[2023-07-06 21:55:17,647] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-07-06 21:55:17,648] multiqc [DEBUG ] No MultiQC config found: /home/mk5636/.multiqc_config.yaml [2023-07-06 21:55:17,648] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-07-06 21:55:17,650] multiqc [DEBUG ] Loading config settings from: /home/mk5636/nf-hpcpipe/test_new/bin/mqc_config.yaml [2023-07-06 21:55:17,650] 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 21:55:17,651] 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 21:55:17,889] multiqc [WARNING] MultiQC Version v1.14 now available! [2023-07-06 21:55:17,889] multiqc [INFO ] This is MultiQC v1.9 [2023-07-06 21:55:17,889] 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 21:55:17,889] multiqc [DEBUG ] Working dir : /scratch/mk5636/nf-pipeline-test/work/94/9b4d1d60d101763d5d75c7d2e56514/1 [2023-07-06 21:55:17,889] multiqc [INFO ] Template : default [2023-07-06 21:55:17,889] 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 21:55:17,889] multiqc [INFO ] Searching : /scratch/mk5636/nf-pipeline-test/work/94/9b4d1d60d101763d5d75c7d2e56514/1 [2023-07-06 21:55:17,890] 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 21:55:17,890] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-35183638/tmpthy7nkzf [2023-07-06 21:55:18,037] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-07-06 21:55:18,039] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-07-06 21:55:18,039] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-07-06 21:55:18,039] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-07-06 21:55:18,039] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-07-06 21:55:18,039] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-07-06 21:55:18,040] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-07-06 21:55:18,269] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-L396B_l01_n02_ADARcdgDNA_fastqc.html [2023-07-06 21:55:18,271] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-L396B_l01_n02_ADARcdgDNA_fastqc.html [2023-07-06 21:55:18,310] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-L396B_l01_n01_undetermined_fastqc.html [2023-07-06 21:55:18,311] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-L396B_l01_n01_undetermined_fastqc.html [2023-07-06 21:55:18,350] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-L396B_l01_n02_Fmr1ADARcdgDNA_fastqc.html [2023-07-06 21:55:18,352] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-L396B_l01_n02_Fmr1ADARcdgDNA_fastqc.html [2023-07-06 21:55:18,390] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-L396B_l01_n02_undetermined_fastqc.html [2023-07-06 21:55:18,392] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-L396B_l01_n02_undetermined_fastqc.html [2023-07-06 21:55:18,431] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-L396B_l01_n01_Fmr1ADARcdgDNA_fastqc.html [2023-07-06 21:55:18,433] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-L396B_l01_n01_Fmr1ADARcdgDNA_fastqc.html [2023-07-06 21:55:18,471] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-L396B_l01_n01_ADARcdgDNA_fastqc.html [2023-07-06 21:55:18,473] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-L396B_l01_n01_ADARcdgDNA_fastqc.html [2023-07-06 21:55:19,185] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-07-06 21:55:19,187] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-07-06 21:55:19,196] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-07-06 21:55:19,198] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 3 samples (table) [2023-07-06 21:55:19,207] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-07-06 21:55:19,212] multiqc [DEBUG ] No samples found: conpair [2023-07-06 21:55:19,217] multiqc [DEBUG ] No samples found: peddy [2023-07-06 21:55:19,223] multiqc [DEBUG ] No samples found: somalier [2023-07-06 21:55:19,227] multiqc [DEBUG ] No samples found: methylQA [2023-07-06 21:55:19,235] multiqc [DEBUG ] No samples found: mosdepth [2023-07-06 21:55:19,240] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-07-06 21:55:19,244] multiqc [DEBUG ] No samples found: qualimap [2023-07-06 21:55:19,258] multiqc [DEBUG ] No samples found: preseq [2023-07-06 21:55:19,263] multiqc [DEBUG ] No samples