[2023-11-22 07:28:01,821] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-11-22 07:28:01,821] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-11-22 07:28:01,821] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-11-22 07:28:01,823] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-11-22 07:28:01,823] 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}} [2023-11-22 07:28:01,823] 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-GJH97/1 [2023-11-22 07:28:01,995] multiqc [WARNING] MultiQC Version v1.17 now available! [2023-11-22 07:28:01,995] multiqc [INFO ] This is MultiQC v1.9 [2023-11-22 07:28:01,995] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/000000000-GJH97/1 [2023-11-22 07:28:01,995] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/000000000-GJH97/1 [2023-11-22 07:28:01,995] multiqc [INFO ] Template : default [2023-11-22 07:28:01,995] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-11-22 07:28:01,995] multiqc [INFO ] Searching : /scratch/gencore/logs/html/000000000-GJH97/1 [2023-11-22 07:28:01,996] 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 [2023-11-22 07:28:01,996] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-40300311/tmpjas4a9v_ [2023-11-22 07:28:02,116] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-GJH97_l01.3_fastqc.html [2023-11-22 07:28:02,118] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-GJH97_l01.3_fastqc.html [2023-11-22 07:28:02,140] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-GJH97_l01.1_fastqc.html [2023-11-22 07:28:02,142] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-GJH97_l01.1_fastqc.html [2023-11-22 07:28:02,163] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-GJH97_l01.2_fastqc.html [2023-11-22 07:28:02,165] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-GJH97_l01.2_fastqc.html [2023-11-22 07:28:02,704] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-11-22 07:28:02,705] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-11-22 07:28:02,709] multiqc.modules.custom_content.custom_content [WARNING] Not able to parse custom data in undetermined_barcodes_mqc.txt [2023-11-22 07:28:02,711] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-11-22 07:28:02,715] multiqc [DEBUG ] No samples found: conpair [2023-11-22 07:28:02,719] multiqc [DEBUG ] No samples found: peddy [2023-11-22 07:28:02,724] multiqc [DEBUG ] No samples found: somalier [2023-11-22 07:28:02,728] multiqc [DEBUG ] No samples found: methylQA [2023-11-22 07:28:02,735] multiqc [DEBUG ] No samples found: mosdepth [2023-11-22 07:28:02,739] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-11-22 07:28:02,743] multiqc [DEBUG ] No samples found: qualimap [2023-11-22 07:28:02,747] multiqc [DEBUG ] No samples found: preseq [2023-11-22 07:28:02,751] multiqc [DEBUG ] No samples found: quast [2023-11-22 07:28:02,755] multiqc [DEBUG ] No samples found: qorts [2023-11-22 07:28:02,760] multiqc [DEBUG ] No samples found: rna_seqc [2023-11-22 07:28:02,764] multiqc [DEBUG ] No samples found: rockhopper [2023-11-22 07:28:02,768] multiqc [DEBUG ] No samples found: rsem [2023-11-22 07:28:02,778] multiqc [DEBUG ] No samples found: rseqc [2023-11-22 07:28:02,781] multiqc [DEBUG ] No samples found: busco [2023-11-22 07:28:02,785] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-11-22 07:28:02,789] multiqc [DEBUG ] No samples found: disambiguate [2023-11-22 07:28:02,794] multiqc [DEBUG ] No samples found: supernova [2023-11-22 07:28:02,804] multiqc [DEBUG ] No samples found: deeptools [2023-11-22 07:28:02,808] multiqc [DEBUG ] No samples found: sargasso [2023-11-22 07:28:02,813] multiqc [DEBUG ] No samples found: verifybamid [2023-11-22 