[2023-11-10 14:06:53,193] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-11-10 14:06:53,193] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-11-10 14:06:53,193] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-11-10 14:06:53,195] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-11-10 14:06:53,195] 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}} [2023-11-10 14:06:53,196] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HJM7CAFX5/merged [2023-11-10 14:06:53,379] multiqc [WARNING] MultiQC Version v1.17 now available! [2023-11-10 14:06:53,379] multiqc [INFO ] This is MultiQC v1.9 [2023-11-10 14:06:53,379] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HJM7CAFX5/merged [2023-11-10 14:06:53,379] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HJM7CAFX5/merged [2023-11-10 14:06:53,379] multiqc [INFO ] Template : default [2023-11-10 14:06:53,379] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-11-10 14:06:53,380] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HJM7CAFX5/merged [2023-11-10 14:06:53,380] 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 [2023-11-10 14:06:53,380] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-39967239/tmphgux3d0f [2023-11-10 14:06:53,498] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-11-10 14:06:53,501] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-11-10 14:06:53,989] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJM7CAFX5_n02_liv_RNA_1_fastqc.html [2023-11-10 14:06:53,991] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJM7CAFX5_n02_liv_RNA_1_fastqc.html [2023-11-10 14:06:54,042] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJM7CAFX5_n02_liv_Hash_1_fastqc.html [2023-11-10 14:06:54,044] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJM7CAFX5_n02_liv_Hash_1_fastqc.html [2023-11-10 14:06:54,106] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJM7CAFX5_n01_liv_RNA_3_fastqc.html [2023-11-10 14:06:54,108] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJM7CAFX5_n01_liv_RNA_3_fastqc.html [2023-11-10 14:06:54,156] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJM7CAFX5_n02_liv_RNA_2_fastqc.html [2023-11-10 14:06:54,158] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJM7CAFX5_n02_liv_RNA_2_fastqc.html [2023-11-10 14:06:54,207] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJM7CAFX5_n02_liv_RNA_3_fastqc.html [2023-11-10 14:06:54,209] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJM7CAFX5_n02_liv_RNA_3_fastqc.html [2023-11-10 14:06:54,258] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJM7CAFX5_n01_undetermined_fastqc.html [2023-11-10 14:06:54,260] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJM7CAFX5_n01_undetermined_fastqc.html [2023-11-10 14:06:54,315] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJM7CAFX5_n01_schiC_1_fastqc.html [2023-11-10 14:06:54,317] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJM7CAFX5_n01_schiC_1_fastqc.html [2023-11-10 14:06:54,374] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJM7CAFX5_n01_liv_Hash_3_fastqc.html [2023-11-10 14:06:54,376] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJM7CAFX5_n01_liv_Hash_3_fastqc.html [2023-11-10 14:06:54,427] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJM7CAFX5_n01_liv_RNA_1_fastqc.html [2023-11-10 14:06:54,429] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJM7CAFX5_n01_liv_RNA_1_fastqc.html [2023-11-10 14:06:54,477] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJM7CAFX5_n02_undetermined_fastqc.html [2023-11-10 14:06:54,479] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJM7CAFX5_n02_undetermined_fastqc.html [2023-11-10 14:06:54,533] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJM7CAFX5_n02_liv_Hash_2_fastqc.html [2023-11-10 14:06:54,535] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJM7CAFX5_n02_liv_Hash_2_fastqc.html [2023-11-10 14:06:54,597] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJM7CAFX5_n01_liv_RNA_2_fastqc.html [2023-11-10 14:06:54,599] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJM7CAFX5_n01_liv_RNA_2_fastqc.html [2023-11-10 14:06:54,647] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJM7CAFX5_n01_liv_Hash_1_fastqc.html [2023-11-10 14:06:54,649] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJM7CAFX5_n01_liv_Hash_1_fastqc.html [2023-11-10 14:06:54,700] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJM7CAFX5_n02_liv_Hash_3_fastqc.html [2023-11-10 14:06:54,702] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJM7CAFX5_n02_liv_Hash_3_fastqc.html [2023-11-10 14:06:54,763] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJM7CAFX5_n01_liv_Hash_2_fastqc.html [2023-11-10 14:06:54,765] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJM7CAFX5_n01_liv_Hash_2_fastqc.html [2023-11-10 