[2023-02-14 06:51:58,368] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-02-14 06:51:58,368] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-02-14 06:51:58,368] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-02-14 06:51:58,371] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-02-14 06:51:58,371] 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}} [2023-02-14 06:51:58,371] 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-KWL6M/1 [2023-02-14 06:51:58,883] multiqc [WARNING] MultiQC Version v1.14 now available! [2023-02-14 06:51:58,884] multiqc [INFO ] This is MultiQC v1.9 [2023-02-14 06:51:58,884] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/000000000-KWL6M/1 [2023-02-14 06:51:58,884] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/000000000-KWL6M/1 [2023-02-14 06:51:58,884] multiqc [INFO ] Template : default [2023-02-14 06:51:58,884] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-02-14 06:51:58,884] multiqc [INFO ] Searching : /scratch/gencore/logs/html/000000000-KWL6M/1 [2023-02-14 06:51:58,884] 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 [2023-02-14 06:51:58,884] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-30209675/tmpp7ss8y2o [2023-02-14 06:51:58,997] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-02-14 06:51:58,999] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-02-14 06:51:58,999] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-02-14 06:51:58,999] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-02-14 06:51:58,999] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-02-14 06:51:58,999] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-02-14 06:51:59,000] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-02-14 06:51:59,029] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-02-14 06:52:00,277] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KWL6M_l01_n01_undetermined_fastqc.html [2023-02-14 06:52:00,278] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KWL6M_l01_n01_undetermined_fastqc.html [2023-02-14 06:52:00,327] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KWL6M_l01_n01_CMVORF_fastqc.html [2023-02-14 06:52:00,329] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KWL6M_l01_n01_CMVORF_fastqc.html [2023-02-14 06:52:00,380] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KWL6M_l01_n01_GibsonORF_fastqc.html [2023-02-14 06:52:00,382] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KWL6M_l01_n01_GibsonORF_fastqc.html [2023-02-14 06:52:00,435] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KWL6M_l01_n01_PresortHighConc_fastqc.html [2023-02-14 06:52:00,437] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KWL6M_l01_n01_PresortHighConc_fastqc.html [2023-02-14 06:52:01,028] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-02-14 06:52:01,029] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-02-14 06:52:01,038] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-02-14 06:52:01,040] multiqc.modules.custom_content.custom_content [INFO ] demux_report-1: Found 4 samples (table) [2023-02-14 06:52:01,050] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-02-14 06:52:01,057] multiqc [DEBUG ] No samples found: conpair [2023-02-14 06:52:01,063] multiqc [DEBUG ] No samples found: peddy [2023-02-14 06:52:01,068] multiqc [DEBUG ] No samples found: somalier [2023-02-14 06:52:01,074] multiqc [DEBUG ] No samples found: methylQA [2023-02-14 06:52:01,088] multiqc [DEBUG ] No samples found: mosdepth [2023-02-14 06:52:01,094] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-02-14 06:52:01,099] multiqc [DEBUG ] No samples found: qualimap [2023-02-14 06:52:01,107] multiqc [DEBUG ] No samples found: preseq [2023-02-14 06:52:01,112] multiqc [DEBUG ] No samples found: quast [2023-02-14 06:52:01,120] multiqc [DEBUG ] No samples found: qorts [2023-02-14 06:52:01,128] multiqc [DEBUG ] No samples found: rna_seqc [2023-02-14 06:52:01,136] multiqc [DEBUG ] No samples found: rockhopper [2023-02-14 06:52:01,142] multiqc [DEBUG ] No samples found: rsem [2023-02-14 06:52:01,158] multiqc [DEBUG ] No samples found: rseqc [2023-02-14 06:52:01,163] multiqc [DEBUG ] No samples found: busco [2023-02-14 