[2023-06-06 21:07:20,251] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-06-06 21:07:20,251] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-06-06 21:07:20,251] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-06-06 21:07:20,254] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-06-06 21:07:20,254] 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}} [2023-06-06 21:07:20,254] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HCMTHBGXT/merged [2023-06-06 21:07:20,494] multiqc [WARNING] MultiQC Version v1.14 now available! [2023-06-06 21:07:20,495] multiqc [INFO ] This is MultiQC v1.9 [2023-06-06 21:07:20,495] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HCMTHBGXT/merged [2023-06-06 21:07:20,495] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HCMTHBGXT/merged [2023-06-06 21:07:20,495] multiqc [INFO ] Template : default [2023-06-06 21:07:20,495] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-06-06 21:07:20,495] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HCMTHBGXT/merged [2023-06-06 21:07:20,495] 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 [2023-06-06 21:07:20,495] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-34296150/tmp0e6g3eti [2023-06-06 21:07:20,650] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HCMTHBGXT_n01_Omer-1_fastqc.html [2023-06-06 21:07:20,653] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HCMTHBGXT_n01_Omer-1_fastqc.html [2023-06-06 21:07:20,696] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-06-06 21:07:20,697] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-06-06 21:07:20,698] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-06-06 21:07:20,698] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-06-06 21:07:20,698] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-06-06 21:07:20,698] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-06-06 21:07:20,698] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-06-06 21:07:20,740] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-06-06 21:07:22,547] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HCMTHBGXT_n01_Omer-2_fastqc.html [2023-06-06 21:07:22,548] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HCMTHBGXT_n01_Omer-2_fastqc.html [2023-06-06 21:07:22,590] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HCMTHBGXT_n02_undetermined_fastqc.html [2023-06-06 21:07:22,592] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HCMTHBGXT_n02_undetermined_fastqc.html [2023-06-06 21:07:22,635] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HCMTHBGXT_n02_Omer-1_fastqc.html [2023-06-06 21:07:22,637] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HCMTHBGXT_n02_Omer-1_fastqc.html [2023-06-06 21:07:22,679] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HCMTHBGXT_n01_undetermined_fastqc.html [2023-06-06 21:07:22,681] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HCMTHBGXT_n01_undetermined_fastqc.html [2023-06-06 21:07:22,723] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HCMTHBGXT_n02_Omer-2_fastqc.html [2023-06-06 21:07:22,724] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HCMTHBGXT_n02_Omer-2_fastqc.html [2023-06-06 21:07:23,282] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-06-06 21:07:23,284] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-06-06 21:07:23,292] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-06-06 21:07:23,294] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 3 samples (table) [2023-06-06 21:07:23,304] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-06-06 21:07:23,331] multiqc [DEBUG ] No samples found: conpair [2023-06-06 21:07:23,380] multiqc [DEBUG ] No samples found: peddy [2023-06-06 21:07:23,400] multiqc [DEBUG ] No samples found: somalier [2023-06-06 21:07:23,422] multiqc [DEBUG ] No samples found: methylQA [2023-06-06 21:07:23,499] multiqc [DEBUG ] No samples found: mosdepth [2023-06-06 21:07:23,521] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-06-06 21:07:23,525] multiqc [DEBUG ] No samples found: qualimap [2023-06-06 21:07:23,555] multiqc [DEBUG ] No samples found: preseq [2023-06-06 21:07:23,601] multiqc [DEBUG ] No samples found: quast [2023-06-06 