] multiqc [DEBUG ] No samples found: dedup [2021-12-18 06:27:23,787] multiqc [DEBUG ] No samples found: damageprofiler [2021-12-18 06:27:23,818] multiqc [DEBUG ] No samples found: biobambam2 [2021-12-18 06:27:23,823] multiqc [DEBUG ] No samples found: mtnucratio [2021-12-18 06:27:23,825] multiqc [DEBUG ] No samples found: picard [2021-12-18 06:27:23,829] multiqc [DEBUG ] No samples found: prokka [2021-12-18 06:27:23,835] multiqc [DEBUG ] No samples found: samblaster [2021-12-18 06:27:23,845] multiqc [DEBUG ] No samples found: samtools [2021-12-18 06:27:23,849] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-12-18 06:27:23,855] multiqc [DEBUG ] No samples found: bamtools [2021-12-18 06:27:23,859] multiqc [DEBUG ] No samples found: jellyfish [2021-12-18 06:27:23,867] multiqc [DEBUG ] No samples found: vcftools [2021-12-18 06:27:23,871] multiqc [DEBUG ] No samples found: longranger [2021-12-18 06:27:23,876] multiqc [DEBUG ] No samples found: stacks [2021-12-18 06:27:23,881] multiqc [DEBUG ] No samples found: varscan2 [2021-12-18 06:27:23,896] multiqc [DEBUG ] No samples found: bbmap [2021-12-18 06:27:23,900] multiqc [DEBUG ] No samples found: bismark [2021-12-18 06:27:23,904] multiqc [DEBUG ] No samples found: biscuit [2021-12-18 06:27:23,909] multiqc [DEBUG ] No samples found: hicexplorer [2021-12-18 06:27:23,913] multiqc [DEBUG ] No samples found: hicup [2021-12-18 06:27:23,917] multiqc [DEBUG ] No samples found: hicpro [2021-12-18 06:27:23,924] multiqc [DEBUG ] No samples found: salmon [2021-12-18 06:27:23,928] multiqc [DEBUG ] No samples found: kallisto [2021-12-18 06:27:23,932] multiqc [DEBUG ] No samples found: slamdunk [2021-12-18 06:27:23,937] multiqc [DEBUG ] No samples found: star [2021-12-18 06:27:23,942] multiqc [DEBUG ] No samples found: hisat2 [2021-12-18 06:27:23,947] multiqc [DEBUG ] No samples found: tophat [2021-12-18 06:27:23,951] multiqc [DEBUG ] No samples found: bowtie2 [2021-12-18 06:27:23,956] multiqc [DEBUG ] No samples found: bowtie1 [2021-12-18 06:27:23,960] multiqc [DEBUG ] No samples found: snpsplit [2021-12-18 06:27:23,965] multiqc [DEBUG ] No samples found: kat [2021-12-18 06:27:23,969] multiqc [DEBUG ] No samples found: leehom [2021-12-18 06:27:23,973] multiqc [DEBUG ] No samples found: adapterRemoval [2021-12-18 06:27:23,977] multiqc [DEBUG ] No samples found: clipandmerge [2021-12-18 06:27:23,981] multiqc [DEBUG ] No samples found: cutadapt [2021-12-18 06:27:23,986] multiqc [DEBUG ] No samples found: flexbar [2021-12-18 06:27:23,990] multiqc [DEBUG ] No samples found: kaiju [2021-12-18 06:27:23,994] multiqc [DEBUG ] No samples found: kraken [2021-12-18 06:27:23,999] multiqc [DEBUG ] No samples found: malt [2021-12-18 06:27:24,004] multiqc [DEBUG ] No samples found: trimmomatic [2021-12-18 06:27:24,009] multiqc [DEBUG ] No samples found: sickle [2021-12-18 06:27:24,013] multiqc [DEBUG ] No samples found: skewer [2021-12-18 06:27:24,018] multiqc [DEBUG ] No samples found: sortmerna [2021-12-18 06:27:24,022] multiqc [DEBUG ] No samples found: biobloomtools [2021-12-18 06:27:24,027] multiqc [DEBUG ] No samples found: fastq_screen [2021-12-18 06:27:24,031] multiqc [DEBUG ] No samples found: afterqc [2021-12-18 06:27:24,036] multiqc [DEBUG ] No samples found: fastp [2021-12-18 06:27:24,101] multiqc.modules.fastqc.fastqc [INFO ] Found 18 reports [2021-12-18 06:27:24,314] multiqc [DEBUG ] No samples found: pycoqc [2021-12-18 06:27:24,319] multiqc [DEBUG ] No samples found: minionqc [2021-12-18 06:27:24,325] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-12-18 06:27:24,330] multiqc [DEBUG ] No samples found: clusterflow [2021-12-18 06:27:24,335] multiqc [DEBUG ] No samples found: bcl2fastq [2021-12-18 06:27:24,339] multiqc [DEBUG ] No samples found: interop [2021-12-18 06:27:24,344] multiqc [DEBUG ] No samples found: ivar [2021-12-18 06:27:24,348] multiqc [DEBUG ] No samples found: flash [2021-12-18 06:27:24,354] multiqc [DEBUG ] No samples found: seqyclean [2021-12-18 06:27:24,354] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2021-12-18 06:27:24,354] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 1 Demultiplexing Report'. [2021-12-18 06:27:24,354] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2021-12-18 06:27:24,354] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-12-18 06:27:24,354] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-12-18 06:27:24,375] multiqc [INFO ] Compressing plot data [2021-12-18 06:27:24,664] multiqc [INFO ] Report : multiqc_report.html [2021-12-18 06:27:24,664] multiqc [INFO ] Data : multiqc_data [2021-12-18 06:27:24,664] multiqc [DEBUG ] Moving data file from '/state/partition1/job-13144100/tmpetx5617g/multiqc_data' to '/scratch/gencore/logs/html/000000000-G992J/1/multiqc_data' [2021-12-18 06:27:24,792] multiqc [INFO ] MultiQC complete