[2022-07-29 04:51:56,194] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-07-29 04:51:56,194] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-07-29 04:51:56,194] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-07-29 04:51:56,195] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-07-29 04:51:56,195] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-07-29 04:51:56,195] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HFWYFDRX2/1 [2022-07-29 04:51:56,914] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-07-29 04:51:56,914] multiqc [INFO ] This is MultiQC v1.9 [2022-07-29 04:51:56,914] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HFWYFDRX2/1 [2022-07-29 04:51:56,914] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HFWYFDRX2/1 [2022-07-29 04:51:56,914] multiqc [INFO ] Template : default [2022-07-29 04:51:56,914] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-07-29 04:51:56,914] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HFWYFDRX2/1 [2022-07-29 04:51:56,915] 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 [2022-07-29 04:51:56,915] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-22959527/tmp6z6sus6k [2022-07-29 04:51:57,034] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFWYFDRX2_l01_n02_WT_3DNAseq_fastqc.html [2022-07-29 04:51:57,037] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFWYFDRX2_l01_n02_WT_3DNAseq_fastqc.html [2022-07-29 04:51:57,079] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-07-29 04:51:57,080] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-07-29 04:51:57,080] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-07-29 04:51:57,080] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-07-29 04:51:57,080] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-07-29 04:51:57,080] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-07-29 04:51:57,080] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-07-29 04:51:57,080] multiqc [DEBUG ] File ignored by snpeff because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-07-29 04:51:57,080] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-07-29 04:52:01,760] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFWYFDRX2_l01_n01_undetermined_fastqc.html [2022-07-29 04:52:01,762] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFWYFDRX2_l01_n01_undetermined_fastqc.html [2022-07-29 04:52:01,801] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFWYFDRX2_l01_n02_WT_2DNAseq_fastqc.html [2022-07-29 04:52:01,803] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFWYFDRX2_l01_n02_WT_2DNAseq_fastqc.html [2022-07-29 04:52:01,842] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFWYFDRX2_l01_n02_WT_1DNAseq_fastqc.html [2022-07-29 04:52:01,844] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFWYFDRX2_l01_n02_WT_1DNAseq_fastqc.html [2022-07-29 04:52:01,883] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFWYFDRX2_l01_n01_WT_1DNAseq_fastqc.html [2022-07-29 04:52:01,884] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFWYFDRX2_l01_n01_WT_1DNAseq_fastqc.html [2022-07-29 04:52:01,923] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFWYFDRX2_l01_n02_undetermined_fastqc.html [2022-07-29 04:52:01,925] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFWYFDRX2_l01_n02_undetermined_fastqc.html [2022-07-29 04:52:01,964] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFWYFDRX2_l01_n01_WT_2DNAseq_fastqc.html [2022-07-29 04:52:01,966] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFWYFDRX2_l01_n01_WT_2DNAseq_fastqc.html [2022-07-29 04:52:02,004] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFWYFDRX2_l01_n01_WT_3DNAseq_fastqc.html [2022-07-29 04:52:02,006] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFWYFDRX2_l01_n01_WT_3DNAseq_fastqc.html [2022-07-29 