[2024-06-13 13:25:32,616] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-06-13 13:25:32,616] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-06-13 13:25:32,616] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-06-13 13:25:32,619] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-06-13 13:25:32,619] 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}} [2024-06-13 13:25:32,619] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-06-13 13:25:32,653] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-06-13 13:25:32,653] multiqc [INFO ] This is MultiQC v1.9 [2024-06-13 13:25:32,653] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-06-13 13:25:32,653] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/52/9b82abe0a3245494c438ac431ce243/merged [2024-06-13 13:25:32,653] multiqc [INFO ] Template : default [2024-06-13 13:25:32,653] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-06-13 13:25:32,653] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/52/9b82abe0a3245494c438ac431ce243/merged [2024-06-13 13:25:32,654] 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 [2024-06-13 13:25:32,654] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-47507762/tmpaqx70egb [2024-06-13 13:25:32,775] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5LHYDRX5_n01_C_A_fastqc.html [2024-06-13 13:25:32,782] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5LHYDRX5_n01_C_A_fastqc.html [2024-06-13 13:25:32,853] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5LHYDRX5_n01_C_B_fastqc.html [2024-06-13 13:25:32,861] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5LHYDRX5_n01_C_B_fastqc.html [2024-06-13 13:25:32,926] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5LHYDRX5_n01_F_A_fastqc.html [2024-06-13 13:25:32,933] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5LHYDRX5_n01_F_A_fastqc.html [2024-06-13 13:25:33,002] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5LHYDRX5_n01_F_B_fastqc.html [2024-06-13 13:25:33,010] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5LHYDRX5_n01_F_B_fastqc.html [2024-06-13 13:25:33,093] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5LHYDRX5_n01_U_A_fastqc.html [2024-06-13 13:25:33,100] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5LHYDRX5_n01_U_A_fastqc.html [2024-06-13 13:25:33,167] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5LHYDRX5_n01_U_B_fastqc.html [2024-06-13 13:25:33,174] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5LHYDRX5_n01_U_B_fastqc.html [2024-06-13 13:25:33,239] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5LHYDRX5_n01_Z_A_fastqc.html [2024-06-13 13:25:33,246] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5LHYDRX5_n01_Z_A_fastqc.html [2024-06-13 13:25:33,311] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5LHYDRX5_n01_Z_B_fastqc.html [2024-06-13 13:25:33,317] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5LHYDRX5_n01_Z_B_fastqc.html [2024-06-13 13:25:33,386] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5LHYDRX5_n01_undetermined_fastqc.html [2024-06-13 13:25:33,393] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5LHYDRX5_n01_undetermined_fastqc.html [2024-06-13 13:25:33,461] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-06-13 13:25:33,468] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-06-13 13:25:33,468] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-06-13 13:25:33,468] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-06-13 13:25:33,468] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-06-13 13:25:33,468] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-06-13 13:25:33,468] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-06-13 13:25:33,525] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-06-13 13:25:36,382] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-06-13 13:25:36,384] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-06-13 13:25:36,396] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 9 samples (table) [2024-06-13 13:25:36,397] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-06-13 13:25:36,407] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-06-13 13:25:36,412] multiqc [DEBUG ] No samples found: conpair [2024-06-13 13:25:36,416] multiqc [DEBUG ] No samples found: peddy [2024-06-13 13:25:36,421] multiqc [DEBUG ] No samples found: somalier [2024-06-13 13:25:36,425] multiqc [DEBUG ] No samples found: methylQA [2024-06-13 13:25:36,433] multiqc [DEBUG ] No samples found: mosdepth [2024-06-13 13:25:36,437] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-06-13 13:25:36,440] multiqc [DEBUG ] No samples found: qualimap [2024-06-13 13:25:36,445] multiqc [DEBUG ] No samples found: preseq [2024-06-13 13:25:36,449] multiqc [DEBUG ] No samples found: quast [2024-06-13 13:25:36,453] multiqc [DEBUG ] No samples found: qorts [2024-06-13 13:25:36,458] multiqc [DEBUG ] No samples found: rna_seqc [2024-06-13 13:25:36,462] multiqc [DEBUG ] No samples found: rockhopper [2024-06-13 13:25:36,467] multiqc [DEBUG ] No samples found: rsem [2024-06-13 13:25:36,477] multiqc [DEBUG ] No samples found: rseqc [2024-06-13 13:25:36,482] multiqc [DEBUG ] No samples found: busco [2024-06-13 13:25:36,487] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-06-13 13:25:36,491] multiqc [DEBUG ] No samples found: disambiguate [2024-06-13 13:25:36,495] multiqc [DEBUG ] No samples found: supernova [2024-06-13 13:25:36,507] multiqc [DEBUG ] No samples found: deeptools [2024-06-13 13:25:36,511] multiqc [DEBUG ] No samples found: sargasso [2024-06-13 13:25:36,516] multiqc [DEBUG ] No samples found: verifybamid [2024-06-13 13:25:36,520] multiqc [DEBUG ] No samples found: mirtrace [2024-06-13 13:25:36,524] multiqc [DEBUG ] No samples found: happy [2024-06-13 13:25:36,529] multiqc [DEBUG ] No samples found: mirtop [2024-06-13 13:25:36,535] multiqc [DEBUG ] No samples found: homer [2024-06-13 13:25:36,539] multiqc [DEBUG ] No samples found: macs2 [2024-06-13 13:25:36,543] multiqc [DEBUG ] No samples found: theta2 [2024-06-13 13:25:36,547] multiqc [DEBUG ] No samples found: snpeff [2024-06-13 13:25:36,553] multiqc [DEBUG ] No samples found: gatk [2024-06-13 13:25:36,558] multiqc [DEBUG ] No samples found: htseq [2024-06-13 13:25:36,563] multiqc [DEBUG ] No samples found: bcftools [2024-06-13 13:25:36,567] multiqc [DEBUG ] No samples found: featureCounts [2024-06-13 13:25:36,573] multiqc [DEBUG ] No samples found: fgbio [2024-06-13 13:25:36,585] multiqc [DEBUG ] No samples found: dragen [2024-06-13 13:25:36,589] multiqc [DEBUG ] No samples found: dedup [2024-06-13 13:25:36,593] multiqc [DEBUG ] No samples found: damageprofiler [2024-06-13 13:25:36,614] multiqc [DEBUG ] No samples found: biobambam2 [2024-06-13 13:25:36,619] multiqc [DEBUG ] No samples found: mtnucratio [2024-06-13 13:25:36,621] multiqc [DEBUG ] No samples found: picard [2024-06-13 13:25:36,626] multiqc [DEBUG ] No samples found: prokka [2024-06-13 13:25:36,630] multiqc [DEBUG ] No samples found: samblaster [2024-06-13 13:25:36,638] multiqc [DEBUG ] No samples found: samtools [2024-06-13 13:25:36,642] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-06-13 13:25:36,647] multiqc [DEBUG ] No samples found: bamtools [2024-06-13 13:25:36,651] multiqc [DEBUG ] No samples found: jellyfish [2024-06-13 13:25:36,658] multiqc [DEBUG ] No samples found: vcftools [2024-06-13 13:25:36,662] multiqc [DEBUG ] No samples found: longranger [2024-06-13 13:25:36,666] multiqc [DEBUG ] No samples found: stacks [2024-06-13 13:25:36,671] multiqc [DEBUG ] No samples found: varscan2 [2024-06-13 13:25:36,684] multiqc [DEBUG ] No samples found: bbmap [2024-06-13 13:25:36,688] multiqc [DEBUG ] No samples found: bismark [2024-06-13 13:25:36,693] multiqc [DEBUG ] No samples found: biscuit [2024-06-13 13:25:36,698] multiqc [DEBUG ] No samples found: hicexplorer [2024-06-13 13:25:36,702] multiqc [DEBUG ] No samples found: hicup [2024-06-13 13:25:36,707] multiqc [DEBUG ] No samples found: hicpro [2024-06-13 13:25:36,711] multiqc [DEBUG ] No samples found: salmon [2024-06-13 13:25:36,715] multiqc [DEBUG ] No samples found: kallisto [2024-06-13 13:25:36,719] multiqc [DEBUG ] No samples found: slamdunk [2024-06-13 13:25:36,724] multiqc [DEBUG ] No samples found: star [2024-06-13 13:25:36,728] multiqc [DEBUG ] No samples found: hisat2 [2024-06-13 13:25:36,732] multiqc [DEBUG ] No samples found: tophat [2024-06-13 13:25:36,737] multiqc [DEBUG ] No samples found: bowtie2 [2024-06-13 13:25:36,741] multiqc [DEBUG ] No samples found: bowtie1 [2024-06-13 13:25:36,745] multiqc [DEBUG ] No samples found: snpsplit [2024-06-13 13:25:36,750] multiqc [DEBUG ] No samples found: kat [2024-06-13 13:25:36,754] multiqc [DEBUG ] No samples found: leehom [2024-06-13 13:25:36,758] multiqc [DEBUG ] No