[2024-07-17 20:07:51,954] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml
[2024-07-17 20:07:51,954] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml
[2024-07-17 20:07:51,955] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml
[2024-07-17 20:07:51,958] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml
[2024-07-17 20:07:51,958] 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}}
[2024-07-17 20:07:51,958] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml .
[2024-07-17 20:07:51,993] multiqc [DEBUG ] Could not connect to multiqc.info for version check: <urlopen error unknown url type: https>
[2024-07-17 20:07:51,994] multiqc [INFO ] This is MultiQC v1.9
[2024-07-17 20:07:51,994] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml .
[2024-07-17 20:07:51,994] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/aa/6e7d24cc674dcdff75afa7aae845ec/1
[2024-07-17 20:07:51,994] multiqc [INFO ] Template : default
[2024-07-17 20:07:51,994] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode]
[2024-07-17 20:07:51,994] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/aa/6e7d24cc674dcdff75afa7aae845ec/1
[2024-07-17 20:07:51,994] 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
[2024-07-17 20:07:51,994] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-48672200/tmp51gxaohf
[2024-07-17 20:07:52,096] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LL9B8_l01.1_fastqc.html
[2024-07-17 20:07:52,105] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LL9B8_l01.1_fastqc.html
[2024-07-17 20:07:52,193] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LL9B8_l01.2_fastqc.html
[2024-07-17 20:07:52,200] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LL9B8_l01.2_fastqc.html
[2024-07-17 20:07:52,263] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LL9B8_l01.3_fastqc.html
[2024-07-17 20:07:52,270] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LL9B8_l01.3_fastqc.html
[2024-07-17 20:07:52,576] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2
[2024-07-17 20:07:52,577] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2
[2024-07-17 20:07:52,581] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table)
[2024-07-17 20:07:52,584] multiqc [DEBUG ] No samples found: conpair
[2024-07-17 20:07:52,586] multiqc [DEBUG ] No samples found: peddy
[2024-07-17 20:07:52,589] multiqc [DEBUG ] No samples found: somalier
[2024-07-17 20:07:52,592] multiqc [DEBUG ] No samples found: methylQA
[2024-07-17 20:07:52,595] multiqc [DEBUG ] No samples found: mosdepth
[2024-07-17 20:07:52,598] multiqc [DEBUG ] No samples found: phantompeakqualtools
[2024-07-17 20:07:52,600] multiqc [DEBUG ] No samples found: qualimap
[2024-07-17 20:07:52,603] multiqc [DEBUG ] No samples found: preseq
[2024-07-17 20:07:52,606] multiqc [DEBUG ] No samples found: quast
[2024-07-17 20:07:52,609] multiqc [DEBUG ] No samples found: qorts
[2024-07-17 20:07:52,611] multiqc [DEBUG ] No samples found: rna_seqc
[2024-07-17 20:07:52,614] multiqc [DEBUG ] No samples found: rockhopper
[2024-07-17 20:07:52,617] multiqc [DEBUG ] No samples found: rsem
[2024-07-17 20:07:52,621] multiqc [DEBUG ] No samples found: rseqc
[2024-07-17 20:07:52,624] multiqc [DEBUG ] No samples found: busco
[2024-07-17 20:07:52,627] multiqc [DEBUG ] No samples found: goleft_indexcov
[2024-07-17 20:07:52,629] multiqc [DEBUG ] No samples found: disambiguate
[2024-07-17 20:07:52,632] multiqc [DEBUG ] No samples found: supernova
