[2023-04-22 15:55:41,925] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-04-22 15:55:41,925] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-04-22 15:55:41,925] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-04-22 15:55:41,928] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-04-22 15:55:41,928] 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}} [2023-04-22 15:55:41,928] 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-KR859/1 [2023-04-22 15:55:42,088] multiqc [WARNING] MultiQC Version v1.14 now available! [2023-04-22 15:55:42,088] multiqc [INFO ] This is MultiQC v1.9 [2023-04-22 15:55:42,088] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/000000000-KR859/1 [2023-04-22 15:55:42,088] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/000000000-KR859/1 [2023-04-22 15:55:42,088] multiqc [INFO ] Template : default [2023-04-22 15:55:42,088] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-04-22 15:55:42,088] multiqc [INFO ] Searching : /scratch/gencore/logs/html/000000000-KR859/1 [2023-04-22 15:55:42,088] 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 [2023-04-22 15:55:42,088] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-32698777/tmp7dbvuvq1 [2023-04-22 15:55:42,193] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KR859_l01_n02_sample10_fastqc.html [2023-04-22 15:55:42,196] multiqc [DEBUG ] File ignored by longranger/invocation because it 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longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-04-22 15:55:42,352] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-04-22 15:55:42,352] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-04-22 15:55:42,352] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-04-22 15:55:42,352] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-04-22 15:55:42,352] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-04-22 15:55:42,408] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize 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000000000-KR859_l01_n02_sample03_fastqc.html [2023-04-22 15:55:45,753] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KR859_l01_n01_sample15_fastqc.html [2023-04-22 15:55:45,755] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KR859_l01_n01_sample15_fastqc.html [2023-04-22 15:55:45,795] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KR859_l01_n01_sample08_fastqc.html [2023-04-22 15:55:45,796] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KR859_l01_n01_sample08_fastqc.html [2023-04-22 15:55:45,837] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KR859_l01_n01_sample11_fastqc.html [2023-04-22 15:55:45,838] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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longranger/invocation because it exceeded search pattern filesize limit: 000000000-KR859_l01_n02_sample11_fastqc.html [2023-04-22 15:55:46,009] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KR859_l01_n02_sample04_fastqc.html [2023-04-22 15:55:46,010] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KR859_l01_n02_sample04_fastqc.html [2023-04-22 15:55:46,051] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KR859_l01_n02_undetermined_fastqc.html [2023-04-22 15:55:46,053] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KR859_l01_n02_undetermined_fastqc.html [2023-04-22 15:55:46,094] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KR859_l01_n02_sample13_fastqc.html [2023-04-22 15:55:46,096] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KR859_l01_n02_sample13_fastqc.html [2023-04-22 15:55:46,139] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KR859_l01_n02_sample01_fastqc.html [2023-04-22 15:55:46,140] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KR859_l01_n02_sample01_fastqc.html [2023-04-22 15:55:46,619] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-04-22 15:55:46,620] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-04-22 15:55:46,634] multiqc.modules.custom_content.custom_content [INFO ] demux_report-1: Found 18 samples (table) [2023-04-22 15:55:46,636] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-04-22 15:55:46,645] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-04-22 15:55:46,649] multiqc [DEBUG ] No samples found: conpair [2023-04-22 15:55:46,653] multiqc [DEBUG ] No samples found: peddy [2023-04-22 15:55:46,657] multiqc [DEBUG ] No samples found: somalier [2023-04-22 15:55:46,661] multiqc [DEBUG ] No samples found: methylQA [2023-04-22 15:55:46,667] multiqc [DEBUG ] No samples found: