[2023-05-20 12:17:55,537] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-05-20 12:17:55,537] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-05-20 12:17:55,537] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-05-20 12:17:55,539] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-05-20 12:17:55,540] 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}} [2023-05-20 12:17:55,540] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/000000000-L2V68/1 [2023-05-20 12:17:55,722] multiqc [WARNING] MultiQC Version v1.14 now available! [2023-05-20 12:17:55,723] multiqc [INFO ] This is MultiQC v1.9 [2023-05-20 12:17:55,723] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/000000000-L2V68/1 [2023-05-20 12:17:55,723] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/000000000-L2V68/1 [2023-05-20 12:17:55,723] multiqc [INFO ] Template : default [2023-05-20 12:17:55,723] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-05-20 12:17:55,723] multiqc [INFO ] Searching : /scratch/gencore/logs/html/000000000-L2V68/1 [2023-05-20 12:17:55,723] 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 [2023-05-20 12:17:55,723] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-33637632/tmpu77l4jbm [2023-05-20 12:17:55,834] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-L2V68_l01_n01_undetermined_fastqc.html [2023-05-20 12:17:55,837] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-L2V68_l01_n01_undetermined_fastqc.html [2023-05-20 12:17:55,877] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-05-20 12:17:55,879] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-05-20 12:17:55,972] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-L2V68_l01_n02_Fmr1ADARcdgDNA_fastqc.html [2023-05-20 12:17:55,974] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-L2V68_l01_n02_Fmr1ADARcdgDNA_fastqc.html [2023-05-20 12:17:56,015] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-L2V68_l01_n02_undetermined_fastqc.html [2023-05-20 12:17:56,017] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-L2V68_l01_n02_undetermined_fastqc.html [2023-05-20 12:17:56,058] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-L2V68_l01_n02_ADARcdgDNA_fastqc.html [2023-05-20 12:17:56,060] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-L2V68_l01_n02_ADARcdgDNA_fastqc.html [2023-05-20 12:17:56,101] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-L2V68_l01_n01_Fmr1ADARcdgDNA_fastqc.html [2023-05-20 12:17:56,103] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-L2V68_l01_n01_Fmr1ADARcdgDNA_fastqc.html [2023-05-20 12:17:56,143] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-L2V68_l01_n01_ADARcdgDNA_fastqc.html [2023-05-20 12:17:56,145] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-L2V68_l01_n01_ADARcdgDNA_fastqc.html [2023-05-20 12:17:56,473] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-05-20 12:17:56,475] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-05-20 12:17:56,484] multiqc.modules.custom_content.custom_content [INFO ] demux_report-1: Found 3 samples (table) [2023-05-20 12:17:56,494] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-05-20 12:17:56,496] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-05-20 12:17:56,501] multiqc [DEBUG ] No samples found: conpair [2023-05-20 12:17:56,506] multiqc [DEBUG ] No samples found: peddy [2023-05-20 12:17:56,512] multiqc [DEBUG ] No samples found: somalier [2023-05-20 12:17:56,517] multiqc [DEBUG ] No samples found: methylQA [2023-05-20 12:17:56,526] multiqc [DEBUG ] No samples found: mosdepth [2023-05-20 12:17:56,531] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-05-20 12:17:56,535] multiqc [DEBUG ] No samples found: qualimap [2023-05-20 12:17:56,540] multiqc [DEBUG ] No samples found: preseq [2023-05-20 12:17:56,545] multiqc [DEBUG ] No samples found: quast [2023-05-20 12:17:56,550] multiqc [DEBUG ] No samples found: qorts [2023-05-20 12:17:56,556] multiqc [DEBUG ] No samples found: rna_seqc [2023-05-20 12:17:56,561] multiqc [DEBUG ] No samples found: rockhopper [2023-05-20 12:17:56,566] multiqc [DEBUG ] No samples found: rsem [2023-05-20 12:17:56,577] multiqc [DEBUG ] No samples found: rseqc [2023-05-20 12:17:56,582] multiqc [DEBUG ] No