21:07:23,638] multiqc [DEBUG ] No samples found: qorts [2023-06-06 21:07:23,687] multiqc [DEBUG ] No samples found: rna_seqc [2023-06-06 21:07:23,720] multiqc [DEBUG ] No samples found: rockhopper [2023-06-06 21:07:23,743] multiqc [DEBUG ] No samples found: rsem [2023-06-06 21:07:23,798] multiqc [DEBUG ] No samples found: rseqc [2023-06-06 21:07:23,831] multiqc [DEBUG ] No samples found: busco [2023-06-06 21:07:23,864] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-06-06 21:07:23,887] multiqc [DEBUG ] No samples found: disambiguate [2023-06-06 21:07:23,909] multiqc [DEBUG ] No samples found: supernova [2023-06-06 21:07:23,987] multiqc [DEBUG ] No samples found: deeptools [2023-06-06 21:07:24,040] multiqc [DEBUG ] No samples found: sargasso [2023-06-06 21:07:24,074] multiqc [DEBUG ] No samples found: verifybamid [2023-06-06 21:07:24,108] multiqc [DEBUG ] No samples found: mirtrace [2023-06-06 21:07:24,139] multiqc [DEBUG ] No samples found: happy [2023-06-06 21:07:24,172] multiqc [DEBUG ] No samples found: mirtop [2023-06-06 21:07:24,205] multiqc [DEBUG ] No samples found: homer [2023-06-06 21:07:24,238] multiqc [DEBUG ] No samples found: macs2 [2023-06-06 21:07:24,272] multiqc [DEBUG ] No samples found: theta2 [2023-06-06 21:07:24,308] multiqc [DEBUG ] No samples found: snpeff [2023-06-06 21:07:24,352] multiqc [DEBUG ] No samples found: gatk [2023-06-06 21:07:24,386] multiqc [DEBUG ] No samples found: htseq [2023-06-06 21:07:24,413] multiqc [DEBUG ] No samples found: bcftools [2023-06-06 21:07:24,446] multiqc [DEBUG ] No samples found: featureCounts [2023-06-06 21:07:24,468] multiqc [DEBUG ] No samples found: fgbio [2023-06-06 21:07:24,515] multiqc [DEBUG ] No samples found: dragen [2023-06-06 21:07:24,537] multiqc [DEBUG ] No samples found: dedup [2023-06-06 21:07:24,560] multiqc [DEBUG ] No samples found: damageprofiler [2023-06-06 21:07:24,674] multiqc [DEBUG ] No samples found: biobambam2 [2023-06-06 21:07:24,718] multiqc [DEBUG ] No samples found: mtnucratio [2023-06-06 21:07:24,720] multiqc [DEBUG ] No samples found: picard [2023-06-06 21:07:24,761] multiqc [DEBUG ] No samples found: prokka [2023-06-06 21:07:24,783] multiqc [DEBUG ] No samples found: samblaster [2023-06-06 21:07:24,830] multiqc [DEBUG ] No samples found: samtools [2023-06-06 21:07:24,847] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-06-06 21:07:24,890] multiqc [DEBUG ] No samples found: bamtools [2023-06-06 21:07:24,924] multiqc [DEBUG ] No samples found: jellyfish [2023-06-06 21:07:24,959] multiqc [DEBUG ] No samples found: vcftools [2023-06-06 21:07:24,978] multiqc [DEBUG ] No samples found: longranger [2023-06-06 21:07:25,001] multiqc [DEBUG ] No samples found: stacks [2023-06-06 21:07:25,023] multiqc [DEBUG ] No samples found: varscan2 [2023-06-06 21:07:25,165] multiqc [DEBUG ] No samples found: bbmap [2023-06-06 21:07:25,181] multiqc [DEBUG ] No samples found: bismark [2023-06-06 21:07:25,215] multiqc [DEBUG ] No samples found: biscuit [2023-06-06 21:07:25,242] multiqc [DEBUG ] No samples found: hicexplorer [2023-06-06 21:07:25,278] multiqc [DEBUG ] No samples found: hicup [2023-06-06 21:07:25,312] multiqc [DEBUG ] No samples found: hicpro [2023-06-06 21:07:25,326] multiqc [DEBUG ] No samples found: salmon [2023-06-06 21:07:25,341] multiqc [DEBUG ] No samples found: kallisto [2023-06-06 21:07:25,374] multiqc [DEBUG ] No samples found: slamdunk [2023-06-06 21:07:25,408] multiqc [DEBUG ] No samples found: star [2023-06-06 21:07:25,430] multiqc [DEBUG ] No samples found: hisat2 [2023-06-06 21:07:25,452] multiqc [DEBUG ] No samples found: tophat [2023-06-06 21:07:25,489] multiqc [DEBUG ] No samples found: bowtie2 [2023-06-06 21:07:25,509] multiqc [DEBUG ] No samples found: bowtie1 [2023-06-06 21:07:25,534] multiqc [DEBUG ] No samples found: snpsplit [2023-06-06 21:07:25,577] multiqc [DEBUG ] No samples found: kat [2023-06-06 21:07:25,623] multiqc [DEBUG ] No samples found: leehom [2023-06-06 21:07:25,650] multiqc [DEBUG ] No samples found: adapterRemoval [2023-06-06 21:07:25,673] multiqc [DEBUG ] No samples found: clipandmerge [2023-06-06 21:07:25,705] multiqc [DEBUG ] No samples found: cutadapt [2023-06-06 