[2023-02-13 14:20:04,148] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-02-13 14:20:04,148] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-02-13 14:20:04,148] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-02-13 14:20:04,150] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-02-13 14:20:04,150] 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}} [2023-02-13 14:20:04,150] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H7K22BGXN/merged [2023-02-13 14:20:04,884] multiqc [WARNING] MultiQC Version v1.14 now available! [2023-02-13 14:20:04,884] multiqc [INFO ] This is MultiQC v1.9 [2023-02-13 14:20:04,884] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H7K22BGXN/merged [2023-02-13 14:20:04,884] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H7K22BGXN/merged [2023-02-13 14:20:04,884] multiqc [INFO ] Template : default [2023-02-13 14:20:04,884] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-02-13 14:20:04,884] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H7K22BGXN/merged [2023-02-13 14:20:04,885] 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 [2023-02-13 14:20:04,885] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-30191427/tmpqh7qqtez [2023-02-13 14:20:05,007] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-02-13 14:20:05,009] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-02-13 14:20:05,010] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-02-13 14:20:05,010] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-02-13 14:20:05,010] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-02-13 14:20:05,010] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-02-13 14:20:05,010] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-02-13 14:20:05,010] multiqc [DEBUG ] File ignored by snpeff because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-02-13 14:20:05,010] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-02-13 14:20:08,944] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7K22BGXN_n01_br317a_fastqc.html [2023-02-13 14:20:08,947] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7K22BGXN_n01_br317a_fastqc.html [2023-02-13 14:20:08,987] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7K22BGXN_n01_br318a_fastqc.html [2023-02-13 14:20:08,989] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7K22BGXN_n01_br318a_fastqc.html [2023-02-13 14:20:09,030] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7K22BGXN_n01_br312a_fastqc.html [2023-02-13 14:20:09,032] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7K22BGXN_n01_br312a_fastqc.html [2023-02-13 14:20:09,075] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7K22BGXN_n01_br314a_fastqc.html [2023-02-13 14:20:09,076] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7K22BGXN_n01_br314a_fastqc.html [2023-02-13 14:20:09,116] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7K22BGXN_n01_br315a_fastqc.html [2023-02-13 14:20:09,118] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7K22BGXN_n01_br315a_fastqc.html [2023-02-13 14:20:09,157] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7K22BGXN_n01_undetermined_fastqc.html [2023-02-13 14:20:09,159] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7K22BGXN_n01_undetermined_fastqc.html [2023-02-13 14:20:09,199] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7K22BGXN_n01_br316a_fastqc.html [2023-02-13 14:20:09,201] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7K22BGXN_n01_br316a_fastqc.html [2023-02-13 14:20:09,241] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7K22BGXN_n01_br313a_fastqc.html [2023-02-13 14:20:09,243] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7K22BGXN_n01_br313a_fastqc.html [2023-02-13 14:20:09,282] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7K22BGXN_n01_br319a_fastqc.html [2023-02-13 14:20:09,284] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7K22BGXN_n01_br319a_fastqc.html [2023-02-13 14:20:09,657] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-02-13 14:20:09,659] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-02-13 14:20:09,667] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-02-13 14:20:09,677] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-02-13 14:20:09,681] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 9 samples (table) [2023-02-13 14:20:09,687] multiqc [DEBUG ] No samples found: conpair [2023-02-13 14:20:09,693] multiqc [DEBUG ] No samples found: peddy [2023-02-13 14:20:09,699] multiqc [DEBUG ] No samples found: somalier [2023-02-13 14:20:09,705] multiqc [DEBUG ] No samples found: methylQA [2023-02-13 14:20:09,716] multiqc [DEBUG ] No samples found: mosdepth [2023-02-13 14:20:09,721] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-02-13 14:20:09,726] multiqc [DEBUG ] No samples found: qualimap [2023-02-13 14:20:09,732] multiqc [DEBUG ] No samples found: preseq [2023-02-13 14:20:09,738] multiqc [DEBUG ] No samples found: quast [2023-02-13 14:20:09,745] multiqc [DEBUG ] No samples found: qorts [2023-02-13 14:20:09,750] multiqc [DEBUG ] No samples found: rna_seqc [2023-02-13 14:20:09,757] multiqc [DEBUG ] No samples found: rockhopper [2023-02-13 14:20:09,763] multiqc [DEBUG ] No samples found: rsem [2023-02-13 14:20:09,779] multiqc [DEBUG ] No samples found: rseqc [2023-02-13 14:20:09,783] multiqc [DEBUG ] No samples found: busco [2023-02-13 14:20:09,789] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-02-13 14:20:09,794] multiqc [DEBUG ] No samples found: disambiguate [2023-02-13 14:20:09,801] multiqc [DEBUG ] No samples found: supernova [2023-02-13 14:20:09,822] multiqc [DEBUG ] No samples found: deeptools [2023-02-13 14:20:09,827] multiqc [DEBUG ] No samples found: sargasso [2023-02-13 14:20:09,834] multiqc [DEBUG ] No samples found: verifybamid [2023-02-13 14:20:09,840] multiqc [DEBUG ] No samples found: mirtrace [2023-02-13 14:20:09,846] multiqc [DEBUG ] No samples found: happy [2023-02-13 14:20:09,852] multiqc [DEBUG ] No samples found: mirtop [2023-02-13 14:20:09,859] multiqc [DEBUG ] No samples found: homer [2023-02-13 14:20:09,866] multiqc [DEBUG ] No samples found: macs2 [2023-02-13 14:20:09,871] multiqc [DEBUG ] No samples found: theta2 [2023-02-13 14:20:09,876] multiqc [DEBUG ] No samples found: snpeff [2023-02-13 14:20:09,885] multiqc [DEBUG ] No samples found: gatk [2023-02-13 14:20:09,891] multiqc [DEBUG ] No samples found: htseq [2023-02-13 14:20:09,897] multiqc [DEBUG ] No samples found: bcftools [2023-02-13 14:20:09,904] multiqc [DEBUG ] No samples found: featureCounts [2023-02-13 14:20:09,912] multiqc [DEBUG ] No samples found: fgbio [2023-02-13 14:20:09,928] multiqc [DEBUG ] No samples found: dragen [2023-02-13 14:20:09,934] multiqc [DEBUG ] No samples found: dedup [2023-02-13 14:20:09,941] multiqc [DEBUG ] No samples found: damageprofiler [2023-02-13 14:20:09,971] multiqc [DEBUG ] No samples found: biobambam2 [2023-02-13 14:20:09,976] multiqc [DEBUG ] No samples found: mtnucratio [2023-02-13 14:20:09,978] multiqc [DEBUG ] No samples found: picard [2023-02-13 14:20:09,983] multiqc [DEBUG ] No samples found: prokka [2023-02-13 14:20:09,989] multiqc [DEBUG ] No samples found: samblaster [2023-02-13 14:20:10,003] multiqc [DEBUG ] No samples found: samtools [2023-02-13 14:20:10,008] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-02-13 14:20:10,016] multiqc [DEBUG ] No samples found: bamtools [2023-02-13 14:20:10,022] multiqc [DEBUG ] No samples found: jellyfish [2023-02-13 14:20:10,032] multiqc [DEBUG ] No samples found: vcftools [2023-02-13 14:20:10,039] multiqc [DEBUG ] No samples found: longranger [2023-02-13 14:20:10,044] multiqc [DEBUG ] No samples found: stacks [2023-02-13 14:20:10,051] multiqc [DEBUG ] No samples found: varscan2 [2023-02-13 14:20:10,071] multiqc [DEBUG ] No samples found: bbmap [2023-02-13 14:20:10,076] multiqc [DEBUG ] No samples found: bismark [2023-02-13 14:20:10,082] multiqc [DEBUG ] No samples found: biscuit [2023-02-13 14:20:10,087] multiqc [DEBUG ] No samples found: hicexplorer [2023-02-13 14:20:10,092] multiqc [DEBUG ] No samples found: hicup [2023-02-13 14:20:10,099] multiqc [DEBUG ] No samples found: hicpro [2023-02-13 14:20:10,103] multiqc [DEBUG ] No samples found: salmon [2023-02-13 14:20:10,109] multiqc [DEBUG ] No samples found: kallisto [2023-02-13 14:20:10,115] multiqc [DEBUG ] No samples found: slamdunk [2023-02-13 14:20:10,121] multiqc [DEBUG ] No samples found: star [2023-02-13 14:20:10,127] multiqc [DEBUG ] No samples found: hisat2 [2023-02-13 14:20:10,132] multiqc [DEBUG ] No samples found: tophat [2023-02-13 14:20:10,138] multiqc [DEBUG ] No samples found: bowtie2 [2023-02-13 14:20:10,143] multiqc [DEBUG ] No samples found: bowtie1 [2023-02-13 14:20:10,148] multiqc [DEBUG ] No samples found: snpsplit [2023-02-13 14:20:10,153] multiqc [DEBUG ] No samples found: kat [2023-02-13 14:20:10,160] multiqc [DEBUG ] No samples