samples found: busco [2023-05-20 12:17:56,588] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-05-20 12:17:56,593] multiqc [DEBUG ] No samples found: disambiguate [2023-05-20 12:17:56,598] multiqc [DEBUG ] No samples found: supernova [2023-05-20 12:17:56,612] multiqc [DEBUG ] No samples found: deeptools [2023-05-20 12:17:56,617] multiqc [DEBUG ] No samples found: sargasso [2023-05-20 12:17:56,623] multiqc [DEBUG ] No samples found: verifybamid [2023-05-20 12:17:56,628] multiqc [DEBUG ] No samples found: mirtrace [2023-05-20 12:17:56,633] multiqc [DEBUG ] No samples found: happy [2023-05-20 12:17:56,638] multiqc [DEBUG ] No samples found: mirtop [2023-05-20 12:17:56,645] multiqc [DEBUG ] No samples found: homer [2023-05-20 12:17:56,650] multiqc [DEBUG ] No samples found: macs2 [2023-05-20 12:17:56,655] multiqc [DEBUG ] No samples found: theta2 [2023-05-20 12:17:56,660] multiqc [DEBUG ] No samples found: snpeff [2023-05-20 12:17:56,667] multiqc [DEBUG ] No samples found: gatk [2023-05-20 12:17:56,672] multiqc [DEBUG ] No samples found: htseq [2023-05-20 12:17:56,678] multiqc [DEBUG ] No samples found: bcftools [2023-05-20 12:17:56,683] multiqc [DEBUG ] No samples found: featureCounts [2023-05-20 12:17:56,690] multiqc [DEBUG ] No samples found: fgbio [2023-05-20 12:17:56,702] multiqc [DEBUG ] No samples found: dragen [2023-05-20 12:17:56,708] multiqc [DEBUG ] No samples found: dedup [2023-05-20 12:17:56,713] multiqc [DEBUG ] No samples found: damageprofiler [2023-05-20 12:17:56,737] multiqc [DEBUG ] No samples found: biobambam2 [2023-05-20 12:17:56,742] multiqc [DEBUG ] No samples found: mtnucratio [2023-05-20 12:17:56,744] multiqc [DEBUG ] No samples found: picard [2023-05-20 12:17:56,749] multiqc [DEBUG ] No samples found: prokka [2023-05-20 12:17:56,756] multiqc [DEBUG ] No samples found: samblaster [2023-05-20 12:17:56,764] multiqc [DEBUG ] No samples found: samtools [2023-05-20 12:17:56,769] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-05-20 12:17:56,775] multiqc [DEBUG ] No samples found: bamtools [2023-05-20 12:17:56,779] multiqc [DEBUG ] No samples found: jellyfish [2023-05-20 12:17:56,786] multiqc [DEBUG ] No samples found: vcftools [2023-05-20 12:17:56,791] multiqc [DEBUG ] No samples found: longranger [2023-05-20 12:17:56,796] multiqc [DEBUG ] No samples found: stacks [2023-05-20 12:17:56,801] multiqc [DEBUG ] No samples found: varscan2 [2023-05-20 12:17:56,816] multiqc [DEBUG ] No samples found: bbmap [2023-05-20 12:17:56,821] multiqc [DEBUG ] No samples found: bismark [2023-05-20 12:17:56,826] multiqc [DEBUG ] No samples found: biscuit [2023-05-20 12:17:56,831] multiqc [DEBUG ] No samples found: hicexplorer [2023-05-20 12:17:56,837] multiqc [DEBUG ] No samples found: hicup [2023-05-20 12:17:56,842] multiqc [DEBUG ] No samples found: hicpro [2023-05-20 12:17:56,847] multiqc [DEBUG ] No samples found: salmon [2023-05-20 12:17:56,852] multiqc [DEBUG ] No samples found: kallisto [2023-05-20 12:17:56,858] multiqc [DEBUG ] No samples found: slamdunk [2023-05-20 12:17:56,863] multiqc [DEBUG ] No samples found: star [2023-05-20 12:17:56,868] multiqc [DEBUG ] No samples found: hisat2 [2023-05-20 12:17:56,873] multiqc [DEBUG ] No samples found: tophat [2023-05-20 12:17:56,878] multiqc [DEBUG ] No samples found: bowtie2 [2023-05-20 12:17:56,883] multiqc [DEBUG ] No samples found: bowtie1 [2023-05-20 12:17:56,889] multiqc [DEBUG ] No samples found: snpsplit [2023-05-20 12:17:56,894] multiqc [DEBUG ] No samples found: kat [2023-05-20 12:17:56,909] multiqc [DEBUG ] No samples found: leehom [2023-05-20 12:17:56,914] multiqc [DEBUG ] No samples found: adapterRemoval [2023-05-20 12:17:56,919] multiqc [DEBUG ] No samples found: clipandmerge [2023-05-20 12:17:56,924] multiqc [DEBUG ] No samples found: cutadapt [2023-05-20 12:17:56,932] multiqc [DEBUG ] No samples found: flexbar [2023-05-20 12:17:56,938] multiqc [DEBUG ] No samples found: kaiju [2023-05-20 12:17:56,943] multiqc [DEBUG ] No samples found: kraken [2023-05-20 12:17:56,948] multiqc [DEBUG ] No samples found: malt [2023-05-20 12:17:56,953] multiqc [DEBUG ] No samples found: trimmomatic [2023-05-20 12:17:56,958] multiqc [DEBUG ] No samples found: sickle [2023-05-20 