[2022-05-10 06:16:41,978] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-05-10 06:16:41,978] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-05-10 06:16:41,978] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-05-10 06:16:41,979] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-05-10 06:16:41,979] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-05-10 06:16:41,979] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HNTVLBGXL/merged [2022-05-10 06:16:42,747] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-05-10 06:16:42,747] multiqc [INFO ] This is MultiQC v1.9 [2022-05-10 06:16:42,747] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HNTVLBGXL/merged [2022-05-10 06:16:42,747] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HNTVLBGXL/merged [2022-05-10 06:16:42,747] multiqc [INFO ] Template : default [2022-05-10 06:16:42,747] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-05-10 06:16:42,747] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HNTVLBGXL/merged [2022-05-10 06:16:42,748] 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 [2022-05-10 06:16:42,748] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-19366904/tmpn7yvn_tr [2022-05-10 06:16:42,853] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-05-10 06:16:42,856] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-05-10 06:16:42,856] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-05-10 06:16:42,856] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-05-10 06:16:42,856] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-05-10 06:16:42,856] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-05-10 06:16:42,856] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-05-10 06:16:43,746] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNTVLBGXL_n01_K562_Essen_R2_fastqc.html [2022-05-10 06:16:43,748] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNTVLBGXL_n01_K562_Essen_R2_fastqc.html [2022-05-10 06:16:43,806] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNTVLBGXL_n01_THP1_Essen_Diff_R2_fastqc.html [2022-05-10 06:16:43,808] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNTVLBGXL_n01_THP1_Essen_Diff_R2_fastqc.html [2022-05-10 06:16:43,861] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNTVLBGXL_n01_GD_eRNA_052022_fastqc.html [2022-05-10 06:16:43,863] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNTVLBGXL_n01_GD_eRNA_052022_fastqc.html [2022-05-10 06:16:43,915] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNTVLBGXL_n01_K562_Essen_R1_fastqc.html [2022-05-10 06:16:43,917] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNTVLBGXL_n01_K562_Essen_R1_fastqc.html [2022-05-10 06:16:43,974] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNTVLBGXL_n01_A375_Essen_R2_fastqc.html [2022-05-10 06:16:43,976] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNTVLBGXL_n01_A375_Essen_R2_fastqc.html [2022-05-10 06:16:44,027] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNTVLBGXL_n01_undetermined_fastqc.html [2022-05-10 06:16:44,029] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNTVLBGXL_n01_undetermined_fastqc.html [2022-05-10 06:16:44,082] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNTVLBGXL_n01_THP1_Essen_Diff_R1_fastqc.html [2022-05-10 06:16:44,084] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNTVLBGXL_n01_THP1_Essen_Diff_R1_fastqc.html [2022-05-10 06:16:44,136] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNTVLBGXL_n01_K562_Diff_R1_fastqc.html [2022-05-10 06:16:44,138] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNTVLBGXL_n01_K562_Diff_R1_fastqc.html [2022-05-10 06:16:44,194] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNTVLBGXL_n01_A375_Essen_R1_fastqc.html [2022-05-10 06:16:44,196] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNTVLBGXL_n01_A375_Essen_R1_fastqc.html [2022-05-10 