06:52:01,169] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-02-14 06:52:01,175] multiqc [DEBUG ] No samples found: disambiguate [2023-02-14 06:52:01,184] multiqc [DEBUG ] No samples found: supernova [2023-02-14 06:52:01,205] multiqc [DEBUG ] No samples found: deeptools [2023-02-14 06:52:01,210] multiqc [DEBUG ] No samples found: sargasso [2023-02-14 06:52:01,217] multiqc [DEBUG ] No samples found: verifybamid [2023-02-14 06:52:01,222] multiqc [DEBUG ] No samples found: mirtrace [2023-02-14 06:52:01,227] multiqc [DEBUG ] No samples found: happy [2023-02-14 06:52:01,231] multiqc [DEBUG ] No samples found: mirtop [2023-02-14 06:52:01,238] multiqc [DEBUG ] No samples found: homer [2023-02-14 06:52:01,244] multiqc [DEBUG ] No samples found: macs2 [2023-02-14 06:52:01,249] multiqc [DEBUG ] No samples found: theta2 [2023-02-14 06:52:01,254] multiqc [DEBUG ] No samples found: snpeff [2023-02-14 06:52:01,264] multiqc [DEBUG ] No samples found: gatk [2023-02-14 06:52:01,271] multiqc [DEBUG ] No samples found: htseq [2023-02-14 06:52:01,277] multiqc [DEBUG ] No samples found: bcftools [2023-02-14 06:52:01,285] multiqc [DEBUG ] No samples found: featureCounts [2023-02-14 06:52:01,293] multiqc [DEBUG ] No samples found: fgbio [2023-02-14 06:52:01,308] multiqc [DEBUG ] No samples found: dragen [2023-02-14 06:52:01,313] multiqc [DEBUG ] No samples found: dedup [2023-02-14 06:52:01,319] multiqc [DEBUG ] No samples found: damageprofiler [2023-02-14 06:52:01,345] multiqc [DEBUG ] No samples found: biobambam2 [2023-02-14 06:52:01,350] multiqc [DEBUG ] No samples found: mtnucratio [2023-02-14 06:52:01,353] multiqc [DEBUG ] No samples found: picard [2023-02-14 06:52:01,358] multiqc [DEBUG ] No samples found: prokka [2023-02-14 06:52:01,364] multiqc [DEBUG ] No samples found: samblaster [2023-02-14 06:52:01,380] multiqc [DEBUG ] No samples found: samtools [2023-02-14 06:52:01,385] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-02-14 06:52:01,392] multiqc [DEBUG ] No samples found: bamtools [2023-02-14 06:52:01,399] multiqc [DEBUG ] No samples found: jellyfish [2023-02-14 06:52:01,410] multiqc [DEBUG ] No samples found: vcftools [2023-02-14 06:52:01,416] multiqc [DEBUG ] No samples found: longranger [2023-02-14 06:52:01,421] multiqc [DEBUG ] No samples found: stacks [2023-02-14 06:52:01,426] multiqc [DEBUG ] No samples found: varscan2 [2023-02-14 06:52:01,443] multiqc [DEBUG ] No samples found: bbmap [2023-02-14 06:52:01,449] multiqc [DEBUG ] No samples found: bismark [2023-02-14 06:52:01,455] multiqc [DEBUG ] No samples found: biscuit [2023-02-14 06:52:01,460] multiqc [DEBUG ] No samples found: hicexplorer [2023-02-14 06:52:01,465] multiqc [DEBUG ] No samples found: hicup [2023-02-14 06:52:01,472] multiqc [DEBUG ] No samples found: hicpro [2023-02-14 06:52:01,476] multiqc [DEBUG ] No samples found: salmon [2023-02-14 06:52:01,481] multiqc [DEBUG ] No samples found: kallisto [2023-02-14 06:52:01,487] multiqc [DEBUG ] No samples found: slamdunk [2023-02-14 06:52:01,494] multiqc [DEBUG ] No samples found: star [2023-02-14 06:52:01,499] multiqc [DEBUG ] No samples found: hisat2 [2023-02-14 06:52:01,504] multiqc [DEBUG ] No samples found: tophat [2023-02-14 06:52:01,509] multiqc [DEBUG ] No samples found: bowtie2 [2023-02-14 06:52:01,514] multiqc [DEBUG ] No samples found: bowtie1 [2023-02-14 06:52:01,521] multiqc [DEBUG ] No samples found: snpsplit [2023-02-14 06:52:01,527] multiqc [DEBUG ] No samples found: kat [2023-02-14 06:52:01,533] multiqc [DEBUG ] No samples found: leehom [2023-02-14 06:52:01,538] multiqc [DEBUG ] No samples found: adapterRemoval [2023-02-14 06:52:01,542] multiqc [DEBUG ] No samples found: clipandmerge [2023-02-14 06:52:01,547] multiqc [DEBUG ] No samples found: cutadapt [2023-02-14 06:52:01,551] multiqc [DEBUG ] No samples found: flexbar [2023-02-14 06:52:01,556] multiqc [DEBUG ] No samples found: kaiju [2023-02-14 06:52:01,562] multiqc [DEBUG ] No samples found: kraken [2023-02-14 06:52:01,567] multiqc [DEBUG ] No samples found: malt [2023-02-14 06:52:01,571] multiqc [DEBUG ] No samples found: trimmomatic [2023-02-14 06:52:01,576] multiqc [DEBUG ] No samples found: sickle [2023-02-14 06:52:01,582] multiqc [DEBUG ] No samples found: skewer [2023-02-14 06:52:01,587] multiqc [DEBUG ] No samples found: sortmerna [2023-02-14 06:52:01,591] multiqc [DEBUG ] No samples found: biobloomtools [2023-02-14 06:52:01,596] multiqc [DEBUG ] No samples found: fastq_screen [2023-02-14 06:52:01,601] multiqc [DEBUG ] No samples found: afterqc [2023-02-14 06:52:01,605] multiqc [DEBUG ] No samples found: fastp [2023-02-14 06:52:01,639] multiqc.modules.fastqc.fastqc [INFO ] Found 4 reports [2023-02-14 06:52:01,698] multiqc [DEBUG ] No samples found: pycoqc [2023-02-14 06:52:01,703] multiqc [DEBUG ] No samples found: minionqc [2023-02-14 06:52:01,707] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-02-14 06:52:01,712] multiqc [DEBUG ] No samples found: clusterflow [2023-02-14 06:52:01,718] multiqc [DEBUG ] No samples found: bcl2fastq [2023-02-14 06:52:01,725] multiqc [DEBUG ] No samples found: interop [2023-02-14 06:52:01,730] multiqc [DEBUG ] No samples found: ivar [2023-02-14 06:52:01,735] multiqc [DEBUG ] No samples found: flash [2023-02-14 06:52:01,739] multiqc [DEBUG ] No samples found: seqyclean [2023-02-14 06:52:01,739] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-02-14 06:52:01,739] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2023-02-14 06:52:01,739] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-02-14 06:52:01,739] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Lane 1 Demultiplexing Report'. [2023-02-14 06:52:01,739] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 1 Demultiplexing Report'. [2023-02-14 06:52:01,739] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Lane 1 Demultiplexing Report'. [2023-02-14 06:52:01,739] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Lane 1 Demultiplexing Report'. [2023-02-14 06:52:01,739] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Lane 1 Demultiplexing Report'. [2023-02-14 06:52:01,739] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Lane 1 Demultiplexing Report'. [2023-02-14 06:52:01,739] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Lane 1 Demultiplexing Report'. [2023-02-14 06:52:01,739] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-02-14 06:52:01,740] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-02-14 06:52:01,740] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-02-14 06:52:01,740] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-02-14 06:52:01,740] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-02-14 06:52:01,740] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-02-14 06:52:01,740] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-02-14 06:52:01,740] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Lane Statistics'. [2023-02-14 06:52:01,740] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2023-02-14 06:52:01,740] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Lane Statistics'. [2023-02-14 06:52:01,740] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Lane Statistics'. [2023-02-14 06:52:01,740] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Lane Statistics'. [2023-02-14 06:52:01,740] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Lane Statistics'. [2023-02-14 06:52:01,740] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Lane Statistics'. [2023-02-14 06:52:01,740] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-02-14 06:52:01,740] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-02-14 06:52:01,740] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-02-14 06:52:01,740] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-02-14 06:52:01,740] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-02-14 06:52:01,740] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-02-14 06:52:01,740] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-02-14 06:52:01,746] multiqc [INFO ] Compressing plot data [2023-02-14 06:52:01,816] multiqc [INFO ] Report : multiqc_report.html [2023-02-14 06:52:01,816] multiqc [INFO ] Data : multiqc_data [2023-02-14 06:52:01,816] multiqc [DEBUG ] Moving data file from '/state/partition1/job-30209675/tmpp7ss8y2o/multiqc_data' to '/scratch/gencore/logs/html/000000000-KWL6M/1/multiqc_data' [2023-02-14 06:52:01,956] multiqc [INFO ] MultiQC complete