07:28:02,817] multiqc [DEBUG ] No samples found: mirtrace [2023-11-22 07:28:02,821] multiqc [DEBUG ] No samples found: happy [2023-11-22 07:28:02,825] multiqc [DEBUG ] No samples found: mirtop [2023-11-22 07:28:02,830] multiqc [DEBUG ] No samples found: homer [2023-11-22 07:28:02,834] multiqc [DEBUG ] No samples found: macs2 [2023-11-22 07:28:02,838] multiqc [DEBUG ] No samples found: theta2 [2023-11-22 07:28:02,842] multiqc [DEBUG ] No samples found: snpeff [2023-11-22 07:28:02,848] multiqc [DEBUG ] No samples found: gatk [2023-11-22 07:28:02,852] multiqc [DEBUG ] No samples found: htseq [2023-11-22 07:28:02,857] multiqc [DEBUG ] No samples found: bcftools [2023-11-22 07:28:02,861] multiqc [DEBUG ] No samples found: featureCounts [2023-11-22 07:28:02,866] multiqc [DEBUG ] No samples found: fgbio [2023-11-22 07:28:02,877] multiqc [DEBUG ] No samples found: dragen [2023-11-22 07:28:02,881] multiqc [DEBUG ] No samples found: dedup [2023-11-22 07:28:02,886] multiqc [DEBUG ] No samples found: damageprofiler [2023-11-22 07:28:02,905] multiqc [DEBUG ] No samples found: biobambam2 [2023-11-22 07:28:02,910] multiqc [DEBUG ] No samples found: mtnucratio [2023-11-22 07:28:02,912] multiqc [DEBUG ] No samples found: picard [2023-11-22 07:28:02,917] multiqc [DEBUG ] No samples found: prokka [2023-11-22 07:28:02,921] multiqc [DEBUG ] No samples found: samblaster [2023-11-22 07:28:02,928] multiqc [DEBUG ] No samples found: samtools [2023-11-22 07:28:02,933] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-11-22 07:28:02,938] multiqc [DEBUG ] No samples found: bamtools [2023-11-22 07:28:02,941] multiqc [DEBUG ] No samples found: jellyfish [2023-11-22 07:28:02,949] multiqc [DEBUG ] No samples found: vcftools [2023-11-22 07:28:02,953] multiqc [DEBUG ] No samples found: longranger [2023-11-22 07:28:02,958] multiqc [DEBUG ] No samples found: stacks [2023-11-22 07:28:02,962] multiqc [DEBUG ] No samples found: varscan2 [2023-11-22 07:28:02,974] multiqc [DEBUG ] No samples found: bbmap [2023-11-22 07:28:02,978] multiqc [DEBUG ] No samples found: bismark [2023-11-22 07:28:02,982] multiqc [DEBUG ] No samples found: biscuit [2023-11-22 07:28:02,987] multiqc [DEBUG ] No samples found: hicexplorer [2023-11-22 07:28:02,991] multiqc [DEBUG ] No samples found: hicup [2023-11-22 07:28:02,996] multiqc [DEBUG ] No samples found: hicpro [2023-11-22 07:28:03,000] multiqc [DEBUG ] No samples found: salmon [2023-11-22 07:28:03,004] multiqc [DEBUG ] No samples found: kallisto [2023-11-22 07:28:03,008] multiqc [DEBUG ] No samples found: slamdunk [2023-11-22 07:28:03,012] multiqc [DEBUG ] No samples found: star [2023-11-22 07:28:03,016] multiqc [DEBUG ] No samples found: hisat2 [2023-11-22 07:28:03,020] multiqc [DEBUG ] No samples found: tophat [2023-11-22 07:28:03,024] multiqc [DEBUG ] No samples found: bowtie2 [2023-11-22 07:28:03,029] multiqc [DEBUG ] No samples found: bowtie1 [2023-11-22 07:28:03,033] multiqc [DEBUG ] No samples found: snpsplit [2023-11-22 07:28:03,037] multiqc [DEBUG ] No samples found: kat [2023-11-22 07:28:03,041] multiqc [DEBUG ] No samples found: leehom [2023-11-22 07:28:03,045] multiqc [DEBUG ] No samples found: adapterRemoval [2023-11-22 07:28:03,049] multiqc [DEBUG ] No samples found: clipandmerge [2023-11-22 07:28:03,053] multiqc [DEBUG ] No samples found: cutadapt [2023-11-22 07:28:03,057] multiqc [DEBUG ] No samples found: flexbar [2023-11-22 07:28:03,061] multiqc [DEBUG ] No samples found: kaiju [2023-11-22 07:28:03,065] multiqc [DEBUG ] No samples found: kraken [2023-11-22 07:28:03,070] multiqc [DEBUG ] No samples found: malt [2023-11-22 07:28:03,076] multiqc [DEBUG ] No samples found: trimmomatic [2023-11-22 