04:52:02,378] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-07-29 04:52:02,380] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-07-29 04:52:02,391] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-07-29 04:52:02,401] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-07-29 04:52:02,403] multiqc.modules.custom_content.custom_content [INFO ] demux_report-1: Found 4 samples (table) [2022-07-29 04:52:02,409] multiqc [DEBUG ] No samples found: conpair [2022-07-29 04:52:02,417] multiqc [DEBUG ] No samples found: peddy [2022-07-29 04:52:02,423] multiqc [DEBUG ] No samples found: somalier [2022-07-29 04:52:02,428] multiqc [DEBUG ] No samples found: methylQA [2022-07-29 04:52:02,443] multiqc [DEBUG ] No samples found: mosdepth [2022-07-29 04:52:02,450] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-07-29 04:52:02,454] multiqc [DEBUG ] No samples found: qualimap [2022-07-29 04:52:02,462] multiqc [DEBUG ] No samples found: preseq [2022-07-29 04:52:02,468] multiqc [DEBUG ] No samples found: quast [2022-07-29 04:52:02,473] multiqc [DEBUG ] No samples found: qorts [2022-07-29 04:52:02,480] multiqc [DEBUG ] No samples found: rna_seqc [2022-07-29 04:52:02,485] multiqc [DEBUG ] No samples found: rockhopper [2022-07-29 04:52:02,492] multiqc [DEBUG ] No samples found: rsem [2022-07-29 04:52:02,511] multiqc [DEBUG ] No samples found: rseqc [2022-07-29 04:52:02,517] multiqc [DEBUG ] No samples found: busco [2022-07-29 04:52:02,524] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-07-29 04:52:02,531] multiqc [DEBUG ] No samples found: disambiguate [2022-07-29 04:52:02,536] multiqc [DEBUG ] No samples found: supernova [2022-07-29 04:52:02,556] multiqc [DEBUG ] No samples found: deeptools [2022-07-29 04:52:02,561] multiqc [DEBUG ] No samples found: sargasso [2022-07-29 04:52:02,566] multiqc [DEBUG ] No samples found: verifybamid [2022-07-29 04:52:02,573] multiqc [DEBUG ] No samples found: mirtrace [2022-07-29 04:52:02,579] multiqc [DEBUG ] No samples found: happy [2022-07-29 04:52:02,585] multiqc [DEBUG ] No samples found: mirtop [2022-07-29 04:52:02,593] multiqc [DEBUG ] No samples found: homer [2022-07-29 04:52:02,600] multiqc [DEBUG ] No samples found: macs2 [2022-07-29 04:52:02,604] multiqc [DEBUG ] No samples found: theta2 [2022-07-29 04:52:02,609] multiqc [DEBUG ] No samples found: snpeff [2022-07-29 04:52:02,619] multiqc [DEBUG ] No samples found: gatk [2022-07-29 04:52:02,625] multiqc [DEBUG ] No samples found: htseq [2022-07-29 04:52:02,632] multiqc [DEBUG ] No samples found: bcftools [2022-07-29 04:52:02,637] multiqc [DEBUG ] No samples found: featureCounts [2022-07-29 04:52:02,647] multiqc [DEBUG ] No samples found: fgbio [2022-07-29 04:52:02,668] multiqc [DEBUG ] No samples found: dragen [2022-07-29 04:52:02,675] multiqc [DEBUG ] No samples found: dedup [2022-07-29 04:52:02,681] multiqc [DEBUG ] No samples found: damageprofiler [2022-07-29 04:52:02,729] multiqc [DEBUG ] No samples found: biobambam2 [2022-07-29 04:52:02,736] multiqc [DEBUG ] No samples found: mtnucratio [2022-07-29 04:52:02,738] multiqc [DEBUG ] No samples found: picard [2022-07-29 04:52:02,744] multiqc [DEBUG ] No samples found: prokka [2022-07-29 04:52:02,749] multiqc [DEBUG ] No samples found: samblaster [2022-07-29 04:52:02,760] multiqc [DEBUG ] No samples found: samtools [2022-07-29 04:52:02,767] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-07-29 04:52:02,775] multiqc [DEBUG ] No samples found: bamtools [2022-07-29 04:52:02,779] multiqc [DEBUG ] No samples found: jellyfish [2022-07-29 04:52:02,789] multiqc [DEBUG ] No samples found: vcftools [2022-07-29 04:52:02,794] multiqc [DEBUG ] No samples found: longranger [2022-07-29 04:52:02,798] multiqc [DEBUG ] No samples found: stacks [2022-07-29 04:52:02,804] multiqc [DEBUG ] No