[2024-01-18 18:57:14,032] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-01-18 18:57:14,032] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-01-18 18:57:14,032] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-01-18 18:57:14,034] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2024-01-18 18:57:14,034] 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}} [2024-01-18 18:57:14,034] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H2L2LDSXC/2 [2024-01-18 18:57:14,205] multiqc [WARNING] MultiQC Version v1.19 now available! [2024-01-18 18:57:14,205] multiqc [INFO ] This is MultiQC v1.9 [2024-01-18 18:57:14,205] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H2L2LDSXC/2 [2024-01-18 18:57:14,205] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H2L2LDSXC/2 [2024-01-18 18:57:14,205] multiqc [INFO ] Template : default [2024-01-18 18:57:14,205] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-01-18 18:57:14,205] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H2L2LDSXC/2 [2024-01-18 18:57:14,205] 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 [2024-01-18 18:57:14,205] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-41889910/tmp6vg6c0u0 [2024-01-18 18:57:14,297] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2L2LDSXC_l02_n02_B_QG3200_fastqc.html [2024-01-18 18:57:14,300] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern 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filesize limit: H2L2LDSXC_l02_n01_A_QG3231_fastqc.html [2024-01-18 18:57:27,348] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2L2LDSXC_l02_n01_undetermined_fastqc.html [2024-01-18 18:57:27,349] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2L2LDSXC_l02_n01_undetermined_fastqc.html [2024-01-18 18:57:27,394] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2L2LDSXC_l02_n01_B_QG3277_fastqc.html [2024-01-18 18:57:27,396] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2L2LDSXC_l02_n01_B_QG3277_fastqc.html [2024-01-18 18:57:27,459] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2L2LDSXC_l02_n02_B_QG3276_fastqc.html [2024-01-18 18:57:27,461] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2L2LDSXC_l02_n02_B_QG3276_fastqc.html [2024-01-18 18:57:27,520] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2L2LDSXC_l02_n02_A_QG3229_fastqc.html [2024-01-18 18:57:27,522] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2L2LDSXC_l02_n02_A_QG3229_fastqc.html [2024-01-18 18:57:27,678] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2L2LDSXC_l02_n01_A_QG3253_fastqc.html [2024-01-18 18:57:27,680] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2L2LDSXC_l02_n01_A_QG3253_fastqc.html [2024-01-18 18:57:27,965] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-01-18 18:57:27,966] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-01-18 18:57:27,973] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-01-18 18:57:28,017] multiqc.modules.custom_content.custom_content [INFO ] demux_report-2: Found 96 samples (table) [2024-01-18 18:57:28,027] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-01-18 18:57:28,029] multiqc [DEBUG ] No samples found: conpair [2024-01-18 18:57:28,032] multiqc [DEBUG ] No samples found: peddy [2024-01-18 18:57:28,035] multiqc [DEBUG ] No samples found: somalier [2024-01-18 18:57:28,038] multiqc [DEBUG ] No samples found: methylQA [2024-01-18 18:57:28,041] multiqc [DEBUG ] No samples found: mosdepth [2024-01-18 18:57:28,044] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-01-18 18:57:28,046] multiqc [DEBUG ] No samples found: qualimap [2024-01-18 18:57:28,049] multiqc [DEBUG ] No samples found: preseq [2024-01-18 18:57:28,052] multiqc [DEBUG ] No samples found: quast [2024-01-18 18:57:28,055] multiqc [DEBUG ] No samples found: qorts [2024-01-18 18:57:28,058] multiqc [DEBUG ] No samples found: rna_seqc [2024-01-18 18:57:28,060] multiqc [DEBUG ] No samples found: rockhopper [2024-01-18 18:57:28,063] multiqc [DEBUG ] No samples found: rsem [2024-01-18 18:57:28,067] multiqc [DEBUG ] No samples found: rseqc [2024-01-18 18:57:28,070] multiqc [DEBUG ] No samples found: busco [2024-01-18 18:57:28,073] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-01-18 