12:17:56,963] multiqc [DEBUG ] No samples found: skewer [2023-05-20 12:17:56,968] multiqc [DEBUG ] No samples found: sortmerna [2023-05-20 12:17:56,973] multiqc [DEBUG ] No samples found: biobloomtools [2023-05-20 12:17:56,978] multiqc [DEBUG ] No samples found: fastq_screen [2023-05-20 12:17:56,982] multiqc [DEBUG ] No samples found: afterqc [2023-05-20 12:17:56,987] multiqc [DEBUG ] No samples found: fastp [2023-05-20 12:17:57,029] multiqc.modules.fastqc.fastqc [INFO ] Found 6 reports [2023-05-20 12:17:57,103] multiqc [DEBUG ] No samples found: pycoqc [2023-05-20 12:17:57,108] multiqc [DEBUG ] No samples found: minionqc [2023-05-20 12:17:57,112] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-05-20 12:17:57,118] multiqc [DEBUG ] No samples found: clusterflow [2023-05-20 12:17:57,122] multiqc [DEBUG ] No samples found: bcl2fastq [2023-05-20 12:17:57,128] multiqc [DEBUG ] No samples found: interop [2023-05-20 12:17:57,132] multiqc [DEBUG ] No samples found: ivar [2023-05-20 12:17:57,137] multiqc [DEBUG ] No samples found: flash [2023-05-20 12:17:57,143] multiqc [DEBUG ] No samples found: seqyclean [2023-05-20 12:17:57,143] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-05-20 12:17:57,143] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2023-05-20 12:17:57,143] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-05-20 12:17:57,143] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Lane 1 Demultiplexing Report'. [2023-05-20 12:17:57,143] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 1 Demultiplexing Report'. [2023-05-20 12:17:57,143] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Lane 1 Demultiplexing Report'. [2023-05-20 12:17:57,143] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Lane 1 Demultiplexing Report'. [2023-05-20 12:17:57,143] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Lane 1 Demultiplexing Report'. [2023-05-20 12:17:57,143] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Lane 1 Demultiplexing Report'. [2023-05-20 12:17:57,143] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Lane 1 Demultiplexing Report'. [2023-05-20 12:17:57,143] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-05-20 12:17:57,143] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-05-20 12:17:57,143] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-05-20 12:17:57,143] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-05-20 12:17:57,143] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-05-20 12:17:57,143] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-05-20 12:17:57,143] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-05-20 12:17:57,143] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Lane Statistics'. [2023-05-20 12:17:57,143] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2023-05-20 12:17:57,143] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Lane Statistics'. [2023-05-20 12:17:57,143] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Lane Statistics'. [2023-05-20 12:17:57,143] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Lane Statistics'. [2023-05-20 12:17:57,143] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Lane Statistics'. [2023-05-20 12:17:57,143] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Lane Statistics'. [2023-05-20 12:17:57,143] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-05-20 12:17:57,143] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-05-20 12:17:57,143] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-05-20 12:17:57,143] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-05-20 12:17:57,143] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-05-20 12:17:57,143] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-05-20 12:17:57,144] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-05-20 12:17:57,151] multiqc [INFO ] Compressing plot data [2023-05-20 12:17:57,255] multiqc [INFO ] Report : multiqc_report.html [2023-05-20 12:17:57,255] multiqc [INFO ] Data : multiqc_data [2023-05-20 12:17:57,255] multiqc [DEBUG ] Moving data file from '/state/partition1/job-33637632/tmpu77l4jbm/multiqc_data' to '/scratch/gencore/logs/html/000000000-L2V68/1/multiqc_data' [2023-05-20 12:17:57,373] multiqc [INFO ] MultiQC complete