21:07:25,742] multiqc [DEBUG ] No samples found: flexbar [2023-06-06 21:07:25,796] multiqc [DEBUG ] No samples found: kaiju [2023-06-06 21:07:25,833] multiqc [DEBUG ] No samples found: kraken [2023-06-06 21:07:25,870] multiqc [DEBUG ] No samples found: malt [2023-06-06 21:07:25,904] multiqc [DEBUG ] No samples found: trimmomatic [2023-06-06 21:07:25,933] multiqc [DEBUG ] No samples found: sickle [2023-06-06 21:07:25,966] multiqc [DEBUG ] No samples found: skewer [2023-06-06 21:07:25,981] multiqc [DEBUG ] No samples found: sortmerna [2023-06-06 21:07:26,004] multiqc [DEBUG ] No samples found: biobloomtools [2023-06-06 21:07:26,012] multiqc [DEBUG ] No samples found: fastq_screen [2023-06-06 21:07:26,033] multiqc [DEBUG ] No samples found: afterqc [2023-06-06 21:07:26,049] multiqc [DEBUG ] No samples found: fastp [2023-06-06 21:07:26,432] multiqc.modules.fastqc.fastqc [INFO ] Found 6 reports [2023-06-06 21:07:26,555] multiqc [DEBUG ] No samples found: pycoqc [2023-06-06 21:07:26,578] multiqc [DEBUG ] No samples found: minionqc [2023-06-06 21:07:26,624] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-06-06 21:07:26,647] multiqc [DEBUG ] No samples found: clusterflow [2023-06-06 21:07:26,685] multiqc [DEBUG ] No samples found: bcl2fastq [2023-06-06 21:07:26,709] multiqc [DEBUG ] No samples found: interop [2023-06-06 21:07:26,734] multiqc [DEBUG ] No samples found: ivar [2023-06-06 21:07:26,750] multiqc [DEBUG ] No samples found: flash [2023-06-06 21:07:26,773] multiqc [DEBUG ] No samples found: seqyclean [2023-06-06 21:07:26,773] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-06-06 21:07:26,773] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-06-06 21:07:26,773] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-06-06 21:07:26,773] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2023-06-06 21:07:26,773] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2023-06-06 21:07:26,773] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2023-06-06 21:07:26,773] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2023-06-06 21:07:26,773] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2023-06-06 21:07:26,773] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2023-06-06 21:07:26,773] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-06-06 21:07:26,773] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-06-06 21:07:26,773] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-06-06 21:07:26,773] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-06-06 21:07:26,773] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-06-06 21:07:26,773] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-06-06 21:07:26,773] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-06-06 21:07:26,773] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-06-06 21:07:26,773] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-06-06 21:07:26,773] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-06-06 21:07:26,773] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-06-06 21:07:26,774] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-06-06 21:07:26,774] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-06-06 21:07:26,774] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-06-06 21:07:26,774] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-06-06 21:07:26,774] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-06-06 21:07:26,774] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-06-06 21:07:26,774] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-06-06 21:07:26,774] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-06-06 21:07:26,774] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-06-06 21:07:26,774] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-06-06 21:07:26,782] multiqc [INFO ] Compressing plot data [2023-06-06 21:07:26,895] multiqc [INFO ] Report : multiqc_report.html [2023-06-06 21:07:26,895] multiqc [INFO ] Data : multiqc_data [2023-06-06 21:07:26,895] multiqc [DEBUG ] Moving data file from '/state/partition1/job-34296150/tmp0e6g3eti/multiqc_data' to '/scratch/gencore/logs/html/HCMTHBGXT/merged/multiqc_data' [2023-06-06 21:07:27,060] multiqc [INFO ] MultiQC complete