mosdepth [2023-04-22 15:55:46,671] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-04-22 15:55:46,674] multiqc [DEBUG ] No samples found: qualimap [2023-04-22 15:55:46,678] multiqc [DEBUG ] No samples found: preseq [2023-04-22 15:55:46,682] multiqc [DEBUG ] No samples found: quast [2023-04-22 15:55:46,685] multiqc [DEBUG ] No samples found: qorts [2023-04-22 15:55:46,696] multiqc [DEBUG ] No samples found: rna_seqc [2023-04-22 15:55:46,700] multiqc [DEBUG ] No samples found: rockhopper [2023-04-22 15:55:46,703] multiqc [DEBUG ] No samples found: rsem [2023-04-22 15:55:46,715] multiqc [DEBUG ] No samples found: rseqc [2023-04-22 15:55:46,718] multiqc [DEBUG ] No samples found: busco [2023-04-22 15:55:46,722] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-04-22 15:55:46,726] multiqc [DEBUG ] No samples found: disambiguate [2023-04-22 15:55:46,730] multiqc [DEBUG ] No samples found: supernova [2023-04-22 15:55:46,739] multiqc [DEBUG ] No samples found: deeptools [2023-04-22 15:55:46,743] multiqc [DEBUG ] No samples found: sargasso [2023-04-22 15:55:46,747] multiqc [DEBUG ] No samples found: verifybamid [2023-04-22 15:55:46,751] multiqc [DEBUG ] No samples found: mirtrace [2023-04-22 15:55:46,754] multiqc [DEBUG ] No samples found: happy [2023-04-22 15:55:46,758] multiqc [DEBUG ] No samples found: mirtop [2023-04-22 15:55:46,771] multiqc [DEBUG ] No samples found: homer [2023-04-22 15:55:46,775] multiqc [DEBUG ] No samples found: macs2 [2023-04-22 15:55:46,780] multiqc [DEBUG ] No samples found: theta2 [2023-04-22 15:55:46,784] multiqc [DEBUG ] No samples found: snpeff [2023-04-22 15:55:46,792] multiqc [DEBUG ] No samples found: gatk [2023-04-22 15:55:46,799] multiqc [DEBUG ] No samples found: htseq [2023-04-22 15:55:46,803] multiqc [DEBUG ] No samples found: bcftools [2023-04-22 15:55:46,807] multiqc [DEBUG ] No samples found: featureCounts [2023-04-22 15:55:46,812] multiqc [DEBUG ] No samples found: fgbio [2023-04-22 15:55:46,822] multiqc [DEBUG ] No samples found: dragen [2023-04-22 15:55:46,826] multiqc [DEBUG ] No samples found: dedup [2023-04-22 15:55:46,829] multiqc [DEBUG ] No samples found: damageprofiler [2023-04-22 15:55:46,846] multiqc [DEBUG ] No samples found: biobambam2 [2023-04-22 15:55:46,849] multiqc [DEBUG ] No samples found: mtnucratio [2023-04-22 15:55:46,852] multiqc [DEBUG ] No samples found: picard [2023-04-22 15:55:46,855] multiqc [DEBUG ] No samples found: prokka [2023-04-22 15:55:46,859] multiqc [DEBUG ] No samples found: samblaster [2023-04-22 15:55:46,868] multiqc [DEBUG ] No samples found: samtools [2023-04-22 15:55:46,872] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-04-22 15:55:46,877] multiqc [DEBUG ] No samples found: bamtools [2023-04-22 15:55:46,881] multiqc [DEBUG ] No samples found: jellyfish [2023-04-22 15:55:46,889] multiqc [DEBUG ] No samples found: vcftools [2023-04-22 15:55:46,893] multiqc [DEBUG ] No samples found: longranger [2023-04-22 15:55:46,896] multiqc [DEBUG ] No samples found: stacks [2023-04-22 15:55:46,900] multiqc [DEBUG ] No samples found: varscan2 [2023-04-22 15:55:46,911] multiqc [DEBUG ] No samples found: bbmap [2023-04-22 15:55:46,915] multiqc [DEBUG ] No samples found: bismark [2023-04-22 15:55:46,925] multiqc [DEBUG ] No samples found: biscuit [2023-04-22 15:55:46,929] multiqc [DEBUG ] No samples found: hicexplorer [2023-04-22 15:55:46,932] multiqc [DEBUG ] No samples found: hicup [2023-04-22 15:55:46,936] multiqc [DEBUG ] No samples found: hicpro [2023-04-22 15:55:46,940] multiqc [DEBUG ] No samples found: salmon [2023-04-22 15:55:46,943] multiqc [DEBUG ] No samples found: kallisto [2023-04-22 15:55:46,947] multiqc [DEBUG ] No samples found: slamdunk [2023-04-22 15:55:46,951] multiqc [DEBUG ] No samples found: star [2023-04-22 15:55:46,955] multiqc [DEBUG ] No samples found: hisat2 [2023-04-22 15:55:46,961] multiqc [DEBUG ] No samples found: tophat [2023-04-22 15:55:46,964] multiqc [DEBUG ] No samples found: bowtie2 [2023-04-22 15:55:46,968] multiqc [DEBUG ] No samples found: bowtie1 [2023-04-22 15:55:46,973] multiqc [DEBUG ] No samples found: snpsplit [2023-04-22 15:55:46,977] multiqc [DEBUG ] No samples found: kat [2023-04-22 15:55:46,980] multiqc [DEBUG ] No samples found: leehom [2023-04-22 15:55:46,984] multiqc [DEBUG ] No samples found: adapterRemoval [2023-04-22 15:55:46,992] multiqc [DEBUG ] No samples found: clipandmerge [2023-04-22 15:55:46,995] multiqc [DEBUG ] No samples found: cutadapt [2023-04-22 15:55:46,999] multiqc [DEBUG ] No samples found: flexbar [2023-04-22 15:55:47,003] multiqc [DEBUG ] No samples found: kaiju [2023-04-22 15:55:47,006] multiqc [DEBUG ] No samples found: kraken [2023-04-22 15:55:47,010] multiqc [DEBUG ] No samples found: malt [2023-04-22 15:55:47,014] multiqc [DEBUG ] No samples found: trimmomatic [2023-04-22 15:55:47,018] multiqc [DEBUG ] No samples found: sickle [2023-04-22 15:55:47,026] multiqc [DEBUG ] No samples found: skewer [2023-04-22 15:55:47,029] multiqc [DEBUG ] No samples found: sortmerna [2023-04-22 15:55:47,033] multiqc [DEBUG ] No samples found: biobloomtools [2023-04-22 15:55:47,049] multiqc [DEBUG ] No samples found: fastq_screen [2023-04-22 15:55:47,053] multiqc [DEBUG ] No samples found: afterqc [2023-04-22 15:55:47,057] multiqc [DEBUG ] No samples found: fastp [2023-04-22 15:55:47,365] multiqc.modules.fastqc.fastqc [INFO ] Found 36 reports [2023-04-22 15:55:47,654] multiqc [DEBUG ] No samples found: pycoqc [2023-04-22 15:55:47,657] multiqc [DEBUG ] No samples found: minionqc [2023-04-22 15:55:47,661] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-04-22 15:55:47,665] multiqc [DEBUG ] No samples found: clusterflow [2023-04-22 15:55:47,669] multiqc [DEBUG ] No samples found: bcl2fastq [2023-04-22 15:55:47,673] multiqc [DEBUG ] No samples found: interop [2023-04-22 15:55:47,677] multiqc [DEBUG ] No samples found: ivar [2023-04-22 15:55:47,681] multiqc [DEBUG ] No samples found: flash [2023-04-22 15:55:47,684] multiqc [DEBUG ] No samples found: seqyclean [2023-04-22 15:55:47,684] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-04-22 15:55:47,685] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2023-04-22 15:55:47,685] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-04-22 15:55:47,685] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Lane 1 Demultiplexing Report'. [2023-04-22 15:55:47,685] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 1 Demultiplexing Report'. [2023-04-22 15:55:47,685] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Lane 1 Demultiplexing Report'. [2023-04-22 15:55:47,685] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Lane 1 Demultiplexing Report'. [2023-04-22 15:55:47,685] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Lane 1 Demultiplexing Report'. [2023-04-22 15:55:47,685] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Lane 1 Demultiplexing Report'. [2023-04-22 15:55:47,685] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Lane 1 Demultiplexing Report'. [2023-04-22 15:55:47,685] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-04-22 15:55:47,685] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-04-22 15:55:47,685] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-04-22 15:55:47,685] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-04-22 15:55:47,685] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-04-22 15:55:47,685] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-04-22 15:55:47,685] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-04-22 15:55:47,685] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Lane Statistics'. [2023-04-22 15:55:47,685] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2023-04-22 15:55:47,685] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Lane Statistics'. [2023-04-22 15:55:47,685] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Lane Statistics'. [2023-04-22 15:55:47,685] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Lane Statistics'. [2023-04-22 15:55:47,685] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Lane Statistics'. [2023-04-22 15:55:47,685] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Lane Statistics'. [2023-04-22 15:55:47,685] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-04-22 15:55:47,685] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-04-22 15:55:47,685] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-04-22 15:55:47,685] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-04-22 15:55:47,685] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-04-22 15:55:47,685] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-04-22 15:55:47,685] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-04-22 15:55:47,727] multiqc [INFO ] Compressing plot data [2023-04-22 15:55:48,216] multiqc [INFO ] Report : multiqc_report.html [2023-04-22 15:55:48,217] multiqc [INFO ] Data : multiqc_data [2023-04-22 15:55:48,217] multiqc [DEBUG ] Moving data file from '/state/partition1/job-32698777/tmp7dbvuvq1/multiqc_data' to '/scratch/gencore/logs/html/000000000-KR859/1/multiqc_data' [2023-04-22 15:55:48,326] multiqc [INFO ] MultiQC complete