samples found: adapterRemoval [2024-06-13 13:25:36,762] multiqc [DEBUG ] No samples found: clipandmerge [2024-06-13 13:25:36,767] multiqc [DEBUG ] No samples found: cutadapt [2024-06-13 13:25:36,771] multiqc [DEBUG ] No samples found: flexbar [2024-06-13 13:25:36,775] multiqc [DEBUG ] No samples found: kaiju [2024-06-13 13:25:36,779] multiqc [DEBUG ] No samples found: kraken [2024-06-13 13:25:36,784] multiqc [DEBUG ] No samples found: malt [2024-06-13 13:25:36,788] multiqc [DEBUG ] No samples found: trimmomatic [2024-06-13 13:25:36,792] multiqc [DEBUG ] No samples found: sickle [2024-06-13 13:25:36,797] multiqc [DEBUG ] No samples found: skewer [2024-06-13 13:25:36,801] multiqc [DEBUG ] No samples found: sortmerna [2024-06-13 13:25:36,805] multiqc [DEBUG ] No samples found: biobloomtools [2024-06-13 13:25:36,809] multiqc [DEBUG ] No samples found: fastq_screen [2024-06-13 13:25:36,814] multiqc [DEBUG ] No samples found: afterqc [2024-06-13 13:25:36,818] multiqc [DEBUG ] No samples found: fastp [2024-06-13 13:25:37,425] multiqc.modules.fastqc.fastqc [INFO ] Found 9 reports [2024-06-13 13:25:37,567] multiqc [DEBUG ] No samples found: pycoqc [2024-06-13 13:25:37,572] multiqc [DEBUG ] No samples found: minionqc [2024-06-13 13:25:37,576] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-06-13 13:25:37,580] multiqc [DEBUG ] No samples found: clusterflow [2024-06-13 13:25:37,585] multiqc [DEBUG ] No samples found: bcl2fastq [2024-06-13 13:25:37,590] multiqc [DEBUG ] No samples found: interop [2024-06-13 13:25:37,594] multiqc [DEBUG ] No samples found: ivar [2024-06-13 13:25:37,599] multiqc [DEBUG ] No samples found: flash [2024-06-13 13:25:37,603] multiqc [DEBUG ] No samples found: seqyclean [2024-06-13 13:25:37,603] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-06-13 13:25:37,603] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-06-13 13:25:37,603] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-06-13 13:25:37,603] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-06-13 13:25:37,603] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-06-13 13:25:37,603] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-06-13 13:25:37,603] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-06-13 13:25:37,604] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-06-13 13:25:37,604] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-06-13 13:25:37,604] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-06-13 13:25:37,604] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-06-13 13:25:37,604] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-06-13 13:25:37,604] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-06-13 13:25:37,604] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-06-13 13:25:37,604] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-06-13 13:25:37,604] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-06-13 13:25:37,604] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-06-13 13:25:37,604] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-06-13 13:25:37,604] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-06-13 13:25:37,604] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-06-13 13:25:37,604] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-06-13 13:25:37,604] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-06-13 13:25:37,604] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-06-13 13:25:37,604] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-06-13 13:25:37,604] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-06-13 13:25:37,604] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-06-13 13:25:37,604] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-06-13 13:25:37,604] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-06-13 13:25:37,604] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-06-13 13:25:37,604] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-06-13 13:25:37,616] multiqc [INFO ] Compressing plot data [2024-06-13 13:25:37,806] multiqc [INFO ] Report : multiqc_report.html [2024-06-13 13:25:37,806] multiqc [INFO ] Data : multiqc_data [2024-06-13 13:25:37,806] multiqc [DEBUG ] Moving data file from '/state/partition1/job-47507762/tmpaqx70egb/multiqc_data' to '/vast/gencore/GENEFLOW/work/52/9b82abe0a3245494c438ac431ce243/merged/multiqc_data' [2024-06-13 13:25:37,963] multiqc [INFO ] MultiQC complete