[2024-08-03 12:52:54,268] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-08-03 12:52:54,268] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-08-03 12:52:54,269] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-08-03 12:52:54,271] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-08-03 12:52:54,271] 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}} [2024-08-03 12:52:54,271] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-08-03 12:52:54,314] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-08-03 12:52:54,314] multiqc [INFO ] This is MultiQC v1.9 [2024-08-03 12:52:54,315] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-08-03 12:52:54,315] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/60/68f79f41a92197f04570f8279cb28a/merged [2024-08-03 12:52:54,315] multiqc [INFO ] Template : default [2024-08-03 12:52:54,315] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-08-03 12:52:54,315] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/60/68f79f41a92197f04570f8279cb28a/merged [2024-08-03 12:52:54,315] 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 [2024-08-03 12:52:54,315] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-49306828/tmpuu0pzfn2 [2024-08-03 12:52:54,453] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7G3VDRX5_1_fastqc.html [2024-08-03 12:52:54,461] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7G3VDRX5_1_fastqc.html [2024-08-03 12:52:54,533] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7G3VDRX5_2_fastqc.html [2024-08-03 12:52:54,539] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7G3VDRX5_2_fastqc.html [2024-08-03 12:52:54,621] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7G3VDRX5_3_fastqc.html [2024-08-03 12:52:54,627] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7G3VDRX5_3_fastqc.html [2024-08-03 12:52:54,696] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7G3VDRX5_4_fastqc.html [2024-08-03 12:52:54,702] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7G3VDRX5_4_fastqc.html [2024-08-03 12:52:55,381] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-08-03 12:52:55,383] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-08-03 12:52:55,389] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-08-03 12:52:55,394] multiqc [DEBUG ] No samples found: conpair [2024-08-03 12:52:55,400] multiqc [DEBUG ] No samples found: peddy [2024-08-03 12:52:55,406] multiqc [DEBUG ] No samples found: somalier [2024-08-03 12:52:55,412] multiqc [DEBUG ] No samples found: methylQA [2024-08-03 12:52:55,421] multiqc [DEBUG ] No samples found: mosdepth [2024-08-03 12:52:55,426] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-08-03 12:52:55,430] multiqc [DEBUG ] No samples found: qualimap [2024-08-03 12:52:55,436] multiqc [DEBUG ] No samples found: preseq [2024-08-03 12:52:55,441] multiqc [DEBUG ] No samples found: quast [2024-08-03 12:52:55,447] multiqc [DEBUG ] No samples found: qorts [2024-08-03 12:52:55,452] multiqc [DEBUG ] No samples found: rna_seqc [2024-08-03 12:52:55,458] multiqc [DEBUG ] No samples found: rockhopper [2024-08-03 12:52:55,464] multiqc [DEBUG ] No samples found: rsem [2024-08-03 12:52:55,477] multiqc [DEBUG ] No samples found: rseqc [2024-08-03 12:52:55,483] multiqc [DEBUG ] No samples found: busco [2024-08-03 12:52:55,489] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-08-03 12:52:55,494] multiqc [DEBUG ] No samples found: disambiguate [2024-08-03 12:52:55,500] multiqc [DEBUG ] No samples found: supernova [2024-08-03 12:52:55,516] multiqc [DEBUG ] No samples found: deeptools [2024-08-03 12:52:55,522] multiqc [DEBUG ] No samples found: sargasso [2024-08-03 12:52:55,528] multiqc [DEBUG ] No samples found: verifybamid [2024-08-03 12:52:55,533] multiqc [DEBUG ] No samples found: mirtrace [2024-08-03 12:52:55,539] multiqc [DEBUG ] No samples found: happy [2024-08-03 12:52:55,544] multiqc [DEBUG ] No samples found: mirtop [2024-08-03 12:52:55,551] multiqc [DEBUG ] No samples found: homer [2024-08-03 12:52:55,557] multiqc [DEBUG ] No samples found: macs2 [2024-08-03 12:52:55,562] multiqc [DEBUG ] No samples found: theta2 [2024-08-03 12:52:55,567] multiqc [DEBUG ] No samples found: snpeff [2024-08-03 12:52:55,575] multiqc [DEBUG ] No samples found: gatk [2024-08-03 12:52:55,580] multiqc [DEBUG ] No samples found: htseq [2024-08-03 12:52:55,587] multiqc [DEBUG ] No samples found: bcftools [2024-08-03 12:52:55,592] multiqc [DEBUG ] No samples found: featureCounts [2024-08-03 12:52:55,599] multiqc [DEBUG ] No samples found: fgbio [2024-08-03 12:52:55,614] multiqc [DEBUG ] No samples found: dragen [2024-08-03 12:52:55,620] multiqc [DEBUG ] No samples found: dedup [2024-08-03 12:52:55,626] multiqc [DEBUG ] No samples found: damageprofiler [2024-08-03 12:52:55,650] multiqc [DEBUG ] No samples found: biobambam2 [2024-08-03 12:52:55,656] multiqc [DEBUG ] No samples found: mtnucratio [2024-08-03 12:52:55,659] multiqc [DEBUG ] No samples found: picard [2024-08-03 12:52:55,665] multiqc [DEBUG ] No samples found: prokka [2024-08-03 12:52:55,669] multiqc [DEBUG ] No samples found: samblaster [2024-08-03 12:52:55,681] multiqc [DEBUG ] No samples found: samtools [2024-08-03 12:52:55,686] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-08-03 