[2023-05-13 17:42:04,421] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-05-13 17:42:04,421] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-05-13 17:42:04,421] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-05-13 17:42:04,423] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-05-13 17:42:04,423] multiqc [DEBUG ] New config 'report_section_order': {'general_stats': {'order': 1000}, 'demux_report': {'order': 900}, 'demux_report-1': {'order': 900}, 'demux_report-2': {'order': 900}, 'undetermined_barcodes': {'order': 800}, 'run_stats': {'order': 700}, 'fastqc': {'order': 500}} [2023-05-13 17:42:04,423] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H7K2JDRX3/merged [2023-05-13 17:42:05,593] multiqc [WARNING] MultiQC Version v1.14 now available! [2023-05-13 17:42:05,593] multiqc [INFO ] This is MultiQC v1.9 [2023-05-13 17:42:05,594] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H7K2JDRX3/merged [2023-05-13 17:42:05,594] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H7K2JDRX3/merged [2023-05-13 17:42:05,594] multiqc [INFO ] Template : default [2023-05-13 17:42:05,594] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-05-13 17:42:05,594] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H7K2JDRX3/merged [2023-05-13 17:42:05,594] 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 [2023-05-13 17:42:05,594] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-33295231/tmpxu51kjtd [2023-05-13 17:42:05,717] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7K2JDRX3_3_fastqc.html [2023-05-13 17:42:05,719] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7K2JDRX3_3_fastqc.html [2023-05-13 17:42:05,775] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7K2JDRX3_1_fastqc.html [2023-05-13 17:42:05,777] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7K2JDRX3_1_fastqc.html [2023-05-13 17:42:05,819] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7K2JDRX3_4_fastqc.html [2023-05-13 17:42:05,821] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7K2JDRX3_4_fastqc.html [2023-05-13 17:42:05,864] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7K2JDRX3_2_fastqc.html [2023-05-13 17:42:05,866] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7K2JDRX3_2_fastqc.html [2023-05-13 17:42:06,626] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-05-13 17:42:06,628] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-05-13 17:42:06,631] multiqc.modules.custom_content.custom_content [WARNING] Not able to parse custom data in undetermined_barcodes_mqc.txt [2023-05-13 17:42:06,634] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-05-13 17:42:06,638] multiqc [DEBUG ] No samples found: conpair [2023-05-13 17:42:06,643] multiqc [DEBUG ] No samples found: peddy [2023-05-13 17:42:06,647] multiqc [DEBUG ] No samples found: somalier [2023-05-13 17:42:06,651] multiqc [DEBUG ] No samples found: methylQA [2023-05-13 17:42:06,659] multiqc [DEBUG ] No samples found: mosdepth [2023-05-13 17:42:06,663] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-05-13 17:42:06,666] multiqc [DEBUG ] No samples found: qualimap [2023-05-13 17:42:06,670] multiqc [DEBUG ] No samples found: preseq [2023-05-13 17:42:06,675] multiqc [DEBUG ] No samples found: quast [2023-05-13 17:42:06,679] multiqc [DEBUG ] No samples found: qorts [2023-05-13 17:42:06,683] multiqc [DEBUG ] No samples found: rna_seqc [2023-05-13 17:42:06,688] multiqc [DEBUG ] No samples found: rockhopper [2023-05-13 17:42:06,692] multiqc [DEBUG ] No samples found: rsem [2023-05-13 17:42:06,701] multiqc [DEBUG ] No samples found: rseqc [2023-05-13 