[2021-06-03 15:16:17,836] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-06-03 15:16:17,836] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-06-03 15:16:17,836] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-06-03 15:16:17,837] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-06-03 15:16:17,837] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-06-03 15:16:17,837] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HNKGJDSXY/merged [2021-06-03 15:16:19,195] multiqc [WARNING] MultiQC Version v1.10.1 now available! [2021-06-03 15:16:19,196] multiqc [INFO ] This is MultiQC v1.9 [2021-06-03 15:16:19,196] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HNKGJDSXY/merged [2021-06-03 15:16:19,196] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HNKGJDSXY/merged [2021-06-03 15:16:19,196] multiqc [INFO ] Template : default [2021-06-03 15:16:19,196] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-06-03 15:16:19,196] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HNKGJDSXY/merged [2021-06-03 15:16:19,196] 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 [2021-06-03 15:16:19,196] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpmrlg__xy [2021-06-03 15:16:19,339] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNKGJDSXY_2_fastqc.html [2021-06-03 15:16:19,341] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNKGJDSXY_2_fastqc.html [2021-06-03 15:16:19,400] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNKGJDSXY_3_fastqc.html [2021-06-03 15:16:19,402] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNKGJDSXY_3_fastqc.html [2021-06-03 15:16:19,447] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNKGJDSXY_1_fastqc.html [2021-06-03 15:16:19,449] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNKGJDSXY_1_fastqc.html [2021-06-03 15:16:19,489] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNKGJDSXY_4_fastqc.html [2021-06-03 15:16:19,491] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNKGJDSXY_4_fastqc.html [2021-06-03 15:16:20,033] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-06-03 15:16:20,034] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-06-03 15:16:20,038] multiqc.modules.custom_content.custom_content [WARNING] Not able to parse custom data in undetermined_barcodes_mqc.txt [2021-06-03 15:16:20,040] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-06-03 15:16:20,046] multiqc [DEBUG ] No samples found: conpair [2021-06-03 15:16:20,052] multiqc [DEBUG ] No samples found: peddy [2021-06-03 15:16:20,058] multiqc [DEBUG ] No samples found: somalier [2021-06-03 15:16:20,062] multiqc [DEBUG ] No samples found: methylQA [2021-06-03 15:16:20,071] multiqc [DEBUG ] No samples found: mosdepth [2021-06-03 15:16:20,076] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-06-03 15:16:20,079] multiqc [DEBUG ] No samples found: qualimap [2021-06-03 15:16:20,085] multiqc [DEBUG ] No samples found: preseq [2021-06-03 15:16:20,090] multiqc [DEBUG ] No samples found: quast [2021-06-03 15:16:20,095] multiqc [DEBUG ] No samples found: qorts [2021-06-03 15:16:20,100] multiqc [DEBUG ] No samples found: rna_seqc [2021-06-03 15:16:20,107] multiqc [DEBUG ] No samples found: rockhopper [2021-06-03 15:16:20,112] multiqc [DEBUG ] No samples found: rsem [2021-06-03 15:16:20,130] multiqc [DEBUG ] No samples found: rseqc [2021-06-03 15:16:20,134] multiqc [DEBUG ] No samples found: busco [2021-06-03 15:16:20,140] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-06-03 15:16:20,144] multiqc [DEBUG ] No samples found: disambiguate [2021-06-03 15:16:20,149] multiqc [DEBUG ] No samples found: supernova [2021-06-03 15:16:20,162] multiqc [DEBUG ] No samples found: deeptools [2021-06-03 15:16:20,167] multiqc [DEBUG ] No samples found: sargasso [2021-06-03 15:16:20,172] multiqc [DEBUG ] No samples found: verifybamid [2021-06-03 15:16:20,177] multiqc [DEBUG ] No samples found: mirtrace [2021-06-03 15:16:20,182] multiqc [DEBUG ] No samples found: happy [2021-06-03 15:16:20,187] multiqc [DEBUG ] No samples found: mirtop [2021-06-03 15:16:20,194] multiqc [DEBUG ] No samples found: homer [2021-06-03 15:16:20,199] multiqc [DEBUG ] No samples found: macs2 [2021-06-03 15:16:20,204] multiqc [DEBUG ] No samples found: theta2 [2021-06-03 15:16:20,209] multiqc [DEBUG ] No samples found: snpeff [2021-06-03 15:16:20,216] multiqc [DEBUG ] No samples found: gatk [2021-06-03 15:16:20,221] multiqc [DEBUG ] No samples found: htseq [2021-06-03 15:16:20,227] multiqc [DEBUG ] No samples found: bcftools [2021-06-03 15:16:20,232] multiqc [DEBUG ] No samples found: featureCounts [2021-06-03 15:16:20,238] multiqc [DEBUG ] No samples found: fgbio [2021-06-03 