14:06:54,816] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJM7CAFX5_n02_schiC_1_fastqc.html [2023-11-10 14:06:54,818] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJM7CAFX5_n02_schiC_1_fastqc.html [2023-11-10 14:06:55,321] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-11-10 14:06:55,324] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-11-10 14:06:55,346] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 8 samples (table) [2023-11-10 14:06:55,348] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-11-10 14:06:55,357] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-11-10 14:06:55,372] multiqc [DEBUG ] No samples found: conpair [2023-11-10 14:06:55,394] multiqc [DEBUG ] No samples found: peddy [2023-11-10 14:06:55,417] multiqc [DEBUG ] No samples found: somalier [2023-11-10 14:06:55,433] multiqc [DEBUG ] No samples found: methylQA [2023-11-10 14:06:55,481] multiqc [DEBUG ] No samples found: mosdepth [2023-11-10 14:06:55,504] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-11-10 14:06:55,514] multiqc [DEBUG ] No samples found: qualimap [2023-11-10 14:06:55,526] multiqc [DEBUG ] No samples found: preseq [2023-11-10 14:06:55,547] multiqc [DEBUG ] No samples found: quast [2023-11-10 14:06:55,569] multiqc [DEBUG ] No samples found: qorts [2023-11-10 14:06:55,583] multiqc [DEBUG ] No samples found: rna_seqc [2023-11-10 14:06:55,602] multiqc [DEBUG ] No samples found: rockhopper [2023-11-10 14:06:55,624] multiqc [DEBUG ] No samples found: rsem [2023-11-10 14:06:55,745] multiqc [DEBUG ] No samples found: rseqc [2023-11-10 14:06:55,767] multiqc [DEBUG ] No samples found: busco [2023-11-10 14:06:55,789] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-11-10 14:06:55,804] multiqc [DEBUG ] No samples found: disambiguate [2023-11-10 14:06:55,815] multiqc [DEBUG ] No samples found: supernova [2023-11-10 14:06:55,921] multiqc [DEBUG ] No samples found: deeptools [2023-11-10 14:06:55,943] multiqc [DEBUG ] No samples found: sargasso [2023-11-10 14:06:55,959] multiqc [DEBUG ] No samples found: verifybamid [2023-11-10 14:06:55,970] multiqc [DEBUG ] No samples found: mirtrace [2023-11-10 14:06:55,985] multiqc [DEBUG ] No samples found: happy [2023-11-10 14:06:56,007] multiqc [DEBUG ] No samples found: mirtop [2023-11-10 14:06:56,051] multiqc [DEBUG ] No samples found: homer [2023-11-10 14:06:56,079] multiqc [DEBUG ] No samples found: macs2 [2023-11-10 14:06:56,101] multiqc [DEBUG ] No samples found: theta2 [2023-11-10 14:06:56,123] multiqc [DEBUG ] No samples found: snpeff [2023-11-10 14:06:56,167] multiqc [DEBUG ] No samples found: gatk [2023-11-10 14:06:56,185] multiqc [DEBUG ] No samples found: htseq [2023-11-10 14:06:56,218] multiqc [DEBUG ] No samples found: bcftools [2023-11-10 14:06:56,240] multiqc [DEBUG ] No samples found: featureCounts [2023-11-10 14:06:56,274] multiqc [DEBUG ] No samples found: fgbio [2023-11-10 14:06:56,368] multiqc [DEBUG ] No samples found: dragen [2023-11-10 14:06:56,381] multiqc [DEBUG ] No samples found: dedup [2023-11-10 14:06:56,390] multiqc [DEBUG ] No samples found: damageprofiler [2023-11-10 14:06:56,487] multiqc [DEBUG ] No samples found: biobambam2 [2023-11-10 14:06:56,492] multiqc [DEBUG ] No samples found: mtnucratio [2023-11-10 14:06:56,494] multiqc [DEBUG ] No samples found: picard [2023-11-10 14:06:56,498] multiqc [DEBUG ] No samples found: prokka [2023-11-10 14:06:56,504] multiqc [DEBUG ] No samples found: samblaster [2023-11-10 14:06:56,557] multiqc [DEBUG ] No samples found: samtools [2023-11-10 14:06:56,579] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-11-10 14:06:56,612] multiqc [DEBUG ] No samples found: bamtools [2023-11-10 14:06:56,634] multiqc [DEBUG ] No samples found: jellyfish [2023-11-10 14:06:56,669] multiqc [DEBUG ] No samples found: vcftools [2023-11-10 14:06:56,679] multiqc [DEBUG ] No samples found: longranger [2023-11-10 14:06:56,701] multiqc [DEBUG ] No samples found: stacks [2023-11-10 14:06:56,723] multiqc [DEBUG ] No samples found: varscan2 [2023-11-10 14:06:56,877] multiqc [DEBUG ] No samples found: bbmap [2023-11-10 14:06:56,899] multiqc [DEBUG ] No samples found: bismark [2023-11-10 14:06:56,923] multiqc [DEBUG ] No samples found: biscuit [2023-11-10 14:06:56,943] multiqc [DEBUG ] No samples found: hicexplorer [2023-11-10 14:06:56,963] multiqc [DEBUG ] No samples found: hicup [2023-11-10 14:06:56,968] multiqc [DEBUG ] No samples found: hicpro [2023-11-10 14:06:56,980] multiqc [DEBUG ] No samples found: salmon [2023-11-10 14:06:56,984] multiqc [DEBUG ] No samples found: kallisto [2023-11-10 14:06:56,988] multiqc [DEBUG ] No samples found: slamdunk [2023-11-10 14:06:56,992] multiqc [DEBUG ] No samples found: star [2023-11-10 14:06:56,997] multiqc [DEBUG ] No samples found: hisat2 [2023-11-10 14:06:57,008] multiqc [DEBUG ] No samples found: tophat [2023-11-10 14:06:57,012] multiqc [DEBUG ] No samples found: bowtie2 [2023-11-10 14:06:57,016] multiqc [DEBUG ] No samples found: bowtie1 [2023-11-10 14:06:57,020] multiqc [DEBUG ] No samples found: snpsplit [2023-11-10 14:06:57,023] multiqc [DEBUG ] No samples found: kat [2023-11-10 14:06:57,029] multiqc [DEBUG ] No samples found: leehom [2023-11-10 14:06:57,033] multiqc [DEBUG ] No samples found: adapterRemoval [2023-11-10 14:06:57,036] multiqc [DEBUG ] No samples found: clipandmerge [2023-11-10 14:06:57,040] multiqc [DEBUG ] No samples found: cutadapt [2023-11-10 14:06:57,044] multiqc [DEBUG ] No samples found: flexbar [2023-11-10 14:06:57,048] multiqc [DEBUG ] No samples found: kaiju [2023-11-10 14:06:57,064] multiqc [DEBUG ] No samples found: kraken [2023-11-10 14:06:57,068] multiqc [DEBUG ] No samples found: malt [2023-11-10 14:06:57,080] multiqc [DEBUG ] No samples found: trimmomatic [2023-11-10 14:06:57,084] multiqc [DEBUG ] No samples found: sickle [2023-11-10 14:06:57,097] multiqc [DEBUG ] No samples found: skewer [2023-11-10 14:06:57,112] multiqc [DEBUG ] No samples found: sortmerna [2023-11-10 14:06:57,142] multiqc [DEBUG ] No samples found: biobloomtools [2023-11-10 14:06:57,157] multiqc [DEBUG ] No samples found: fastq_screen [2023-11-10 14:06:57,170] multiqc [DEBUG ] No samples found: afterqc [2023-11-10 14:06:57,191] multiqc [DEBUG ] No samples found: fastp [2023-11-10 14:06:57,565] multiqc.modules.fastqc.fastqc [INFO ] Found 16 reports [2023-11-10 14:06:57,706] multiqc [DEBUG ] No samples found: pycoqc [2023-11-10 14:06:57,727] multiqc [DEBUG ] No samples found: minionqc [2023-11-10 14:06:57,750] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-11-10 14:06:57,771] multiqc [DEBUG ] No samples found: clusterflow [2023-11-10 14:06:57,794] multiqc [DEBUG ] No samples found: bcl2fastq [2023-11-10 14:06:57,815] multiqc [DEBUG ] No samples found: interop [2023-11-10 14:06:57,827] multiqc [DEBUG ] No samples found: ivar [2023-11-10 14:06:57,848] multiqc [DEBUG ] No samples found: flash [2023-11-10 14:06:57,871] multiqc [DEBUG ] No samples found: seqyclean [2023-11-10 14:06:57,871] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-11-10 14:06:57,871] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-11-10 14:06:57,871] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-11-10 14:06:57,872] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2023-11-10 14:06:57,872] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2023-11-10 14:06:57,872] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2023-11-10 14:06:57,872] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2023-11-10 14:06:57,872] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2023-11-10 14:06:57,872] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2023-11-10 14:06:57,872] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-11-10 14:06:57,872] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-11-10 14:06:57,872] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-11-10 14:06:57,872] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-11-10 14:06:57,872] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-11-10 14:06:57,872] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-11-10 14:06:57,872] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-11-10 14:06:57,872] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-11-10 14:06:57,872] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-11-10 14:06:57,872] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-11-10 14:06:57,872] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-11-10 14:06:57,872] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-11-10 14:06:57,872] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-11-10 14:06:57,872] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-11-10 14:06:57,872] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-11-10 14:06:57,872] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-11-10 14:06:57,872] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-11-10 14:06:57,872] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-11-10 14:06:57,872] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-11-10 14:06:57,872] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-11-10 14:06:57,872] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-11-10 14:06:57,892] multiqc [INFO ] Compressing plot data [2023-11-10 14:06:58,137] multiqc [INFO ] Report : multiqc_report.html [2023-11-10 14:06:58,137] multiqc [INFO ] Data : multiqc_data [2023-11-10 14:06:58,137] multiqc [DEBUG ] Moving data file from '/state/partition1/job-39967239/tmphgux3d0f/multiqc_data' to '/scratch/gencore/logs/html/HJM7CAFX5/merged/multiqc_data' [2023-11-10 14:06:58,256] multiqc [INFO ] MultiQC complete