found: leehom [2023-02-13 14:20:10,165] multiqc [DEBUG ] No samples found: adapterRemoval [2023-02-13 14:20:10,170] multiqc [DEBUG ] No samples found: clipandmerge [2023-02-13 14:20:10,175] multiqc [DEBUG ] No samples found: cutadapt [2023-02-13 14:20:10,179] multiqc [DEBUG ] No samples found: flexbar [2023-02-13 14:20:10,185] multiqc [DEBUG ] No samples found: kaiju [2023-02-13 14:20:10,191] multiqc [DEBUG ] No samples found: kraken [2023-02-13 14:20:10,196] multiqc [DEBUG ] No samples found: malt [2023-02-13 14:20:10,201] multiqc [DEBUG ] No samples found: trimmomatic [2023-02-13 14:20:10,206] multiqc [DEBUG ] No samples found: sickle [2023-02-13 14:20:10,213] multiqc [DEBUG ] No samples found: skewer [2023-02-13 14:20:10,218] multiqc [DEBUG ] No samples found: sortmerna [2023-02-13 14:20:10,224] multiqc [DEBUG ] No samples found: biobloomtools [2023-02-13 14:20:10,229] multiqc [DEBUG ] No samples found: fastq_screen [2023-02-13 14:20:10,235] multiqc [DEBUG ] No samples found: afterqc [2023-02-13 14:20:10,240] multiqc [DEBUG ] No samples found: fastp [2023-02-13 14:20:10,851] multiqc.modules.fastqc.fastqc [INFO ] Found 9 reports [2023-02-13 14:20:11,052] multiqc [DEBUG ] No samples found: pycoqc [2023-02-13 14:20:11,057] multiqc [DEBUG ] No samples found: minionqc [2023-02-13 14:20:11,063] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-02-13 14:20:11,068] multiqc [DEBUG ] No samples found: clusterflow [2023-02-13 14:20:11,074] multiqc [DEBUG ] No samples found: bcl2fastq [2023-02-13 14:20:11,081] multiqc [DEBUG ] No samples found: interop [2023-02-13 14:20:11,086] multiqc [DEBUG ] No samples found: ivar [2023-02-13 14:20:11,092] multiqc [DEBUG ] No samples found: flash [2023-02-13 14:20:11,097] multiqc [DEBUG ] No samples found: seqyclean [2023-02-13 14:20:11,097] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-02-13 14:20:11,097] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-02-13 14:20:11,097] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-02-13 14:20:11,097] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2023-02-13 14:20:11,097] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2023-02-13 14:20:11,097] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2023-02-13 14:20:11,097] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2023-02-13 14:20:11,097] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2023-02-13 14:20:11,097] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2023-02-13 14:20:11,097] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-02-13 14:20:11,097] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-02-13 14:20:11,097] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-02-13 14:20:11,097] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-02-13 14:20:11,097] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-02-13 14:20:11,097] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-02-13 14:20:11,097] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-02-13 14:20:11,097] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-02-13 14:20:11,097] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-02-13 14:20:11,097] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-02-13 14:20:11,097] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-02-13 14:20:11,097] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-02-13 14:20:11,097] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-02-13 14:20:11,098] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-02-13 14:20:11,098] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-02-13 14:20:11,098] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-02-13 14:20:11,098] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-02-13 14:20:11,098] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-02-13 14:20:11,098] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-02-13 14:20:11,098] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-02-13 14:20:11,098] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-02-13 14:20:11,109] multiqc [INFO ] Compressing plot data [2023-02-13 14:20:11,271] multiqc [INFO ] Report : multiqc_report.html [2023-02-13 14:20:11,271] multiqc [INFO ] Data : multiqc_data [2023-02-13 14:20:11,271] multiqc [DEBUG ] Moving data file from '/state/partition1/job-30191427/tmpqh7qqtez/multiqc_data' to '/scratch/gencore/logs/html/H7K22BGXN/merged/multiqc_data' [2023-02-13 14:20:11,435] multiqc [INFO ] MultiQC complete