17:42:06,705] multiqc [DEBUG ] No samples found: busco [2023-05-13 17:42:06,710] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-05-13 17:42:06,714] multiqc [DEBUG ] No samples found: disambiguate [2023-05-13 17:42:06,718] multiqc [DEBUG ] No samples found: supernova [2023-05-13 17:42:06,729] multiqc [DEBUG ] No samples found: deeptools [2023-05-13 17:42:06,734] multiqc [DEBUG ] No samples found: sargasso [2023-05-13 17:42:06,738] multiqc [DEBUG ] No samples found: verifybamid [2023-05-13 17:42:06,743] multiqc [DEBUG ] No samples found: mirtrace [2023-05-13 17:42:06,747] multiqc [DEBUG ] No samples found: happy [2023-05-13 17:42:06,751] multiqc [DEBUG ] No samples found: mirtop [2023-05-13 17:42:06,757] multiqc [DEBUG ] No samples found: homer [2023-05-13 17:42:06,761] multiqc [DEBUG ] No samples found: macs2 [2023-05-13 17:42:06,765] multiqc [DEBUG ] No samples found: theta2 [2023-05-13 17:42:06,769] multiqc [DEBUG ] No samples found: snpeff [2023-05-13 17:42:06,775] multiqc [DEBUG ] No samples found: gatk [2023-05-13 17:42:06,779] multiqc [DEBUG ] No samples found: htseq [2023-05-13 17:42:06,784] multiqc [DEBUG ] No samples found: bcftools [2023-05-13 17:42:06,788] multiqc [DEBUG ] No samples found: featureCounts [2023-05-13 17:42:06,794] multiqc [DEBUG ] No samples found: fgbio [2023-05-13 17:42:06,806] multiqc [DEBUG ] No samples found: dragen [2023-05-13 17:42:06,810] multiqc [DEBUG ] No samples found: dedup [2023-05-13 17:42:06,815] multiqc [DEBUG ] No samples found: damageprofiler [2023-05-13 17:42:06,835] multiqc [DEBUG ] No samples found: biobambam2 [2023-05-13 17:42:06,840] multiqc [DEBUG ] No samples found: mtnucratio [2023-05-13 17:42:06,843] multiqc [DEBUG ] No samples found: picard [2023-05-13 17:42:06,847] multiqc [DEBUG ] No samples found: prokka [2023-05-13 17:42:06,851] multiqc [DEBUG ] No samples found: samblaster [2023-05-13 17:42:06,858] multiqc [DEBUG ] No samples found: samtools [2023-05-13 17:42:06,863] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-05-13 17:42:06,868] multiqc [DEBUG ] No samples found: bamtools [2023-05-13 17:42:06,872] multiqc [DEBUG ] No samples found: jellyfish [2023-05-13 17:42:06,878] multiqc [DEBUG ] No samples found: vcftools [2023-05-13 17:42:06,882] multiqc [DEBUG ] No samples found: longranger [2023-05-13 17:42:06,887] multiqc [DEBUG ] No samples found: stacks [2023-05-13 17:42:06,891] multiqc [DEBUG ] No samples found: varscan2 [2023-05-13 17:42:06,903] multiqc [DEBUG ] No samples found: bbmap [2023-05-13 17:42:06,907] multiqc [DEBUG ] No samples found: bismark [2023-05-13 17:42:06,912] multiqc [DEBUG ] No samples found: biscuit [2023-05-13 17:42:06,917] multiqc [DEBUG ] No samples found: hicexplorer [2023-05-13 17:42:06,921] multiqc [DEBUG ] No samples found: hicup [2023-05-13 17:42:06,925] multiqc [DEBUG ] No samples found: hicpro [2023-05-13 17:42:06,929] multiqc [DEBUG ] No samples found: salmon [2023-05-13 17:42:06,934] multiqc [DEBUG ] No samples found: kallisto [2023-05-13 17:42:06,938] multiqc [DEBUG ] No samples found: slamdunk [2023-05-13 17:42:06,942] multiqc [DEBUG ] No samples found: star [2023-05-13 17:42:06,947] multiqc [DEBUG ] No samples found: hisat2 [2023-05-13 17:42:06,951] multiqc [DEBUG ] No samples found: tophat [2023-05-13 17:42:06,955] multiqc [DEBUG ] No samples found: bowtie2 [2023-05-13 17:42:06,959] multiqc [DEBUG ] No samples found: bowtie1 [2023-05-13 17:42:06,964] multiqc [DEBUG ] No samples found: snpsplit [2023-05-13 17:42:06,968] multiqc [DEBUG ] No samples found: kat [2023-05-13 17:42:06,971] multiqc [DEBUG ] No samples found: leehom [2023-05-13 