15:16:20,251] multiqc [DEBUG ] No samples found: dragen [2021-06-03 15:16:20,256] multiqc [DEBUG ] No samples found: dedup [2021-06-03 15:16:20,261] multiqc [DEBUG ] No samples found: damageprofiler [2021-06-03 15:16:20,294] multiqc [DEBUG ] No samples found: biobambam2 [2021-06-03 15:16:20,300] multiqc [DEBUG ] No samples found: mtnucratio [2021-06-03 15:16:20,302] multiqc [DEBUG ] No samples found: picard [2021-06-03 15:16:20,308] multiqc [DEBUG ] No samples found: prokka [2021-06-03 15:16:20,312] multiqc [DEBUG ] No samples found: samblaster [2021-06-03 15:16:20,321] multiqc [DEBUG ] No samples found: samtools [2021-06-03 15:16:20,326] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-06-03 15:16:20,331] multiqc [DEBUG ] No samples found: bamtools [2021-06-03 15:16:20,336] multiqc [DEBUG ] No samples found: jellyfish [2021-06-03 15:16:20,343] multiqc [DEBUG ] No samples found: vcftools [2021-06-03 15:16:20,348] multiqc [DEBUG ] No samples found: longranger [2021-06-03 15:16:20,353] multiqc [DEBUG ] No samples found: stacks [2021-06-03 15:16:20,358] multiqc [DEBUG ] No samples found: varscan2 [2021-06-03 15:16:20,370] multiqc [DEBUG ] No samples found: bbmap [2021-06-03 15:16:20,375] multiqc [DEBUG ] No samples found: bismark [2021-06-03 15:16:20,381] multiqc [DEBUG ] No samples found: biscuit [2021-06-03 15:16:20,386] multiqc [DEBUG ] No samples found: hicexplorer [2021-06-03 15:16:20,391] multiqc [DEBUG ] No samples found: hicup [2021-06-03 15:16:20,397] multiqc [DEBUG ] No samples found: hicpro [2021-06-03 15:16:20,404] multiqc [DEBUG ] No samples found: salmon [2021-06-03 15:16:20,409] multiqc [DEBUG ] No samples found: kallisto [2021-06-03 15:16:20,414] multiqc [DEBUG ] No samples found: slamdunk [2021-06-03 15:16:20,419] multiqc [DEBUG ] No samples found: star [2021-06-03 15:16:20,424] multiqc [DEBUG ] No samples found: hisat2 [2021-06-03 15:16:20,429] multiqc [DEBUG ] No samples found: tophat [2021-06-03 15:16:20,434] multiqc [DEBUG ] No samples found: bowtie2 [2021-06-03 15:16:20,439] multiqc [DEBUG ] No samples found: bowtie1 [2021-06-03 15:16:20,443] multiqc [DEBUG ] No samples found: snpsplit [2021-06-03 15:16:20,448] multiqc [DEBUG ] No samples found: kat [2021-06-03 15:16:20,452] multiqc [DEBUG ] No samples found: leehom [2021-06-03 15:16:20,457] multiqc [DEBUG ] No samples found: adapterRemoval [2021-06-03 15:16:20,462] multiqc [DEBUG ] No samples found: clipandmerge [2021-06-03 15:16:20,467] multiqc [DEBUG ] No samples found: cutadapt [2021-06-03 15:16:20,471] multiqc [DEBUG ] No samples found: flexbar [2021-06-03 15:16:20,476] multiqc [DEBUG ] No samples found: kaiju [2021-06-03 15:16:20,481] multiqc [DEBUG ] No samples found: kraken [2021-06-03 15:16:20,486] multiqc [DEBUG ] No samples found: malt [2021-06-03 15:16:20,490] multiqc [DEBUG ] No samples found: trimmomatic [2021-06-03 15:16:20,495] multiqc [DEBUG ] No samples found: sickle [2021-06-03 15:16:20,499] multiqc [DEBUG ] No samples found: skewer [2021-06-03 15:16:20,504] multiqc [DEBUG ] No samples found: sortmerna [2021-06-03 15:16:20,508] multiqc [DEBUG ] No samples found: biobloomtools [2021-06-03 15:16:20,513] multiqc [DEBUG ] No samples found: fastq_screen [2021-06-03 15:16:20,519] multiqc [DEBUG ] No samples found: afterqc [2021-06-03 15:16:20,527] multiqc [DEBUG ] No samples found: fastp [2021-06-03 15:16:20,958] multiqc.modules.fastqc.fastqc [INFO ] Found 4 reports [2021-06-03 15:16:21,004] multiqc [DEBUG ] No samples found: pycoqc [2021-06-03 15:16:21,009] multiqc [DEBUG ] No samples found: minionqc [2021-06-03 15:16:21,014] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-06-03 15:16:21,019] multiqc [DEBUG ] No samples found: clusterflow [2021-06-03 15:16:21,024] multiqc [DEBUG ] No samples found: bcl2fastq [2021-06-03 15:16:21,029] multiqc [DEBUG ] No samples found: interop [2021-06-03 15:16:21,034] multiqc [DEBUG ] No samples found: ivar [2021-06-03 15:16:21,039] multiqc [DEBUG ] No samples found: flash [2021-06-03 15:16:21,044] multiqc [DEBUG ] No samples found: seqyclean [2021-06-03 15:16:21,044] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2021-06-03 15:16:21,044] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-06-03 15:16:21,044] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-06-03 15:16:21,050] multiqc [INFO ] Compressing plot data [2021-06-03 15:16:21,123] multiqc [INFO ] Report : multiqc_report.html [2021-06-03 15:16:21,123] multiqc [INFO ] Data : multiqc_data [2021-06-03 15:16:21,123] multiqc [DEBUG ] Moving data file from '/tmp/tmpmrlg__xy/multiqc_data' to '/scratch/gencore/logs/html/HNKGJDSXY/merged/multiqc_data' [2021-06-03 15:16:21,249] multiqc [INFO ] MultiQC complete