[2023-08-30 23:18:29,825] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-08-30 23:18:29,825] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-08-30 23:18:29,825] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-08-30 23:18:29,828] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-08-30 23:18:29,828] 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}} [2023-08-30 23:18:29,828] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H7Y7KDRX3/merged [2023-08-30 23:18:30,018] multiqc [WARNING] MultiQC Version v1.15 now available! [2023-08-30 23:18:30,018] multiqc [INFO ] This is MultiQC v1.9 [2023-08-30 23:18:30,019] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H7Y7KDRX3/merged [2023-08-30 23:18:30,019] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H7Y7KDRX3/merged [2023-08-30 23:18:30,019] multiqc [INFO ] Template : default [2023-08-30 23:18:30,019] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-08-30 23:18:30,019] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H7Y7KDRX3/merged [2023-08-30 23:18:30,019] 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 [2023-08-30 23:18:30,019] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-37051690/tmpmxsxrwtv [2023-08-30 23:18:30,137] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7Y7KDRX3_1_fastqc.html [2023-08-30 23:18:30,139] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7Y7KDRX3_1_fastqc.html [2023-08-30 23:18:30,200] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7Y7KDRX3_4_fastqc.html [2023-08-30 23:18:30,202] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7Y7KDRX3_4_fastqc.html [2023-08-30 23:18:30,295] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7Y7KDRX3_2_fastqc.html [2023-08-30 23:18:30,297] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7Y7KDRX3_2_fastqc.html [2023-08-30 23:18:30,351] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7Y7KDRX3_3_fastqc.html [2023-08-30 23:18:30,353] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7Y7KDRX3_3_fastqc.html [2023-08-30 23:18:30,895] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-08-30 23:18:30,896] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-08-30 23:18:30,900] multiqc.modules.custom_content.custom_content [WARNING] Not able to parse custom data in undetermined_barcodes_mqc.txt [2023-08-30 23:18:30,903] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-08-30 23:18:30,908] multiqc [DEBUG ] No samples found: conpair [2023-08-30 23:18:30,913] multiqc [DEBUG ] No samples found: peddy [2023-08-30 23:18:30,918] multiqc [DEBUG ] No samples found: somalier [2023-08-30 23:18:30,922] multiqc [DEBUG ] No samples found: methylQA [2023-08-30 23:18:30,930] multiqc [DEBUG ] No samples found: mosdepth [2023-08-30 23:18:30,934] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-08-30 23:18:30,938] multiqc [DEBUG ] No samples found: qualimap [2023-08-30 23:18:30,942] multiqc [DEBUG ] No samples found: preseq [2023-08-30 23:18:30,947] multiqc [DEBUG ] No samples found: quast [2023-08-30 23:18:30,951] multiqc [DEBUG ] No samples found: qorts [2023-08-30 23:18:30,955] multiqc [DEBUG ] No samples found: rna_seqc [2023-08-30 23:18:30,960] multiqc [DEBUG ] No samples found: rockhopper [2023-08-30 23:18:30,964] multiqc [DEBUG ] No samples found: rsem [2023-08-30 23:18:30,974] multiqc [DEBUG ] No samples found: rseqc [2023-08-30 23:18:30,978] multiqc [DEBUG ] No samples found: busco [2023-08-30 23:18:30,983] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-08-30 23:18:30,987] multiqc [DEBUG ] No samples found: disambiguate [2023-08-30 23:18:30,991] multiqc [DEBUG ] No samples found: supernova [2023-08-30 23:18:31,003] multiqc [DEBUG ] No samples found: deeptools [2023-08-30 23:18:31,008] multiqc [DEBUG ] No samples found: sargasso [2023-08-30 23:18:31,013] multiqc [DEBUG ] No samples found: verifybamid [2023-08-30 23:18:31,017] multiqc [DEBUG ] No samples found: mirtrace [2023-08-30 23:18:31,023] multiqc [DEBUG ] No samples found: happy [2023-08-30 23:18:31,028] multiqc [DEBUG ] No samples found: mirtop [2023-08-30 23:18:31,033] multiqc [DEBUG ] No samples found: homer [2023-08-30 23:18:31,038] multiqc [DEBUG ] No samples found: macs2 [2023-08-30 23:18:31,042] multiqc [DEBUG ] No samples found: theta2 [2023-08-30 23:18:31,046] multiqc [DEBUG ] No samples found: snpeff [2023-08-30 23:18:31,052] multiqc [DEBUG ] No samples found: gatk [2023-08-30 23:18:31,056] multiqc [DEBUG ] No samples found: htseq [2023-08-30 23:18:31,061] multiqc [DEBUG ] No samples found: bcftools [2023-08-30 23:18:31,066] multiqc [DEBUG ] No samples found: featureCounts [2023-08-30 23:18:31,072] multiqc [DEBUG ] No samples found: fgbio [2023-08-30 23:18:31,084] multiqc [DEBUG ] No samples found: dragen [2023-08-30 23:18:31,088] multiqc [DEBUG ] No samples found: dedup [2023-08-30 23:18:31,092] multiqc [DEBUG ] No samples found: damageprofiler [2023-08-30 23:18:31,114] multiqc [DEBUG ] No samples found: biobambam2 [2023-08-30 23:18:31,119] multiqc [DEBUG ] No samples found: mtnucratio [2023-08-30 23:18:31,121] multiqc [DEBUG ] No samples found: picard [2023-08-30 23:18:31,126] multiqc [DEBUG ] No samples found: prokka [2023-08-30 23:18:31,130] multiqc [DEBUG ] No samples found: samblaster [2023-08-30 23:18:31,139] multiqc [DEBUG ] No samples