found: quast [2023-07-06 21:55:19,268] multiqc [DEBUG ] No samples found: qorts [2023-07-06 21:55:19,273] multiqc [DEBUG ] No samples found: rna_seqc [2023-07-06 21:55:19,278] multiqc [DEBUG ] No samples found: rockhopper [2023-07-06 21:55:19,283] multiqc [DEBUG ] No samples found: rsem [2023-07-06 21:55:19,293] multiqc [DEBUG ] No samples found: rseqc [2023-07-06 21:55:19,302] multiqc [DEBUG ] No samples found: busco [2023-07-06 21:55:19,311] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-07-06 21:55:19,324] multiqc [DEBUG ] No samples found: disambiguate [2023-07-06 21:55:19,330] multiqc [DEBUG ] No samples found: supernova [2023-07-06 21:55:19,344] multiqc [DEBUG ] No samples found: deeptools [2023-07-06 21:55:19,349] multiqc [DEBUG ] No samples found: sargasso [2023-07-06 21:55:19,353] multiqc [DEBUG ] No samples found: verifybamid [2023-07-06 21:55:19,358] multiqc [DEBUG ] No samples found: mirtrace [2023-07-06 21:55:19,362] multiqc [DEBUG ] No samples found: happy [2023-07-06 21:55:19,367] multiqc [DEBUG ] No samples found: mirtop [2023-07-06 21:55:19,382] multiqc [DEBUG ] No samples found: homer [2023-07-06 21:55:19,387] multiqc [DEBUG ] No samples found: macs2 [2023-07-06 21:55:19,391] multiqc [DEBUG ] No samples found: theta2 [2023-07-06 21:55:19,396] multiqc [DEBUG ] No samples found: snpeff [2023-07-06 21:55:19,402] multiqc [DEBUG ] No samples found: gatk [2023-07-06 21:55:19,419] multiqc [DEBUG ] No samples found: htseq [2023-07-06 21:55:19,424] multiqc [DEBUG ] No samples found: bcftools [2023-07-06 21:55:19,428] multiqc [DEBUG ] No samples found: featureCounts [2023-07-06 21:55:19,434] multiqc [DEBUG ] No samples found: fgbio [2023-07-06 21:55:19,447] multiqc [DEBUG ] No samples found: dragen [2023-07-06 21:55:19,453] multiqc [DEBUG ] No samples found: dedup [2023-07-06 21:55:19,458] multiqc [DEBUG ] No samples found: damageprofiler [2023-07-06 21:55:19,501] multiqc [DEBUG ] No samples found: biobambam2 [2023-07-06 21:55:19,519] multiqc [DEBUG ] No samples found: mtnucratio [2023-07-06 21:55:19,522] multiqc [DEBUG ] No samples found: picard [2023-07-06 21:55:19,526] multiqc [DEBUG ] No samples found: prokka [2023-07-06 21:55:19,531] multiqc [DEBUG ] No samples found: samblaster [2023-07-06 21:55:19,540] multiqc [DEBUG ] No samples found: samtools [2023-07-06 21:55:19,544] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-07-06 21:55:19,549] multiqc [DEBUG ] No samples found: bamtools [2023-07-06 21:55:19,553] multiqc [DEBUG ] No samples found: jellyfish [2023-07-06 21:55:19,563] multiqc [DEBUG ] No samples found: vcftools [2023-07-06 21:55:19,568] multiqc [DEBUG ] No samples found: longranger [2023-07-06 21:55:19,575] multiqc [DEBUG ] No samples found: stacks [2023-07-06 21:55:19,579] multiqc [DEBUG ] No samples found: varscan2 [2023-07-06 21:55:19,594] multiqc [DEBUG ] No samples found: bbmap [2023-07-06 21:55:19,601] multiqc [DEBUG ] No samples found: bismark [2023-07-06 21:55:19,606] multiqc [DEBUG ] No samples found: biscuit [2023-07-06 21:55:19,629] multiqc [DEBUG ] No samples found: hicexplorer [2023-07-06 21:55:19,634] multiqc [DEBUG ] No samples found: hicup [2023-07-06 21:55:19,639] multiqc [DEBUG ] No samples found: hicpro [2023-07-06 21:55:19,643] multiqc [DEBUG ] No samples found: salmon [2023-07-06 21:55:19,658] multiqc [DEBUG ] No samples found: kallisto [2023-07-06 21:55:19,668] multiqc [DEBUG ] No samples found: slamdunk [2023-07-06 21:55:19,673] multiqc [DEBUG ] No samples found: star [2023-07-06 21:55:19,679] multiqc [DEBUG ] No samples found: hisat2 [2023-07-06 21:55:19,692] multiqc [DEBUG ] No samples found: tophat [2023-07-06 21:55:19,697] multiqc [DEBUG ] No samples found: bowtie2 [2023-07-06 21:55:19,701] multiqc [DEBUG ] No samples found: bowtie1 [2023-07-06 21:55:19,712] multiqc [DEBUG ] No samples found: snpsplit [2023-07-06 21:55:19,729] multiqc [DEBUG ] No samples found: kat [2023-07-06 21:55:19,735] multiqc [DEBUG ] No samples found: leehom [2023-07-06 21:55:19,742] multiqc [DEBUG ] No samples found: adapterRemoval [2023-07-06 21:55:19,748] multiqc [DEBUG ] No samples found: clipandmerge [2023-07-06 21:55:19,753] multiqc [DEBUG ] No samples found: cutadapt [2023-07-06 