[2022-06-18 03:09:08,949] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-06-18 03:09:08,949] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-06-18 03:09:08,949] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-06-18 03:09:08,950] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-06-18 03:09:08,950] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-06-18 03:09:08,951] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H3WMNBGXM/merged [2022-06-18 03:09:09,774] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-06-18 03:09:09,774] multiqc [INFO ] This is MultiQC v1.9 [2022-06-18 03:09:09,775] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H3WMNBGXM/merged [2022-06-18 03:09:09,775] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H3WMNBGXM/merged [2022-06-18 03:09:09,775] multiqc [INFO ] Template : default [2022-06-18 03:09:09,775] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-06-18 03:09:09,775] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H3WMNBGXM/merged [2022-06-18 03:09:09,775] 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 [2022-06-18 03:09:09,775] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-21167629/tmpx5tbumko [2022-06-18 03:09:09,886] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-06-18 03:09:09,888] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-06-18 03:09:10,419] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3WMNBGXM_n01_Alex1_R13_fastqc.html [2022-06-18 03:09:10,421] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3WMNBGXM_n01_Alex1_R13_fastqc.html [2022-06-18 03:09:10,478] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3WMNBGXM_n01_undetermined_fastqc.html [2022-06-18 03:09:10,480] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3WMNBGXM_n01_undetermined_fastqc.html [2022-06-18 03:09:10,525] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3WMNBGXM_n01_GD_R21_fastqc.html [2022-06-18 03:09:10,527] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3WMNBGXM_n01_GD_R21_fastqc.html [2022-06-18 03:09:10,582] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3WMNBGXM_n01_GD_eRNA_R02_A375_Rep0_fastqc.html [2022-06-18 03:09:10,584] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3WMNBGXM_n01_GD_eRNA_R02_A375_Rep0_fastqc.html [2022-06-18 03:09:10,637] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3WMNBGXM_n01_GD_eRNA_R24_K562_A375_fastqc.html [2022-06-18 03:09:10,639] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3WMNBGXM_n01_GD_eRNA_R24_K562_A375_fastqc.html [2022-06-18 03:09:10,689] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3WMNBGXM_n01_GD_R20_fastqc.html [2022-06-18 03:09:10,691] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3WMNBGXM_n01_GD_R20_fastqc.html [2022-06-18 03:09:10,742] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3WMNBGXM_n01_Alex2_R14_fastqc.html [2022-06-18 03:09:10,743] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3WMNBGXM_n01_Alex2_R14_fastqc.html [2022-06-18 03:09:11,104] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-06-18 03:09:11,105] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-06-18 03:09:11,113] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-06-18 03:09:11,117] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 7 samples (table) [2022-06-18 03:09:11,126] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-06-18 03:09:11,132] multiqc [DEBUG ] No samples found: conpair [2022-06-18 03:09:11,137] multiqc [DEBUG ] No samples