12:52:55,692] multiqc [DEBUG ] No samples found: bamtools [2024-08-03 12:52:55,697] multiqc [DEBUG ] No samples found: jellyfish [2024-08-03 12:52:55,706] multiqc [DEBUG ] No samples found: vcftools [2024-08-03 12:52:55,712] multiqc [DEBUG ] No samples found: longranger [2024-08-03 12:52:55,717] multiqc [DEBUG ] No samples found: stacks [2024-08-03 12:52:55,722] multiqc [DEBUG ] No samples found: varscan2 [2024-08-03 12:52:55,737] multiqc [DEBUG ] No samples found: bbmap [2024-08-03 12:52:55,743] multiqc [DEBUG ] No samples found: bismark [2024-08-03 12:52:55,750] multiqc [DEBUG ] No samples found: biscuit [2024-08-03 12:52:55,755] multiqc [DEBUG ] No samples found: hicexplorer [2024-08-03 12:52:55,761] multiqc [DEBUG ] No samples found: hicup [2024-08-03 12:52:55,766] multiqc [DEBUG ] No samples found: hicpro [2024-08-03 12:52:55,771] multiqc [DEBUG ] No samples found: salmon [2024-08-03 12:52:55,776] multiqc [DEBUG ] No samples found: kallisto [2024-08-03 12:52:55,781] multiqc [DEBUG ] No samples found: slamdunk [2024-08-03 12:52:55,787] multiqc [DEBUG ] No samples found: star [2024-08-03 12:52:55,792] multiqc [DEBUG ] No samples found: hisat2 [2024-08-03 12:52:55,797] multiqc [DEBUG ] No samples found: tophat [2024-08-03 12:52:55,802] multiqc [DEBUG ] No samples found: bowtie2 [2024-08-03 12:52:55,807] multiqc [DEBUG ] No samples found: bowtie1 [2024-08-03 12:52:55,813] multiqc [DEBUG ] No samples found: snpsplit [2024-08-03 12:52:55,818] multiqc [DEBUG ] No samples found: kat [2024-08-03 12:52:55,823] multiqc [DEBUG ] No samples found: leehom [2024-08-03 12:52:55,829] multiqc [DEBUG ] No samples found: adapterRemoval [2024-08-03 12:52:55,834] multiqc [DEBUG ] No samples found: clipandmerge [2024-08-03 12:52:55,839] multiqc [DEBUG ] No samples found: cutadapt [2024-08-03 12:52:55,844] multiqc [DEBUG ] No samples found: flexbar [2024-08-03 12:52:55,849] multiqc [DEBUG ] No samples found: kaiju [2024-08-03 12:52:55,855] multiqc [DEBUG ] No samples found: kraken [2024-08-03 12:52:55,860] multiqc [DEBUG ] No samples found: malt [2024-08-03 12:52:55,865] multiqc [DEBUG ] No samples found: trimmomatic [2024-08-03 12:52:55,871] multiqc [DEBUG ] No samples found: sickle [2024-08-03 12:52:55,876] multiqc [DEBUG ] No samples found: skewer [2024-08-03 12:52:55,881] multiqc [DEBUG ] No samples found: sortmerna [2024-08-03 12:52:55,886] multiqc [DEBUG ] No samples found: biobloomtools [2024-08-03 12:52:55,891] multiqc [DEBUG ] No samples found: fastq_screen [2024-08-03 12:52:55,896] multiqc [DEBUG ] No samples found: afterqc [2024-08-03 12:52:55,902] multiqc [DEBUG ] No samples found: fastp [2024-08-03 12:52:56,061] multiqc.modules.fastqc.fastqc [INFO ] Found 4 reports [2024-08-03 12:52:56,110] multiqc [DEBUG ] No samples found: pycoqc [2024-08-03 12:52:56,116] multiqc [DEBUG ] No samples found: minionqc [2024-08-03 12:52:56,121] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-08-03 12:52:56,126] multiqc [DEBUG ] No samples found: clusterflow [2024-08-03 12:52:56,132] multiqc [DEBUG ] No samples found: bcl2fastq [2024-08-03 12:52:56,137] multiqc [DEBUG ] No samples found: interop [2024-08-03 12:52:56,142] multiqc [DEBUG ] No samples found: ivar [2024-08-03 12:52:56,147] multiqc [DEBUG ] No samples found: flash [2024-08-03 12:52:56,153] multiqc [DEBUG ] No samples found: seqyclean [2024-08-03 12:52:56,153] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-08-03 12:52:56,153] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2024-08-03 12:52:56,153] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-08-03 12:52:56,153] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-08-03 12:52:56,153] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found. [2024-08-03 12:52:56,153] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-08-03 12:52:56,153] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-08-03 12:52:56,153] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-08-03 12:52:56,153] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-08-03 12:52:56,153] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-08-03 12:52:56,153] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-08-03 12:52:56,153] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-08-03 12:52:56,153] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-08-03 12:52:56,153] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-08-03 12:52:56,153] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-08-03 12:52:56,153] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-08-03 12:52:56,153] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-08-03 12:52:56,153] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-08-03 12:52:56,154] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-08-03 12:52:56,160] multiqc [INFO ] Compressing plot data [2024-08-03 12:52:56,239] multiqc [INFO ] Report : multiqc_report.html [2024-08-03 12:52:56,239] multiqc [INFO ] Data : multiqc_data [2024-08-03 12:52:56,239] multiqc [DEBUG ] Moving data file from '/state/partition1/job-49306828/tmpuu0pzfn2/multiqc_data' to '/vast/gencore/GENEFLOW/work/60/68f79f41a92197f04570f8279cb28a/merged/multiqc_data' [2024-08-03 12:52:56,414] multiqc [INFO ] MultiQC complete