[2021-06-22 02:08:55,848] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-06-22 02:08:55,848] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-06-22 02:08:55,848] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-06-22 02:08:55,849] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-06-22 02:08:55,849] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-06-22 02:08:55,850] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H55KCBGXJ/merged [2021-06-22 02:08:57,293] multiqc [WARNING] MultiQC Version v1.10.1 now available! [2021-06-22 02:08:57,293] multiqc [INFO ] This is MultiQC v1.9 [2021-06-22 02:08:57,293] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H55KCBGXJ/merged [2021-06-22 02:08:57,293] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H55KCBGXJ/merged [2021-06-22 02:08:57,293] multiqc [INFO ] Template : default [2021-06-22 02:08:57,294] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-06-22 02:08:57,294] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H55KCBGXJ/merged [2021-06-22 02:08:57,294] 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 [2021-06-22 02:08:57,294] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-7887308/tmpaond7ibo [2021-06-22 02:08:57,402] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H55KCBGXJ_n01_undetermined_fastqc.html [2021-06-22 02:08:57,407] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H55KCBGXJ_n01_undetermined_fastqc.html [2021-06-22 02:08:57,451] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-06-22 02:08:57,452] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-06-22 02:08:57,577] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H55KCBGXJ_n01_AKM244_fastqc.html [2021-06-22 02:08:57,579] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H55KCBGXJ_n01_AKM244_fastqc.html [2021-06-22 02:08:57,621] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H55KCBGXJ_n01_AKM253_fastqc.html [2021-06-22 02:08:57,623] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H55KCBGXJ_n01_AKM253_fastqc.html [2021-06-22 02:08:57,667] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H55KCBGXJ_n01_AKM248_fastqc.html [2021-06-22 02:08:57,669] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H55KCBGXJ_n01_AKM248_fastqc.html [2021-06-22 02:08:57,711] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H55KCBGXJ_n01_AKM247_fastqc.html [2021-06-22 02:08:57,713] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H55KCBGXJ_n01_AKM247_fastqc.html [2021-06-22 02:08:57,757] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H55KCBGXJ_n01_AKM252_fastqc.html [2021-06-22 02:08:57,758] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H55KCBGXJ_n01_AKM252_fastqc.html [2021-06-22 02:08:57,801] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H55KCBGXJ_n01_AKM263_fastqc.html [2021-06-22 02:08:57,803] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H55KCBGXJ_n01_AKM263_fastqc.html [2021-06-22 02:08:57,847] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H55KCBGXJ_n01_AKM261_fastqc.html [2021-06-22 02:08:57,849] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H55KCBGXJ_n01_AKM261_fastqc.html [2021-06-22 02:08:57,892] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H55KCBGXJ_n01_AKM257_fastqc.html [2021-06-22 02:08:57,894] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H55KCBGXJ_n01_AKM257_fastqc.html [2021-06-22 02:08:57,936] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H55KCBGXJ_n01_AKM256_fastqc.html [2021-06-22 02:08:57,938] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H55KCBGXJ_n01_AKM256_fastqc.html [2021-06-22 02:08:57,980] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H55KCBGXJ_n01_AKM259_fastqc.html [2021-06-22 02:08:57,982] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H55KCBGXJ_n01_AKM259_fastqc.html [2021-06-22 02:08:58,024] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H55KCBGXJ_n01_AKM264_fastqc.html [2021-06-22 02:08:58,026] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H55KCBGXJ_n01_AKM264_fastqc.html [2021-06-22 02:08:58,070] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H55KCBGXJ_n01_AKM245_fastqc.html [2021-06-22 02:08:58,072] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H55KCBGXJ_n01_AKM245_fastqc.html [2021-06-22 02:08:58,114] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H55KCBGXJ_n01_AKM246_fastqc.html [2021-06-22 02:08:58,116] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H55KCBGXJ_n01_AKM246_fastqc.html [2021-06-22 02:08:58,158] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H55KCBGXJ_n01_AKM250_fastqc.html [2021-06-22 02:08:58,160] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H55KCBGXJ_n01_AKM250_fastqc.html [2021-06-22 02:08:58,203] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H55KCBGXJ_n01_AKM255_fastqc.html [2021-06-22 02:08:58,205] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H55KCBGXJ_n01_AKM255_fastqc.html [2021-06-22 02:08:58,248] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H55KCBGXJ_n01_AKM249_fastqc.html [2021-06-22 02:08:58,250] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H55KCBGXJ_n01_AKM249_fastqc.html [2021-06-22 02:08:58,293] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H55KCBGXJ_n01_AKM251_fastqc.html [2021-06-22 02:08:58,294] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H55KCBGXJ_n01_AKM251_fastqc.html [2021-06-22 02:08:58,338] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H55KCBGXJ_n01_AKM260_fastqc.html [2021-06-22 02:08:58,340] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H55KCBGXJ_n01_AKM260_fastqc.html [2021-06-22 02:08:58,381] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H55KCBGXJ_n01_AKM265_fastqc.html [2021-06-22 02:08:58,383] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H55KCBGXJ_n01_AKM265_fastqc.html [2021-06-22 02:08:58,424] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H55KCBGXJ_n01_AKM243_fastqc.html [2021-06-22 02:08:58,425] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H55KCBGXJ_n01_AKM243_fastqc.html [2021-06-22 02:08:58,466] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H55KCBGXJ_n01_AKM254_fastqc.html [2021-06-22 02:08:58,468] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H55KCBGXJ_n01_AKM254_fastqc.html [2021-06-22 02:08:58,510] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H55KCBGXJ_n01_AKM258_fastqc.html [2021-06-22 02:08:58,512] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H55KCBGXJ_n01_AKM258_fastqc.html [2021-06-22 02:08:58,554] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H55KCBGXJ_n01_AKM262_fastqc.html [2021-06-22 02:08:58,556] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H55KCBGXJ_n01_AKM262_fastqc.html [2021-06-22 02:08:58,600] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H55KCBGXJ_n01_AKM266_fastqc.html [2021-06-22 02:08:58,602] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H55KCBGXJ_n01_AKM266_fastqc.html [2021-06-22 02:08:59,223] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-06-22 02:08:59,225] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-06-22 02:08:59,243] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 25 samples (table) [2021-06-22 02:08:59,245] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-06-22 02:08:59,255] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-06-22 02:08:59,260] multiqc [DEBUG ] No samples found: conpair [2021-06-22 02:08:59,265] multiqc [DEBUG ] No samples found: peddy [2021-06-22 02:08:59,270] multiqc [DEBUG ] No samples found: somalier [2021-06-22 02:08:59,275] multiqc [DEBUG ] No samples found: methylQA [2021-06-22 02:08:59,283] multiqc [DEBUG ] No samples found: mosdepth [2021-06-22 02:08:59,287] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-06-22 02:08:59,290] multiqc [DEBUG ] No samples found: qualimap [2021-06-22 02:08:59,295] multiqc [DEBUG ] No samples found: preseq [2021-06-22 02:08:59,301] multiqc [DEBUG ] No samples found: quast [2021-06-22 02:08:59,305] multiqc [DEBUG ] No samples found: qorts [2021-06-22 02:08:59,310] multiqc [DEBUG ] No samples found: rna_seqc [2021-06-22 02:08:59,315] multiqc [DEBUG ] No samples found: rockhopper [2021-06-22 02:08:59,320] multiqc [DEBUG ] No samples found: rsem [2021-06-22 02:08:59,331] multiqc [DEBUG ] No samples found: rseqc [2021-06-22 02:08:59,335] multiqc [DEBUG ] No samples found: busco [2021-06-22 02:08:59,340] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-06-22 02:08:59,345] multiqc [DEBUG ] No samples found: disambiguate [2021-06-22 02:08:59,350] multiqc [DEBUG ] No samples found: supernova [2021-06-22 02:08:59,362] multiqc [DEBUG ] No samples found: deeptools [2021-06-22 02:08:59,367] multiqc [DEBUG ] No samples found: sargasso [2021-06-22 02:08:59,372] multiqc [DEBUG ] No samples found: verifybamid [2021-06-22 02:08:59,377] multiqc [DEBUG ] No samples found: mirtrace [2021-06-22 02:08:59,381] multiqc [DEBUG ] No samples found: happy [2021-06-22 02:08:59,386] multiqc [DEBUG ] No samples found: mirtop [2021-06-22 02:08:59,392] multiqc [DEBUG ] No samples found: homer [2021-06-22 02:08:59,397] multiqc [DEBUG ] No samples found: macs2 [2021-06-22 02:08:59,402] multiqc [DEBUG ] No samples found: theta2 [2021-06-22 02:08:59,407] multiqc [DEBUG ] No samples found: snpeff [2021-06-22 02:08:59,414] multiqc [DEBUG ] No samples found: gatk [2021-06-22 02:08:59,418] multiqc [DEBUG ] No samples found: htseq [2021-06-22 02:08:59,424] multiqc [DEBUG ] No samples found: bcftools [2021-06-22 02:08:59,428] multiqc [DEBUG ] No samples found: featureCounts [2021-06-22 02:08:59,435] multiqc [DEBUG ] No samples found: fgbio [2021-06-22 02:08:59,448] multiqc [DEBUG ] No samples found: dragen [2021-06-22 02:08:59,452] multiqc [DEBUG ] No samples found: dedup [2021-06-22 02:08:59,457] multiqc [DEBUG ] No samples found: damageprofiler [2021-06-22 02:08:59,480] multiqc [DEBUG ] No samples found: biobambam2 [2021-06-22 02:08:59,485] multiqc [DEBUG ] No samples found: mtnucratio [2021-06-22 02:08:59,487] multiqc [DEBUG ] No samples found: picard [2021-06-22 02:08:59,492] multiqc [DEBUG ] No samples found: prokka [2021-06-22 02:08:59,496] multiqc [DEBUG ] No samples found: samblaster [2021-06-22 02:08:59,504] multiqc [DEBUG ] No samples found: samtools [2021-06-22 02:08:59,509] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-06-22 02:08:59,514] multiqc [DEBUG ] No samples found: bamtools [2021-06-22 02:08:59,518] multiqc [DEBUG ] No samples found: jellyfish [2021-06-22 02:08:59,525] multiqc [DEBUG ] No samples found: vcftools [2021-06-22 02:08:59,530] multiqc [DEBUG ] No samples found: longranger [2021-06-22 02:08:59,535] multiqc [DEBUG ] No samples found: stacks [2021-06-22 02:08:59,540] multiqc [DEBUG ] No samples found: varscan2 [2021-06-22 02:08:59,554] multiqc [DEBUG ] No samples found: bbmap [2021-06-22 02:08:59,559] multiqc [DEBUG ] No samples found: bismark [2021-06-22 02:08:59,564] multiqc [DEBUG ] No samples found: biscuit [2021-06-22 02:08:59,569] multiqc [DEBUG ] No samples found: hicexplorer [2021-06-22 02:08:59,575] multiqc [DEBUG ] No samples found: hicup [2021-06-22 02:08:59,579] multiqc [DEBUG ] No samples found: hicpro [2021-06-22 02:08:59,584] multiqc [DEBUG ] No samples found: salmon [2021-06-22 02:08:59,589] multiqc [DEBUG ] No samples found: kallisto [2021-06-22 02:08:59,594] multiqc [DEBUG ] No samples found: slamdunk [2021-06-22 02:08:59,599] multiqc [DEBUG ] No samples found: star [2021-06-22 02:08:59,603] multiqc [DEBUG ] No samples found: hisat2 [2021-06-22 02:08:59,608] multiqc [DEBUG ] No samples found: tophat [2021-06-22 02:08:59,613] multiqc [DEBUG ] No samples found: bowtie2 [2021-06-22 02:08:59,618] multiqc [DEBUG ] No samples found: bowtie1 [2021-06-22 02:08:59,622] multiqc [DEBUG ] No samples found: snpsplit [2021-06-22 02:08:59,627] multiqc [DEBUG ] No samples found: kat [2021-06-22 02:08:59,631] multiqc [DEBUG ] No samples found: leehom [2021-06-22 02:08:59,636] multiqc [DEBUG ] No samples found: adapterRemoval [2021-06-22 02:08:59,640] multiqc [DEBUG ] No samples found: clipandmerge [2021-06-22 02:08:59,645] multiqc [DEBUG ] No samples found: cutadapt [2021-06-22 02:08:59,650] multiqc [DEBUG ] No samples found: flexbar [2021-06-22 02:08:59,655] multiqc [DEBUG ] No samples found: kaiju [2021-06-22 02:08:59,660] multiqc [DEBUG ] No samples found: kraken [2021-06-22 02:08:59,665] multiqc [DEBUG ] No samples found: malt [2021-06-22 02:08:59,669] multiqc [DEBUG ] No samples found: trimmomatic [2021-06-22 02:08:59,674] multiqc [DEBUG ] No samples found: sickle [2021-06-22 02:08:59,679] multiqc [DEBUG ] No samples found: skewer [2021-06-22 02:08:59,683] multiqc [DEBUG ] No samples found: sortmerna [2021-06-22 02:08:59,687] multiqc [DEBUG ] No samples found: biobloomtools [2021-06-22 02:08:59,692] multiqc [DEBUG ] No samples found: fastq_screen [2021-06-22 02:08:59,697] multiqc [DEBUG ] No samples found: afterqc [2021-06-22 02:08:59,702] multiqc [DEBUG ] No samples found: fastp [2021-06-22 02:09:01,389] multiqc.modules.fastqc.fastqc [INFO ] Found 25 reports [2021-06-22 02:09:01,920] multiqc [DEBUG ] No samples found: pycoqc [2021-06-22 02:09:01,925] multiqc [DEBUG ] No samples found: minionqc [2021-06-22 02:09:01,930] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-06-22 02:09:01,935] multiqc [DEBUG ] No samples found: clusterflow [2021-06-22 02:09:01,940] multiqc [DEBUG ] No samples found: bcl2fastq [2021-06-22 02:09:01,945] multiqc [DEBUG ] No samples found: interop [2021-06-22 02:09:01,949] multiqc [DEBUG ] No samples found: ivar [2021-06-22 02:09:01,954] multiqc [DEBUG ] No samples found: flash [2021-06-22 02:09:01,959] multiqc [DEBUG ] No samples found: seqyclean [2021-06-22 02:09:01,959] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-06-22 02:09:01,959] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-06-22 02:09:01,959] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-06-22 02:09:01,959] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-06-22 02:09:01,988] multiqc [INFO ] Compressing plot data [2021-06-22 02:09:02,440] multiqc [INFO ] Report : multiqc_report.html [2021-06-22 02:09:02,440] multiqc [INFO ] Data : multiqc_data [2021-06-22 02:09:02,440] multiqc [DEBUG ] Moving data file from '/state/partition1/job-7887308/tmpaond7ibo/multiqc_data' to '/scratch/gencore/logs/html/H55KCBGXJ/merged/multiqc_data' [2021-06-22 02:09:02,563] multiqc [INFO ] MultiQC complete