21:55:19,757] multiqc [DEBUG ] No samples found: flexbar [2023-07-06 21:55:19,762] multiqc [DEBUG ] No samples found: kaiju [2023-07-06 21:55:19,769] multiqc [DEBUG ] No samples found: kraken [2023-07-06 21:55:19,773] multiqc [DEBUG ] No samples found: malt [2023-07-06 21:55:19,778] multiqc [DEBUG ] No samples found: trimmomatic [2023-07-06 21:55:19,782] multiqc [DEBUG ] No samples found: sickle [2023-07-06 21:55:19,787] multiqc [DEBUG ] No samples found: skewer [2023-07-06 21:55:19,793] multiqc [DEBUG ] No samples found: sortmerna [2023-07-06 21:55:19,798] multiqc [DEBUG ] No samples found: biobloomtools [2023-07-06 21:55:19,802] multiqc [DEBUG ] No samples found: fastq_screen [2023-07-06 21:55:19,808] multiqc [DEBUG ] No samples found: afterqc [2023-07-06 21:55:19,812] multiqc [DEBUG ] No samples found: fastp [2023-07-06 21:55:19,871] multiqc.modules.fastqc.fastqc [INFO ] Found 6 reports [2023-07-06 21:55:20,021] multiqc [DEBUG ] No samples found: pycoqc [2023-07-06 21:55:20,031] multiqc [DEBUG ] No samples found: minionqc [2023-07-06 21:55:20,048] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-07-06 21:55:20,053] multiqc [DEBUG ] No samples found: clusterflow [2023-07-06 21:55:20,058] multiqc [DEBUG ] No samples found: bcl2fastq [2023-07-06 21:55:20,062] multiqc [DEBUG ] No samples found: interop [2023-07-06 21:55:20,068] multiqc [DEBUG ] No samples found: ivar [2023-07-06 21:55:20,087] multiqc [DEBUG ] No samples found: flash [2023-07-06 21:55:20,092] multiqc [DEBUG ] No samples found: seqyclean [2023-07-06 21:55:20,092] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-07-06 21:55:20,092] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-07-06 21:55:20,092] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-07-06 21:55:20,092] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2023-07-06 21:55:20,092] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2023-07-06 21:55:20,092] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2023-07-06 21:55:20,092] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2023-07-06 21:55:20,092] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2023-07-06 21:55:20,092] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2023-07-06 21:55:20,092] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-07-06 21:55:20,092] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-07-06 21:55:20,092] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-07-06 21:55:20,092] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-07-06 21:55:20,092] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-07-06 21:55:20,092] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-07-06 21:55:20,092] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-07-06 21:55:20,092] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-07-06 21:55:20,093] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-07-06 21:55:20,093] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-07-06 21:55:20,093] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-07-06 21:55:20,093] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-07-06 21:55:20,093] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-07-06 21:55:20,093] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-07-06 21:55:20,093] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-07-06 21:55:20,093] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-07-06 21:55:20,093] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-07-06 21:55:20,093] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-07-06 21:55:20,093] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-07-06 21:55:20,093] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-07-06 21:55:20,093] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-07-06 21:55:20,101] multiqc [INFO ] Compressing plot data [2023-07-06 21:55:20,216] multiqc [INFO ] Report : multiqc_report.html [2023-07-06 21:55:20,216] multiqc [INFO ] Data : multiqc_data [2023-07-06 21:55:20,216] multiqc [DEBUG ] Moving data file from '/state/partition1/job-35183638/tmpthy7nkzf/multiqc_data' to '/scratch/mk5636/nf-pipeline-test/work/94/9b4d1d60d101763d5d75c7d2e56514/1/multiqc_data' [2023-07-06 21:55:20,387] multiqc [INFO ] MultiQC complete