07:28:03,083] multiqc [DEBUG ] No samples found: sickle [2023-11-22 07:28:03,092] multiqc [DEBUG ] No samples found: skewer [2023-11-22 07:28:03,096] multiqc [DEBUG ] No samples found: sortmerna [2023-11-22 07:28:03,100] multiqc [DEBUG ] No samples found: biobloomtools [2023-11-22 07:28:03,104] multiqc [DEBUG ] No samples found: fastq_screen [2023-11-22 07:28:03,108] multiqc [DEBUG ] No samples found: afterqc [2023-11-22 07:28:03,112] multiqc [DEBUG ] No samples found: fastp [2023-11-22 07:28:03,119] multiqc.modules.fastqc.fastqc [INFO ] Found 3 reports [2023-11-22 07:28:03,120] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: '000000000-GJH97_l01.1' [2023-11-22 07:28:03,120] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: '000000000-GJH97_l01.2' [2023-11-22 07:28:03,120] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: '000000000-GJH97_l01.3' [2023-11-22 07:28:03,126] multiqc.modules.fastqc.fastqc [DEBUG ] sequence_quality not found in FastQC reports [2023-11-22 07:28:03,126] multiqc.modules.fastqc.fastqc [DEBUG ] per_seq_quality not found in FastQC reports [2023-11-22 07:28:03,140] multiqc.modules.fastqc.fastqc [DEBUG ] adapter_content not found in FastQC reports [2023-11-22 07:28:03,148] multiqc [DEBUG ] No samples found: pycoqc [2023-11-22 07:28:03,153] multiqc [DEBUG ] No samples found: minionqc [2023-11-22 07:28:03,157] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-11-22 07:28:03,162] multiqc [DEBUG ] No samples found: clusterflow [2023-11-22 07:28:03,166] multiqc [DEBUG ] No samples found: bcl2fastq [2023-11-22 07:28:03,170] multiqc [DEBUG ] No samples found: interop [2023-11-22 07:28:03,175] multiqc [DEBUG ] No samples found: ivar [2023-11-22 07:28:03,179] multiqc [DEBUG ] No samples found: flash [2023-11-22 07:28:03,185] multiqc [DEBUG ] No samples found: seqyclean [2023-11-22 07:28:03,185] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-11-22 07:28:03,185] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2023-11-22 07:28:03,185] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-11-22 07:28:03,185] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-11-22 07:28:03,185] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found. [2023-11-22 07:28:03,185] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-11-22 07:28:03,185] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-11-22 07:28:03,185] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-11-22 07:28:03,185] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-11-22 07:28:03,185] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-11-22 07:28:03,185] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-11-22 07:28:03,185] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-11-22 07:28:03,185] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-11-22 07:28:03,185] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-11-22 07:28:03,185] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-11-22 07:28:03,185] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-11-22 07:28:03,185] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-11-22 07:28:03,185] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-11-22 07:28:03,185] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-11-22 07:28:03,190] multiqc [INFO ] Compressing plot data [2023-11-22 07:28:03,210] multiqc [INFO ] Report : multiqc_report.html [2023-11-22 07:28:03,210] multiqc [INFO ] Data : multiqc_data [2023-11-22 07:28:03,210] multiqc [DEBUG ] Moving data file from '/state/partition1/job-40300311/tmpjas4a9v_/multiqc_data' to '/scratch/gencore/logs/html/000000000-GJH97/1/multiqc_data' [2023-11-22 07:28:03,331] multiqc [INFO ] MultiQC complete