18:57:28,076] multiqc [DEBUG ] No samples found: disambiguate [2024-01-18 18:57:28,078] multiqc [DEBUG ] No samples found: supernova [2024-01-18 18:57:28,083] multiqc [DEBUG ] No samples found: deeptools [2024-01-18 18:57:28,086] multiqc [DEBUG ] No samples found: sargasso [2024-01-18 18:57:28,089] multiqc [DEBUG ] No samples found: verifybamid [2024-01-18 18:57:28,091] multiqc [DEBUG ] No samples found: mirtrace [2024-01-18 18:57:28,094] multiqc [DEBUG ] No samples found: happy [2024-01-18 18:57:28,097] multiqc [DEBUG ] No samples found: mirtop [2024-01-18 18:57:28,100] multiqc [DEBUG ] No samples found: homer [2024-01-18 18:57:28,103] multiqc [DEBUG ] No samples found: macs2 [2024-01-18 18:57:28,105] multiqc [DEBUG ] No samples found: theta2 [2024-01-18 18:57:28,108] multiqc [DEBUG ] No samples found: snpeff [2024-01-18 18:57:28,111] multiqc [DEBUG ] No samples found: gatk [2024-01-18 18:57:28,114] multiqc [DEBUG ] No samples found: htseq [2024-01-18 18:57:28,117] multiqc [DEBUG ] No samples found: bcftools [2024-01-18 18:57:28,120] multiqc [DEBUG ] No samples found: featureCounts [2024-01-18 18:57:28,123] multiqc [DEBUG ] No samples found: fgbio [2024-01-18 18:57:28,128] multiqc [DEBUG ] No samples found: dragen [2024-01-18 18:57:28,130] multiqc [DEBUG ] No samples found: dedup [2024-01-18 18:57:28,133] multiqc [DEBUG ] No samples found: damageprofiler [2024-01-18 18:57:28,140] multiqc [DEBUG ] No samples found: biobambam2 [2024-01-18 18:57:28,143] multiqc [DEBUG ] No samples found: mtnucratio [2024-01-18 18:57:28,145] multiqc [DEBUG ] No samples found: picard [2024-01-18 18:57:28,148] multiqc [DEBUG ] No samples found: prokka [2024-01-18 18:57:28,151] multiqc [DEBUG ] No samples found: samblaster [2024-01-18 18:57:28,154] multiqc [DEBUG ] No samples found: samtools [2024-01-18 18:57:28,157] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-01-18 18:57:28,160] multiqc [DEBUG ] No samples found: bamtools [2024-01-18 18:57:28,163] multiqc [DEBUG ] No samples found: jellyfish [2024-01-18 18:57:28,166] multiqc [DEBUG ] No samples found: vcftools [2024-01-18 18:57:28,169] multiqc [DEBUG ] No samples found: longranger [2024-01-18 18:57:28,172] multiqc [DEBUG ] No samples found: stacks [2024-01-18 18:57:28,174] multiqc [DEBUG ] No samples found: varscan2 [2024-01-18 18:57:28,179] multiqc [DEBUG ] No samples found: bbmap [2024-01-18 18:57:28,182] multiqc [DEBUG ] No samples found: bismark [2024-01-18 18:57:28,185] multiqc [DEBUG ] No samples found: biscuit [2024-01-18 18:57:28,188] multiqc [DEBUG ] No samples found: hicexplorer [2024-01-18 18:57:28,190] multiqc [DEBUG ] No samples found: hicup [2024-01-18 18:57:28,193] multiqc [DEBUG ] No samples found: hicpro [2024-01-18 18:57:28,196] multiqc [DEBUG ] No samples found: salmon [2024-01-18 18:57:28,198] multiqc [DEBUG ] No samples found: kallisto [2024-01-18 18:57:28,201] multiqc [DEBUG ] No samples found: slamdunk [2024-01-18 18:57:28,204] multiqc [DEBUG ] No samples found: star [2024-01-18 18:57:28,207] multiqc [DEBUG ] No samples found: hisat2 [2024-01-18 18:57:28,209] multiqc [DEBUG ] No samples found: tophat [2024-01-18 18:57:28,212] multiqc [DEBUG ] No samples found: bowtie2 [2024-01-18 18:57:28,215] multiqc [DEBUG ] No samples found: bowtie1 [2024-01-18 18:57:28,218] multiqc [DEBUG ] No samples found: snpsplit [2024-01-18 18:57:28,220] multiqc [DEBUG ] No samples found: kat [2024-01-18 18:57:28,223] multiqc [DEBUG ] No samples found: leehom [2024-01-18 18:57:28,226] multiqc [DEBUG ] No samples found: adapterRemoval [2024-01-18 18:57:28,228] multiqc [DEBUG ] No samples found: clipandmerge [2024-01-18 18:57:28,231] multiqc [DEBUG ] No samples found: cutadapt [2024-01-18 18:57:28,234] multiqc [DEBUG ] No samples found: flexbar [2024-01-18 18:57:28,236] multiqc [DEBUG ] No samples found: kaiju [2024-01-18 18:57:28,239] multiqc [DEBUG ] No samples found: kraken [2024-01-18 18:57:28,242] multiqc [DEBUG ] No samples found: malt [2024-01-18 18:57:28,245] multiqc [DEBUG ] No samples found: trimmomatic [2024-01-18 18:57:28,247] multiqc [DEBUG ] No samples found: sickle [2024-01-18 18:57:28,250] multiqc [DEBUG ] No samples