samples found: varscan2 [2022-07-29 04:52:02,831] multiqc [DEBUG ] No samples found: bbmap [2022-07-29 04:52:02,836] multiqc [DEBUG ] No samples found: bismark [2022-07-29 04:52:02,844] multiqc [DEBUG ] No samples found: biscuit [2022-07-29 04:52:02,849] multiqc [DEBUG ] No samples found: hicexplorer [2022-07-29 04:52:02,853] multiqc [DEBUG ] No samples found: hicup [2022-07-29 04:52:02,858] multiqc [DEBUG ] No samples found: hicpro [2022-07-29 04:52:02,865] multiqc [DEBUG ] No samples found: salmon [2022-07-29 04:52:02,871] multiqc [DEBUG ] No samples found: kallisto [2022-07-29 04:52:02,878] multiqc [DEBUG ] No samples found: slamdunk [2022-07-29 04:52:02,883] multiqc [DEBUG ] No samples found: star [2022-07-29 04:52:02,888] multiqc [DEBUG ] No samples found: hisat2 [2022-07-29 04:52:02,894] multiqc [DEBUG ] No samples found: tophat [2022-07-29 04:52:02,899] multiqc [DEBUG ] No samples found: bowtie2 [2022-07-29 04:52:02,904] multiqc [DEBUG ] No samples found: bowtie1 [2022-07-29 04:52:02,911] multiqc [DEBUG ] No samples found: snpsplit [2022-07-29 04:52:02,917] multiqc [DEBUG ] No samples found: kat [2022-07-29 04:52:02,923] multiqc [DEBUG ] No samples found: leehom [2022-07-29 04:52:02,931] multiqc [DEBUG ] No samples found: adapterRemoval [2022-07-29 04:52:02,937] multiqc [DEBUG ] No samples found: clipandmerge [2022-07-29 04:52:02,944] multiqc [DEBUG ] No samples found: cutadapt [2022-07-29 04:52:02,950] multiqc [DEBUG ] No samples found: flexbar [2022-07-29 04:52:02,958] multiqc [DEBUG ] No samples found: kaiju [2022-07-29 04:52:02,963] multiqc [DEBUG ] No samples found: kraken [2022-07-29 04:52:02,970] multiqc [DEBUG ] No samples found: malt [2022-07-29 04:52:02,976] multiqc [DEBUG ] No samples found: trimmomatic [2022-07-29 04:52:02,981] multiqc [DEBUG ] No samples found: sickle [2022-07-29 04:52:02,986] multiqc [DEBUG ] No samples found: skewer [2022-07-29 04:52:02,994] multiqc [DEBUG ] No samples found: sortmerna [2022-07-29 04:52:03,000] multiqc [DEBUG ] No samples found: biobloomtools [2022-07-29 04:52:03,005] multiqc [DEBUG ] No samples found: fastq_screen [2022-07-29 04:52:03,010] multiqc [DEBUG ] No samples found: afterqc [2022-07-29 04:52:03,016] multiqc [DEBUG ] No samples found: fastp [2022-07-29 04:52:03,207] multiqc.modules.fastqc.fastqc [INFO ] Found 8 reports [2022-07-29 04:52:03,292] multiqc [DEBUG ] No samples found: pycoqc [2022-07-29 04:52:03,298] multiqc [DEBUG ] No samples found: minionqc [2022-07-29 04:52:03,304] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-07-29 04:52:03,312] multiqc [DEBUG ] No samples found: clusterflow [2022-07-29 04:52:03,317] multiqc [DEBUG ] No samples found: bcl2fastq [2022-07-29 04:52:03,323] multiqc [DEBUG ] No samples found: interop [2022-07-29 04:52:03,330] multiqc [DEBUG ] No samples found: ivar [2022-07-29 04:52:03,335] multiqc [DEBUG ] No samples found: flash [2022-07-29 04:52:03,342] multiqc [DEBUG ] No samples found: seqyclean [2022-07-29 04:52:03,342] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2022-07-29 04:52:03,342] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2022-07-29 04:52:03,342] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-07-29 04:52:03,343] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 1 Demultiplexing Report'. [2022-07-29 04:52:03,343] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-07-29 04:52:03,353] multiqc [INFO ] Compressing plot data [2022-07-29 04:52:03,499] multiqc [INFO ] Report : multiqc_report.html [2022-07-29 04:52:03,499] multiqc [INFO ] Data : multiqc_data [2022-07-29 04:52:03,499] multiqc [DEBUG ] Moving data file from '/state/partition1/job-22959527/tmp6z6sus6k/multiqc_data' to '/scratch/gencore/logs/html/HFWYFDRX2/1/multiqc_data' [2022-07-29 04:52:03,631] multiqc [INFO ] MultiQC complete