[2023-07-06 17:38:53,861] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-07-06 17:38:53,862] multiqc [DEBUG ] No MultiQC config found: /home/mk5636/.multiqc_config.yaml [2023-07-06 17:38:53,862] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-07-06 17:38:53,864] multiqc [DEBUG ] Loading config settings from: /home/mk5636/nf-hpcpipe/test_new/bin/mqc_config.yaml [2023-07-06 17:38:53,864] 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}} [2023-07-06 17:38:53,864] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/mk5636/nf-hpcpipe/test_new/bin/mqc_config.yaml . [2023-07-06 17:38:54,043] multiqc [WARNING] MultiQC Version v1.14 now available! [2023-07-06 17:38:54,044] multiqc [INFO ] This is MultiQC v1.9 [2023-07-06 17:38:54,044] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/mk5636/nf-hpcpipe/test_new/bin/mqc_config.yaml . [2023-07-06 17:38:54,044] multiqc [DEBUG ] Working dir : /scratch/mk5636/nf-pipeline-test/work/bd/602e788c50dbc09fff2bc8e9563143/4 [2023-07-06 17:38:54,044] multiqc [INFO ] Template : default [2023-07-06 17:38:54,044] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-07-06 17:38:54,044] multiqc [INFO ] Searching : /scratch/mk5636/nf-pipeline-test/work/bd/602e788c50dbc09fff2bc8e9563143/4 [2023-07-06 17:38:54,044] 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 [2023-07-06 17:38:54,044] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-35180271/tmp9xli3o_l [2023-07-06 17:38:54,138] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l04_n01_15G_1-11_fastqc.html [2023-07-06 17:38:54,141] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52YHDSX7_l04_n01_15G_1-11_fastqc.html [2023-07-06 17:38:54,193] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l04_n01_10R_1-5_fastqc.html [2023-07-06 17:38:54,195] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52YHDSX7_l04_n01_10R_1-5_fastqc.html [2023-07-06 17:38:54,246] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l04_n01_15R_1-5_fastqc.html [2023-07-06 17:38:54,248] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52YHDSX7_l04_n01_15R_1-5_fastqc.html [2023-07-06 17:38:54,298] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l04_n01_4G_1-5_fastqc.html [2023-07-06 17:38:54,300] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52YHDSX7_l04_n01_4G_1-5_fastqc.html [2023-07-06 17:38:54,352] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l04_n01_14G_1-5_fastqc.html [2023-07-06 17:38:54,354] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52YHDSX7_l04_n01_14G_1-5_fastqc.html [2023-07-06 17:38:54,404] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l04_n01_12R_1-5_fastqc.html [2023-07-06 17:38:54,406] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52YHDSX7_l04_n01_12R_1-5_fastqc.html [2023-07-06 17:38:54,456] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H52YHDSX7_l04_n01_7R_1-5_fastqc.html [2023-07-06 17:38:54,458] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H52YHDSX7_l04_n01_7R_1-5_fastqc.html [2023-07-06 17:38:54,787] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-07-06 17:38:54,788] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-07-06 17:38:54,839] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 98 samples (table) [2023-07-06 17:38:54,849] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-07-06 17:38:54,851] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-07-06 17:38:54,854] multiqc [DEBUG ] No samples found: conpair [2023-07-06 17:38:54,857] multiqc [DEBUG ] No samples found: peddy [2023-07-06 17:38:54,860] multiqc [DEBUG ] No samples found: somalier [2023-07-06 17:38:54,863] multiqc [DEBUG ] No samples found: methylQA [2023-07-06 17:38:54,867] multiqc [DEBUG ] No samples found: mosdepth [2023-07-06 17:38:54,869] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-07-06 17:38:54,872] multiqc [DEBUG ] No samples found: qualimap [2023-07-06 17:38:54,875] multiqc [DEBUG ] No samples found: preseq [2023-07-06 17:38:54,878] multiqc [DEBUG ] No samples found: quast [2023-07-06 17:38:54,881] multiqc [DEBUG ] No samples found: qorts [2023-07-06 17:38:54,884] multiqc [DEBUG ] No samples found: rna_seqc [2023-07-06 17:38:54,887] multiqc [DEBUG ] No samples found: rockhopper [2023-07-06 17:38:54,890] multiqc [DEBUG ] No samples found: rsem [2023-07-06 17:38:54,895] multiqc [DEBUG ] No samples found: rseqc [2023-07-06 17:38:54,897] multiqc [DEBUG ] No samples found: busco [2023-07-06 17:38:54,900] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-07-06 17:38:54,903] multiqc [DEBUG ] No samples found: disambiguate [2023-07-06 17:38:54,906] multiqc [DEBUG ] No samples found: supernova [2023-07-06 17:38:54,911] multiqc [DEBUG ] No samples found: deeptools [2023-07-06 17:38:54,914] multiqc [DEBUG ] No samples found: sargasso [2023-07-06 17:38:54,917] multiqc [DEBUG ] No samples found: verifybamid [2023-07-06 17:38:54,920] multiqc [DEBUG ] No samples found: mirtrace [2023-07-06 17:38:54,923] multiqc [DEBUG ] No samples found: happy [2023-07-06 17:38:54,926] multiqc [DEBUG ] No samples found: mirtop [2023-07-06 17:38:54,929] multiqc [DEBUG ] No samples found: homer [2023-07-06 17:38:54,932] multiqc [DEBUG ] No samples found: macs2 [2023-07-06 17:38:54,935] multiqc [DEBUG ] No samples found: theta2 [2023-07-06 17:38:54,938] multiqc [DEBUG ] No samples found: snpeff [2023-07-06 17:38:54,941] multiqc [DEBUG ] No samples found: gatk [2023-07-06 17:38:54,944] multiqc [DEBUG ] No samples found: htseq [2023-07-06 17:38:54,947] multiqc [DEBUG ] No samples found: bcftools [2023-07-06 17:38:54,950] multiqc [DEBUG ] No samples found: featureCounts [2023-07-06 17:38:54,954] multiqc [DEBUG ] No samples found: fgbio [2023-07-06 17:38:54,959] multiqc [DEBUG ] No samples found: dragen [2023-07-06 17:38:54,962] multiqc [DEBUG ] No samples found: dedup [2023-07-06 17:38:54,964] multiqc [DEBUG ] No samples found: damageprofiler [2023-07-06 17:38:54,973] multiqc [DEBUG ] No samples found: biobambam2 [2023-07-06 17:38:54,975] multiqc [DEBUG ] No samples found: mtnucratio [2023-07-06 17:38:54,978] multiqc [DEBUG ] No samples found: picard [2023-07-06 17:38:54,980] multiqc [DEBUG ] No samples found: prokka [2023-07-06 17:38:54,983] multiqc [DEBUG ] No samples found: samblaster [2023-07-06 17:38:54,987] multiqc [DEBUG ] No samples found: samtools [2023-07-06 17:38:54,990] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-07-06 17:38:54,993] multiqc [DEBUG ] No samples found: bamtools [2023-07-06 17:38:54,996] multiqc [DEBUG ] No samples found: jellyfish [2023-07-06 17:38:55,000] multiqc [DEBUG ] No samples found: vcftools [2023-07-06 17:38:55,003] multiqc [DEBUG ] No samples found: longranger [2023-07-06 17:38:55,005] multiqc [DEBUG ] No samples found: stacks [2023-07-06 17:38:55,008] multiqc [DEBUG ] No samples found: varscan2 [2023-07-06 17:38:55,014] multiqc [DEBUG ] No samples found: bbmap [2023-07-06 17:38:55,017] multiqc [DEBUG ] No samples found: bismark [2023-07-06 17:38:55,020] multiqc [DEBUG ] No samples found: biscuit [2023-07-06 17:38:55,023] multiqc [DEBUG ] No samples found: hicexplorer [2023-07-06 17:38:55,026] multiqc [DEBUG ] No samples found: hicup [2023-07-06 17:38:55,029] multiqc [DEBUG ] No samples found: hicpro [2023-07-06 17:38:55,032] multiqc [DEBUG ] No samples found: salmon [2023-07-06 17:38:55,034] multiqc [DEBUG ] No samples found: kallisto [2023-07-06 17:38:55,038] multiqc [DEBUG ] No samples found: slamdunk [2023-07-06 17:38:55,040] multiqc [DEBUG ] No samples found: star [2023-07-06 17:38:55,043] multiqc [DEBUG ] No samples found: hisat2 [2023-07-06 17:38:55,046] multiqc [DEBUG ] No samples found: tophat [2023-07-06 17:38:55,049] multiqc [DEBUG ] No samples found: bowtie2 [2023-07-06 17:38:55,052] multiqc [DEBUG ] No samples found: bowtie1 [2023-07-06 17:38:55,055] multiqc [DEBUG ] No samples found: snpsplit [2023-07-06 17:38:55,057] multiqc [DEBUG ] No samples found: kat [2023-07-06 17:38:55,060] multiqc [DEBUG ] No samples found: leehom [2023-07-06 17:38:55,063] multiqc [DEBUG ] No samples found: adapterRemoval [2023-07-06 17:38:55,066] multiqc [DEBUG ] No samples found: clipandmerge [2023-07-06 17:38:55,069] multiqc [DEBUG ] No samples found: cutadapt [2023-07-06 17:38:55,072] multiqc [DEBUG ] No samples found: flexbar [2023-07-06 17:38:55,075] multiqc [DEBUG ] No samples found: kaiju [2023-07-06 17:38:55,077] multiqc [DEBUG ] No samples found: kraken [2023-07-06 17:38:55,080] multiqc [DEBUG ] No samples found: malt [2023-07-06 17:38:55,083] multiqc [DEBUG ] No samples found: trimmomatic [2023-07-06 17:38:55,086] multiqc [DEBUG ] No samples found: sickle [2023-07-06 17:38:55,089] multiqc [DEBUG ] No samples found: skewer [2023-07-06 17:38:55,092] multiqc [DEBUG ] No samples found: sortmerna [2023-07-06 17:38:55,094] multiqc [DEBUG ] No samples found: biobloomtools [2023-07-06 17:38:55,097] multiqc [DEBUG ] No samples found: fastq_screen [2023-07-06 17:38:55,100] multiqc [DEBUG ] No samples found: afterqc [2023-07-06 17:38:55,103] multiqc [DEBUG ] No samples found: fastp [2023-07-06 17:38:56,425] multiqc.modules.fastqc.fastqc [INFO ] Found 7 reports [2023-07-06 17:38:56,539] multiqc [DEBUG ] No samples found: pycoqc [2023-07-06 17:38:56,542] multiqc [DEBUG ] No samples found: minionqc [2023-07-06 17:38:56,545] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-07-06 17:38:56,548] multiqc [DEBUG ] No samples found: clusterflow [2023-07-06 17:38:56,551] multiqc [DEBUG ] No samples found: bcl2fastq [2023-07-06 17:38:56,554] multiqc [DEBUG ] No samples found: interop [2023-07-06 17:38:56,557] multiqc [DEBUG ] No samples found: ivar [2023-07-06 17:38:56,560] multiqc [DEBUG ] No samples found: flash [2023-07-06 17:38:56,563] multiqc [DEBUG ] No samples found: seqyclean [2023-07-06 17:38:56,563] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-07-06 17:38:56,563] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-07-06 17:38:56,563] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-07-06 17:38:56,563] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2023-07-06 17:38:56,563] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2023-07-06 17:38:56,564] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2023-07-06 17:38:56,564] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2023-07-06 17:38:56,564] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2023-07-06 17:38:56,564] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2023-07-06 17:38:56,564] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-07-06 17:38:56,564] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-07-06 17:38:56,564] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-07-06 17:38:56,564] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-07-06 17:38:56,564] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-07-06 17:38:56,564] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-07-06 17:38:56,564] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-07-06 17:38:56,564] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-07-06 17:38:56,564] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-07-06 17:38:56,564] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-07-06 17:38:56,564] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-07-06 17:38:56,564] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-07-06 17:38:56,564] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-07-06 17:38:56,564] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-07-06 17:38:56,564] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-07-06 17:38:56,564] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-07-06 17:38:56,564] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-07-06 17:38:56,564] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-07-06 17:38:56,564] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-07-06 17:38:56,564] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-07-06 17:38:56,564] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-07-06 17:38:56,574] multiqc [INFO ] Compressing plot data [2023-07-06 17:38:56,716] multiqc [INFO ] Report : multiqc_report.html [2023-07-06 17:38:56,717] multiqc [INFO ] Data : multiqc_data [2023-07-06 17:38:56,717] multiqc [DEBUG ] Moving data file from '/state/partition1/job-35180271/tmp9xli3o_l/multiqc_data' to '/scratch/mk5636/nf-pipeline-test/work/bd/602e788c50dbc09fff2bc8e9563143/4/multiqc_data' [2023-07-06 17:38:56,884] multiqc [INFO ] MultiQC complete