found: samtools [2023-08-30 23:18:31,144] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-08-30 23:18:31,149] multiqc [DEBUG ] No samples found: bamtools [2023-08-30 23:18:31,153] multiqc [DEBUG ] No samples found: jellyfish [2023-08-30 23:18:31,161] multiqc [DEBUG ] No samples found: vcftools [2023-08-30 23:18:31,166] multiqc [DEBUG ] No samples found: longranger [2023-08-30 23:18:31,173] multiqc [DEBUG ] No samples found: stacks [2023-08-30 23:18:31,178] multiqc [DEBUG ] No samples found: varscan2 [2023-08-30 23:18:31,191] multiqc [DEBUG ] No samples found: bbmap [2023-08-30 23:18:31,196] multiqc [DEBUG ] No samples found: bismark [2023-08-30 23:18:31,200] multiqc [DEBUG ] No samples found: biscuit [2023-08-30 23:18:31,205] multiqc [DEBUG ] No samples found: hicexplorer [2023-08-30 23:18:31,209] multiqc [DEBUG ] No samples found: hicup [2023-08-30 23:18:31,213] multiqc [DEBUG ] No samples found: hicpro [2023-08-30 23:18:31,217] multiqc [DEBUG ] No samples found: salmon [2023-08-30 23:18:31,222] multiqc [DEBUG ] No samples found: kallisto [2023-08-30 23:18:31,227] multiqc [DEBUG ] No samples found: slamdunk [2023-08-30 23:18:31,232] multiqc [DEBUG ] No samples found: star [2023-08-30 23:18:31,238] multiqc [DEBUG ] No samples found: hisat2 [2023-08-30 23:18:31,242] multiqc [DEBUG ] No samples found: tophat [2023-08-30 23:18:31,247] multiqc [DEBUG ] No samples found: bowtie2 [2023-08-30 23:18:31,251] multiqc [DEBUG ] No samples found: bowtie1 [2023-08-30 23:18:31,255] multiqc [DEBUG ] No samples found: snpsplit [2023-08-30 23:18:31,259] multiqc [DEBUG ] No samples found: kat [2023-08-30 23:18:31,263] multiqc [DEBUG ] No samples found: leehom [2023-08-30 23:18:31,269] multiqc [DEBUG ] No samples found: adapterRemoval [2023-08-30 23:18:31,273] multiqc [DEBUG ] No samples found: clipandmerge [2023-08-30 23:18:31,279] multiqc [DEBUG ] No samples found: cutadapt [2023-08-30 23:18:31,283] multiqc [DEBUG ] No samples found: flexbar [2023-08-30 23:18:31,288] multiqc [DEBUG ] No samples found: kaiju [2023-08-30 23:18:31,292] multiqc [DEBUG ] No samples found: kraken [2023-08-30 23:18:31,297] multiqc [DEBUG ] No samples found: malt [2023-08-30 23:18:31,303] multiqc [DEBUG ] No samples found: trimmomatic [2023-08-30 23:18:31,307] multiqc [DEBUG ] No samples found: sickle [2023-08-30 23:18:31,311] multiqc [DEBUG ] No samples found: skewer [2023-08-30 23:18:31,315] multiqc [DEBUG ] No samples found: sortmerna [2023-08-30 23:18:31,319] multiqc [DEBUG ] No samples found: biobloomtools [2023-08-30 23:18:31,324] multiqc [DEBUG ] No samples found: fastq_screen [2023-08-30 23:18:31,328] multiqc [DEBUG ] No samples found: afterqc [2023-08-30 23:18:31,333] multiqc [DEBUG ] No samples found: fastp [2023-08-30 23:18:31,658] multiqc.modules.fastqc.fastqc [INFO ] Found 4 reports [2023-08-30 23:18:31,707] multiqc [DEBUG ] No samples found: pycoqc [2023-08-30 23:18:31,711] multiqc [DEBUG ] No samples found: minionqc [2023-08-30 23:18:31,716] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-08-30 23:18:31,720] multiqc [DEBUG ] No samples found: clusterflow [2023-08-30 23:18:31,725] multiqc [DEBUG ] No samples found: bcl2fastq [2023-08-30 23:18:31,729] multiqc [DEBUG ] No samples found: interop [2023-08-30 23:18:31,733] multiqc [DEBUG ] No samples found: ivar [2023-08-30 23:18:31,738] multiqc [DEBUG ] No samples found: flash [2023-08-30 23:18:31,742] multiqc [DEBUG ] No samples found: seqyclean [2023-08-30 23:18:31,742] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-08-30 23:18:31,742] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2023-08-30 23:18:31,742] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-08-30 23:18:31,742] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-08-30 23:18:31,742] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found. [2023-08-30 23:18:31,742] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-08-30 23:18:31,742] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-08-30 23:18:31,742] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-08-30 23:18:31,742] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-08-30 23:18:31,742] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-08-30 23:18:31,742] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-08-30 23:18:31,742] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-08-30 23:18:31,742] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-08-30 23:18:31,742] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-08-30 23:18:31,742] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-08-30 23:18:31,742] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-08-30 23:18:31,743] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-08-30 23:18:31,743] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-08-30 23:18:31,743] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-08-30 23:18:31,748] multiqc [INFO ] Compressing plot data [2023-08-30 23:18:31,822] multiqc [INFO ] Report : multiqc_report.html [2023-08-30 23:18:31,822] multiqc [INFO ] Data : multiqc_data [2023-08-30 23:18:31,822] multiqc [DEBUG ] Moving data file from '/state/partition1/job-37051690/tmpmxsxrwtv/multiqc_data' to '/scratch/gencore/logs/html/H7Y7KDRX3/merged/multiqc_data' [2023-08-30 23:18:31,944] multiqc [INFO ] MultiQC complete