17:42:06,976] multiqc [DEBUG ] No samples found: adapterRemoval [2023-05-13 17:42:06,980] multiqc [DEBUG ] No samples found: clipandmerge [2023-05-13 17:42:06,984] multiqc [DEBUG ] No samples found: cutadapt [2023-05-13 17:42:06,988] multiqc [DEBUG ] No samples found: flexbar [2023-05-13 17:42:06,992] multiqc [DEBUG ] No samples found: kaiju [2023-05-13 17:42:06,997] multiqc [DEBUG ] No samples found: kraken [2023-05-13 17:42:07,001] multiqc [DEBUG ] No samples found: malt [2023-05-13 17:42:07,005] multiqc [DEBUG ] No samples found: trimmomatic [2023-05-13 17:42:07,009] multiqc [DEBUG ] No samples found: sickle [2023-05-13 17:42:07,014] multiqc [DEBUG ] No samples found: skewer [2023-05-13 17:42:07,018] multiqc [DEBUG ] No samples found: sortmerna [2023-05-13 17:42:07,022] multiqc [DEBUG ] No samples found: biobloomtools [2023-05-13 17:42:07,026] multiqc [DEBUG ] No samples found: fastq_screen [2023-05-13 17:42:07,031] multiqc [DEBUG ] No samples found: afterqc [2023-05-13 17:42:07,035] multiqc [DEBUG ] No samples found: fastp [2023-05-13 17:42:07,184] multiqc.modules.fastqc.fastqc [INFO ] Found 4 reports [2023-05-13 17:42:07,234] multiqc [DEBUG ] No samples found: pycoqc [2023-05-13 17:42:07,239] multiqc [DEBUG ] No samples found: minionqc [2023-05-13 17:42:07,243] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-05-13 17:42:07,247] multiqc [DEBUG ] No samples found: clusterflow [2023-05-13 17:42:07,252] multiqc [DEBUG ] No samples found: bcl2fastq [2023-05-13 17:42:07,256] multiqc [DEBUG ] No samples found: interop [2023-05-13 17:42:07,260] multiqc [DEBUG ] No samples found: ivar [2023-05-13 17:42:07,264] multiqc [DEBUG ] No samples found: flash [2023-05-13 17:42:07,268] multiqc [DEBUG ] No samples found: seqyclean [2023-05-13 17:42:07,268] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-05-13 17:42:07,269] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2023-05-13 17:42:07,269] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-05-13 17:42:07,269] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-05-13 17:42:07,269] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found. [2023-05-13 17:42:07,269] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-05-13 17:42:07,269] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-05-13 17:42:07,269] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-05-13 17:42:07,269] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-05-13 17:42:07,269] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-05-13 17:42:07,269] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-05-13 17:42:07,269] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-05-13 17:42:07,269] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-05-13 17:42:07,269] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-05-13 17:42:07,269] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-05-13 17:42:07,269] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-05-13 17:42:07,269] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-05-13 17:42:07,269] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-05-13 17:42:07,269] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-05-13 17:42:07,275] multiqc [INFO ] Compressing plot data [2023-05-13 17:42:07,351] multiqc [INFO ] Report : multiqc_report.html [2023-05-13 17:42:07,351] multiqc [INFO ] Data : multiqc_data [2023-05-13 17:42:07,351] multiqc [DEBUG ] Moving data file from '/state/partition1/job-33295231/tmpxu51kjtd/multiqc_data' to '/scratch/gencore/logs/html/H7K2JDRX3/merged/multiqc_data' [2023-05-13 17:42:07,483] multiqc [INFO ] MultiQC complete