found: peddy [2022-06-18 03:09:11,143] multiqc [DEBUG ] No samples found: somalier [2022-06-18 03:09:11,149] multiqc [DEBUG ] No samples found: methylQA [2022-06-18 03:09:11,156] multiqc [DEBUG ] No samples found: mosdepth [2022-06-18 03:09:11,160] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-06-18 03:09:11,164] multiqc [DEBUG ] No samples found: qualimap [2022-06-18 03:09:11,168] multiqc [DEBUG ] No samples found: preseq [2022-06-18 03:09:11,173] multiqc [DEBUG ] No samples found: quast [2022-06-18 03:09:11,177] multiqc [DEBUG ] No samples found: qorts [2022-06-18 03:09:11,182] multiqc [DEBUG ] No samples found: rna_seqc [2022-06-18 03:09:11,187] multiqc [DEBUG ] No samples found: rockhopper [2022-06-18 03:09:11,191] multiqc [DEBUG ] No samples found: rsem [2022-06-18 03:09:11,203] multiqc [DEBUG ] No samples found: rseqc [2022-06-18 03:09:11,207] multiqc [DEBUG ] No samples found: busco [2022-06-18 03:09:11,211] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-06-18 03:09:11,215] multiqc [DEBUG ] No samples found: disambiguate [2022-06-18 03:09:11,220] multiqc [DEBUG ] No samples found: supernova [2022-06-18 03:09:11,233] multiqc [DEBUG ] No samples found: deeptools [2022-06-18 03:09:11,238] multiqc [DEBUG ] No samples found: sargasso [2022-06-18 03:09:11,242] multiqc [DEBUG ] No samples found: verifybamid [2022-06-18 03:09:11,246] multiqc [DEBUG ] No samples found: mirtrace [2022-06-18 03:09:11,251] multiqc [DEBUG ] No samples found: happy [2022-06-18 03:09:11,255] multiqc [DEBUG ] No samples found: mirtop [2022-06-18 03:09:11,261] multiqc [DEBUG ] No samples found: homer [2022-06-18 03:09:11,265] multiqc [DEBUG ] No samples found: macs2 [2022-06-18 03:09:11,269] multiqc [DEBUG ] No samples found: theta2 [2022-06-18 03:09:11,275] multiqc [DEBUG ] No samples found: snpeff [2022-06-18 03:09:11,285] multiqc [DEBUG ] No samples found: gatk [2022-06-18 03:09:11,289] multiqc [DEBUG ] No samples found: htseq [2022-06-18 03:09:11,294] multiqc [DEBUG ] No samples found: bcftools [2022-06-18 03:09:11,300] multiqc [DEBUG ] No samples found: featureCounts [2022-06-18 03:09:11,306] multiqc [DEBUG ] No samples found: fgbio [2022-06-18 03:09:11,322] multiqc [DEBUG ] No samples found: dragen [2022-06-18 03:09:11,326] multiqc [DEBUG ] No samples found: dedup [2022-06-18 03:09:11,331] multiqc [DEBUG ] No samples found: damageprofiler [2022-06-18 03:09:11,353] multiqc [DEBUG ] No samples found: biobambam2 [2022-06-18 03:09:11,357] multiqc [DEBUG ] No samples found: mtnucratio [2022-06-18 03:09:11,360] multiqc [DEBUG ] No samples found: picard [2022-06-18 03:09:11,364] multiqc [DEBUG ] No samples found: prokka [2022-06-18 03:09:11,369] multiqc [DEBUG ] No samples found: samblaster [2022-06-18 03:09:11,381] multiqc [DEBUG ] No samples found: samtools [2022-06-18 03:09:11,385] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-06-18 03:09:11,390] multiqc [DEBUG ] No samples found: bamtools [2022-06-18 03:09:11,394] multiqc [DEBUG ] No samples found: jellyfish [2022-06-18 03:09:11,402] multiqc [DEBUG ] No samples found: vcftools [2022-06-18 03:09:11,407] multiqc [DEBUG ] No samples found: longranger [2022-06-18 03:09:11,411] multiqc [DEBUG ] No samples found: stacks [2022-06-18 03:09:11,416] multiqc [DEBUG ] No samples found: varscan2 [2022-06-18 03:09:11,430] multiqc [DEBUG ] No samples found: bbmap [2022-06-18 03:09:11,434] multiqc [DEBUG ] No samples found: bismark [2022-06-18 03:09:11,439] multiqc [DEBUG ] No