06:16:44,248] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNTVLBGXL_n01_K562_Diff_R2_fastqc.html [2022-05-10 06:16:44,249] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNTVLBGXL_n01_K562_Diff_R2_fastqc.html [2022-05-10 06:16:44,731] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-05-10 06:16:44,733] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-05-10 06:16:44,745] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 10 samples (table) [2022-05-10 06:16:44,746] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-05-10 06:16:44,756] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-05-10 06:16:44,761] multiqc [DEBUG ] No samples found: conpair [2022-05-10 06:16:44,766] multiqc [DEBUG ] No samples found: peddy [2022-05-10 06:16:44,771] multiqc [DEBUG ] No samples found: somalier [2022-05-10 06:16:44,775] multiqc [DEBUG ] No samples found: methylQA [2022-05-10 06:16:44,783] multiqc [DEBUG ] No samples found: mosdepth [2022-05-10 06:16:44,788] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-05-10 06:16:44,791] multiqc [DEBUG ] No samples found: qualimap [2022-05-10 06:16:44,796] multiqc [DEBUG ] No samples found: preseq [2022-05-10 06:16:44,801] multiqc [DEBUG ] No samples found: quast [2022-05-10 06:16:44,806] multiqc [DEBUG ] No samples found: qorts [2022-05-10 06:16:44,811] multiqc [DEBUG ] No samples found: rna_seqc [2022-05-10 06:16:44,815] multiqc [DEBUG ] No samples found: rockhopper [2022-05-10 06:16:44,820] multiqc [DEBUG ] No samples found: rsem [2022-05-10 06:16:44,830] multiqc [DEBUG ] No samples found: rseqc [2022-05-10 06:16:44,834] multiqc [DEBUG ] No samples found: busco [2022-05-10 06:16:44,838] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-05-10 06:16:44,843] multiqc [DEBUG ] No samples found: disambiguate [2022-05-10 06:16:44,847] multiqc [DEBUG ] No samples found: supernova [2022-05-10 06:16:44,859] multiqc [DEBUG ] No samples found: deeptools [2022-05-10 06:16:44,864] multiqc [DEBUG ] No samples found: sargasso [2022-05-10 06:16:44,868] multiqc [DEBUG ] No samples found: verifybamid [2022-05-10 06:16:44,873] multiqc [DEBUG ] No samples found: mirtrace [2022-05-10 06:16:44,877] multiqc [DEBUG ] No samples found: happy [2022-05-10 06:16:44,881] multiqc [DEBUG ] No samples found: mirtop [2022-05-10 06:16:44,887] multiqc [DEBUG ] No samples found: homer [2022-05-10 06:16:44,892] multiqc [DEBUG ] No samples found: macs2 [2022-05-10 06:16:44,896] multiqc [DEBUG ] No samples found: theta2 [2022-05-10 06:16:44,900] multiqc [DEBUG ] No samples found: snpeff [2022-05-10 06:16:44,907] multiqc [DEBUG ] No samples found: gatk [2022-05-10 06:16:44,911] multiqc [DEBUG ] No samples found: htseq [2022-05-10 06:16:44,916] multiqc [DEBUG ] No samples found: bcftools [2022-05-10 06:16:44,921] multiqc [DEBUG ] No samples found: featureCounts [2022-05-10 06:16:44,927] multiqc [DEBUG ] No samples found: fgbio [2022-05-10 06:16:44,939] multiqc [DEBUG ] No samples found: dragen [2022-05-10 06:16:44,944] multiqc [DEBUG ] No samples found: dedup [2022-05-10 06:16:44,948] multiqc [DEBUG ] No samples found: damageprofiler [2022-05-10 06:16:44,970] multiqc [DEBUG ] No samples found: biobambam2 [2022-05-10 06:16:44,974] multiqc [DEBUG ] No samples found: mtnucratio [2022-05-10 06:16:44,976] multiqc [DEBUG ] No samples found: picard [2022-05-10 06:16:44,981] multiqc [DEBUG ] No samples found: prokka [2022-05-10 06:16:44,984] multiqc [DEBUG ] No samples found: samblaster [2022-05-10 06:16:44,992] multiqc [DEBUG ] No samples found: samtools [2022-05-10 06:16:44,997] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-05-10 06:16:45,001] multiqc [DEBUG ] No samples found: bamtools [2022-05-10 06:16:45,005] multiqc [DEBUG ] No samples found: jellyfish [2022-05-10 06:16:45,012] multiqc [DEBUG ] No samples found: vcftools [2022-05-10 06:16:45,017] multiqc [DEBUG ] No samples found: longranger [2022-05-10 06:16:45,021] multiqc [DEBUG ] No samples found: stacks [2022-05-10 06:16:45,026] multiqc [DEBUG ] No samples found: varscan2 [2022-05-10 06:16:45,039] multiqc [DEBUG ] No samples found: bbmap [2022-05-10 06:16:45,044] multiqc [DEBUG ] No samples found: bismark [2022-05-10 06:16:45,049] multiqc [DEBUG ] No samples found: biscuit [2022-05-10 06:16:45,053] multiqc [DEBUG ] No samples found: hicexplorer [2022-05-10 06:16:45,057] multiqc [DEBUG ] No samples found: hicup [2022-05-10 06:16:45,062] multiqc [DEBUG ] No samples found: hicpro [2022-05-10 06:16:45,067] multiqc [DEBUG ] No samples found: salmon [2022-05-10 06:16:45,072] multiqc [DEBUG ] No samples found: kallisto [2022-05-10 06:16:45,076] multiqc [DEBUG ] No samples found: slamdunk [2022-05-10 06:16:45,081] multiqc [DEBUG ] No samples found: star [2022-05-10 06:16:45,085] multiqc [DEBUG ] No samples found: hisat2 [2022-05-10 06:16:45,089] multiqc [DEBUG ] No samples found: tophat [2022-05-10 06:16:45,094] multiqc [DEBUG ] No samples found: bowtie2 [2022-05-10 06:16:45,098] multiqc [DEBUG ] No samples found: bowtie1 [2022-05-10 06:16:45,103] multiqc [DEBUG ] No samples found: snpsplit [2022-05-10 06:16:45,107] multiqc [DEBUG ] No samples found: kat [2022-05-10 06:16:45,111] multiqc [DEBUG ] No samples found: leehom [2022-05-10 06:16:45,115] multiqc [DEBUG ] No samples found: adapterRemoval [2022-05-10 06:16:45,119] multiqc [DEBUG ] No samples found: clipandmerge [2022-05-10 06:16:45,123] multiqc [DEBUG ] No samples found: cutadapt [2022-05-10 06:16:45,128] multiqc [DEBUG ] No samples found: flexbar [2022-05-10 06:16:45,132] multiqc [DEBUG ] No samples found: kaiju [2022-05-10 06:16:45,136] multiqc [DEBUG ] No samples found: kraken [2022-05-10 06:16:45,141] multiqc [DEBUG ] No samples found: malt [2022-05-10 06:16:45,145] multiqc [DEBUG ] No samples found: trimmomatic [2022-05-10 06:16:45,149] multiqc [DEBUG ] No samples found: sickle [2022-05-10 06:16:45,154] multiqc [DEBUG ] No samples found: skewer [2022-05-10 06:16:45,158] multiqc [DEBUG ] No samples found: sortmerna [2022-05-10 06:16:45,162] multiqc [DEBUG ] No samples found: biobloomtools [2022-05-10 06:16:45,166] multiqc [DEBUG ] No samples found: fastq_screen [2022-05-10 06:16:45,170] multiqc [DEBUG ] No samples found: afterqc [2022-05-10 06:16:45,175] multiqc [DEBUG ] No samples found: fastp [2022-05-10 06:16:45,774] multiqc.modules.fastqc.fastqc [INFO ] Found 10 reports [2022-05-10 06:16:45,870] multiqc [DEBUG ] No samples found: pycoqc [2022-05-10 06:16:45,875] multiqc [DEBUG ] No samples found: minionqc [2022-05-10 06:16:45,879] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-05-10 06:16:45,884] multiqc [DEBUG ] No samples found: clusterflow [2022-05-10 06:16:45,888] multiqc [DEBUG ] No samples found: bcl2fastq [2022-05-10 06:16:45,893] multiqc [DEBUG ] No samples found: interop [2022-05-10 06:16:45,897] multiqc [DEBUG ] No samples found: ivar [2022-05-10 06:16:45,902] multiqc [DEBUG ] No samples found: flash [2022-05-10 06:16:45,906] multiqc [DEBUG ] No samples found: seqyclean [2022-05-10 06:16:45,906] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-05-10 06:16:45,906] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-05-10 06:16:45,906] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-05-10 06:16:45,906] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-05-10 06:16:45,919] multiqc [INFO ] Compressing plot data [2022-05-10 06:16:46,077] multiqc [INFO ] Report : multiqc_report.html [2022-05-10 06:16:46,077] multiqc [INFO ] Data : multiqc_data [2022-05-10 06:16:46,077] multiqc [DEBUG ] Moving data file from '/state/partition1/job-19366904/tmpn7yvn_tr/multiqc_data' to '/scratch/gencore/logs/html/HNTVLBGXL/merged/multiqc_data' [2022-05-10 06:16:46,196] multiqc [INFO ] MultiQC complete