found: skewer [2024-01-18 18:57:28,253] multiqc [DEBUG ] No samples found: sortmerna [2024-01-18 18:57:28,255] multiqc [DEBUG ] No samples found: biobloomtools [2024-01-18 18:57:28,258] multiqc [DEBUG ] No samples found: fastq_screen [2024-01-18 18:57:28,261] multiqc [DEBUG ] No samples found: afterqc [2024-01-18 18:57:28,263] multiqc [DEBUG ] No samples found: fastp [2024-01-18 18:58:01,971] multiqc.modules.fastqc.fastqc [INFO ] Found 192 reports [2024-01-18 18:58:22,041] multiqc [DEBUG ] No samples found: pycoqc [2024-01-18 18:58:22,044] multiqc [DEBUG ] No samples found: minionqc [2024-01-18 18:58:22,047] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-01-18 18:58:22,050] multiqc [DEBUG ] No samples found: clusterflow [2024-01-18 18:58:22,052] multiqc [DEBUG ] No samples found: bcl2fastq [2024-01-18 18:58:22,055] multiqc [DEBUG ] No samples found: interop [2024-01-18 18:58:22,058] multiqc [DEBUG ] No samples found: ivar [2024-01-18 18:58:22,061] multiqc [DEBUG ] No samples found: flash [2024-01-18 18:58:22,063] multiqc [DEBUG ] No samples found: seqyclean [2024-01-18 18:58:22,063] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-01-18 18:58:22,063] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2024-01-18 18:58:22,063] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-01-18 18:58:22,063] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Lane 2 Demultiplexing Report'. [2024-01-18 18:58:22,063] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 2 Demultiplexing Report'. [2024-01-18 18:58:22,063] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Lane 2 Demultiplexing Report'. [2024-01-18 18:58:22,064] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Lane 2 Demultiplexing Report'. [2024-01-18 18:58:22,064] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Lane 2 Demultiplexing Report'. [2024-01-18 18:58:22,064] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Lane 2 Demultiplexing Report'. [2024-01-18 18:58:22,064] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Lane 2 Demultiplexing Report'. [2024-01-18 18:58:22,064] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-01-18 18:58:22,064] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-01-18 18:58:22,064] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-01-18 18:58:22,064] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-01-18 18:58:22,064] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-01-18 18:58:22,064] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-01-18 18:58:22,064] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-01-18 18:58:22,064] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Lane Statistics'. [2024-01-18 18:58:22,064] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2024-01-18 18:58:22,064] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Lane Statistics'. [2024-01-18 18:58:22,064] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Lane Statistics'. [2024-01-18 18:58:22,064] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Lane Statistics'. [2024-01-18 18:58:22,064] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Lane Statistics'. [2024-01-18 18:58:22,064] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Lane Statistics'. [2024-01-18 18:58:22,064] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-01-18 18:58:22,064] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-01-18 18:58:22,064] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-01-18 18:58:22,064] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-01-18 18:58:22,064] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-01-18 18:58:22,064] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-01-18 18:58:22,064] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-01-18 18:58:22,283] multiqc [INFO ] Compressing plot data [2024-01-18 18:58:22,347] multiqc [INFO ] Report : multiqc_report.html [2024-01-18 18:58:22,348] multiqc [INFO ] Data : multiqc_data [2024-01-18 18:58:22,348] multiqc [DEBUG ] Moving data file from '/state/partition1/job-41889910/tmp6vg6c0u0/multiqc_data' to '/scratch/gencore/logs/html/H2L2LDSXC/2/multiqc_data' [2024-01-18 19:11:00,677] multiqc [INFO ] MultiQC complete