samples found: biscuit [2022-06-18 03:09:11,443] multiqc [DEBUG ] No samples found: hicexplorer [2022-06-18 03:09:11,448] multiqc [DEBUG ] No samples found: hicup [2022-06-18 03:09:11,452] multiqc [DEBUG ] No samples found: hicpro [2022-06-18 03:09:11,456] multiqc [DEBUG ] No samples found: salmon [2022-06-18 03:09:11,460] multiqc [DEBUG ] No samples found: kallisto [2022-06-18 03:09:11,465] multiqc [DEBUG ] No samples found: slamdunk [2022-06-18 03:09:11,469] multiqc [DEBUG ] No samples found: star [2022-06-18 03:09:11,473] multiqc [DEBUG ] No samples found: hisat2 [2022-06-18 03:09:11,478] multiqc [DEBUG ] No samples found: tophat [2022-06-18 03:09:11,482] multiqc [DEBUG ] No samples found: bowtie2 [2022-06-18 03:09:11,486] multiqc [DEBUG ] No samples found: bowtie1 [2022-06-18 03:09:11,490] multiqc [DEBUG ] No samples found: snpsplit [2022-06-18 03:09:11,494] multiqc [DEBUG ] No samples found: kat [2022-06-18 03:09:11,498] multiqc [DEBUG ] No samples found: leehom [2022-06-18 03:09:11,503] multiqc [DEBUG ] No samples found: adapterRemoval [2022-06-18 03:09:11,507] multiqc [DEBUG ] No samples found: clipandmerge [2022-06-18 03:09:11,511] multiqc [DEBUG ] No samples found: cutadapt [2022-06-18 03:09:11,515] multiqc [DEBUG ] No samples found: flexbar [2022-06-18 03:09:11,519] multiqc [DEBUG ] No samples found: kaiju [2022-06-18 03:09:11,524] multiqc [DEBUG ] No samples found: kraken [2022-06-18 03:09:11,528] multiqc [DEBUG ] No samples found: malt [2022-06-18 03:09:11,532] multiqc [DEBUG ] No samples found: trimmomatic [2022-06-18 03:09:11,536] multiqc [DEBUG ] No samples found: sickle [2022-06-18 03:09:11,542] multiqc [DEBUG ] No samples found: skewer [2022-06-18 03:09:11,546] multiqc [DEBUG ] No samples found: sortmerna [2022-06-18 03:09:11,550] multiqc [DEBUG ] No samples found: biobloomtools [2022-06-18 03:09:11,554] multiqc [DEBUG ] No samples found: fastq_screen [2022-06-18 03:09:11,558] multiqc [DEBUG ] No samples found: afterqc [2022-06-18 03:09:11,563] multiqc [DEBUG ] No samples found: fastp [2022-06-18 03:09:11,990] multiqc.modules.fastqc.fastqc [INFO ] Found 7 reports [2022-06-18 03:09:12,067] multiqc [DEBUG ] No samples found: pycoqc [2022-06-18 03:09:12,073] multiqc [DEBUG ] No samples found: minionqc [2022-06-18 03:09:12,078] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-06-18 03:09:12,083] multiqc [DEBUG ] No samples found: clusterflow [2022-06-18 03:09:12,087] multiqc [DEBUG ] No samples found: bcl2fastq [2022-06-18 03:09:12,092] multiqc [DEBUG ] No samples found: interop [2022-06-18 03:09:12,096] multiqc [DEBUG ] No samples found: ivar [2022-06-18 03:09:12,100] multiqc [DEBUG ] No samples found: flash [2022-06-18 03:09:12,105] multiqc [DEBUG ] No samples found: seqyclean [2022-06-18 03:09:12,105] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-06-18 03:09:12,105] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-06-18 03:09:12,105] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-06-18 03:09:12,105] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-06-18 03:09:12,114] multiqc [INFO ] Compressing plot data [2022-06-18 03:09:12,231] multiqc [INFO ] Report : multiqc_report.html [2022-06-18 03:09:12,231] multiqc [INFO ] Data : multiqc_data [2022-06-18 03:09:12,232] multiqc [DEBUG ] Moving data file from '/state/partition1/job-21167629/tmpx5tbumko/multiqc_data' to '/scratch/gencore/logs/html/H3WMNBGXM/merged/multiqc_data' [2022-06-18 03:09:12,368] multiqc [INFO ] MultiQC complete