[2024-07-17 20:07:52,637] multiqc [DEBUG ] No samples found: deeptools
[2024-07-17 20:07:52,639] multiqc [DEBUG ] No samples found: sargasso
[2024-07-17 20:07:52,642] multiqc [DEBUG ] No samples found: verifybamid
[2024-07-17 20:07:52,645] multiqc [DEBUG ] No samples found: mirtrace
[2024-07-17 20:07:52,647] multiqc [DEBUG ] No samples found: happy
[2024-07-17 20:07:52,650] multiqc [DEBUG ] No samples found: mirtop
[2024-07-17 20:07:52,653] multiqc [DEBUG ] No samples found: homer
[2024-07-17 20:07:52,656] multiqc [DEBUG ] No samples found: macs2
[2024-07-17 20:07:52,659] multiqc [DEBUG ] No samples found: theta2
[2024-07-17 20:07:52,661] multiqc [DEBUG ] No samples found: snpeff
[2024-07-17 20:07:52,664] multiqc [DEBUG ] No samples found: gatk
[2024-07-17 20:07:52,667] multiqc [DEBUG ] No samples found: htseq
[2024-07-17 20:07:52,670] multiqc [DEBUG ] No samples found: bcftools
[2024-07-17 20:07:52,673] multiqc [DEBUG ] No samples found: featureCounts
[2024-07-17 20:07:52,676] multiqc [DEBUG ] No samples found: fgbio
[2024-07-17 20:07:52,681] multiqc [DEBUG ] No samples found: dragen
[2024-07-17 20:07:52,683] multiqc [DEBUG ] No samples found: dedup
[2024-07-17 20:07:52,686] multiqc [DEBUG ] No samples found: damageprofiler
[2024-07-17 20:07:52,693] multiqc [DEBUG ] No samples found: biobambam2
[2024-07-17 20:07:52,696] multiqc [DEBUG ] No samples found: mtnucratio
[2024-07-17 20:07:52,698] multiqc [DEBUG ] No samples found: picard
[2024-07-17 20:07:52,701] multiqc [DEBUG ] No samples found: prokka
[2024-07-17 20:07:52,703] multiqc [DEBUG ] No samples found: samblaster
[2024-07-17 20:07:52,707] multiqc [DEBUG ] No samples found: samtools
[2024-07-17 20:07:52,709] multiqc [DEBUG ] No samples found: sexdeterrmine
[2024-07-17 20:07:52,712] multiqc [DEBUG ] No samples found: bamtools
[2024-07-17 20:07:52,715] multiqc [DEBUG ] No samples found: jellyfish
[2024-07-17 20:07:52,718] multiqc [DEBUG ] No samples found: vcftools
[2024-07-17 20:07:52,721] multiqc [DEBUG ] No samples found: longranger
[2024-07-17 20:07:52,724] multiqc [DEBUG ] No samples found: stacks
[2024-07-17 20:07:52,726] multiqc [DEBUG ] No samples found: varscan2
[2024-07-17 20:07:52,731] multiqc [DEBUG ] No samples found: bbmap
[2024-07-17 20:07:52,734] multiqc [DEBUG ] No samples found: bismark
[2024-07-17 20:07:52,737] multiqc [DEBUG ] No samples found: biscuit
[2024-07-17 20:07:52,740] multiqc [DEBUG ] No samples found: hicexplorer
[2024-07-17 20:07:52,742] multiqc [DEBUG ] No samples found: hicup
[2024-07-17 20:07:52,745] multiqc [DEBUG ] No samples found: hicpro
[2024-07-17 20:07:52,747] multiqc [DEBUG ] No samples found: salmon
[2024-07-17 20:07:52,750] multiqc [DEBUG ] No samples found: kallisto
[2024-07-17 20:07:52,753] multiqc [DEBUG ] No samples found: slamdunk
[2024-07-17 20:07:52,756] multiqc [DEBUG ] No samples found: star
[2024-07-17 20:07:52,758] multiqc [DEBUG ] No samples found: hisat2
[2024-07-17 20:07:52,761] multiqc [DEBUG ] No samples found: tophat
[2024-07-17 20:07:52,764] multiqc [DEBUG ] No samples found: bowtie2
[2024-07-17 20:07:52,766] multiqc [DEBUG ] No samples found: bowtie1
[2024-07-17 20:07:52,769] multiqc [DEBUG ] No samples found: snpsplit
[2024-07-17 20:07:52,771] multiqc [DEBUG ] No samples found: kat
[2024-07-17 20:07:52,774] multiqc [DEBUG ] No samples found: leehom
[2024-07-17 20:07:52,777] multiqc [DEBUG ] No samples found: adapterRemoval
[2024-07-17 20:07:52,780] multiqc [DEBUG ] No samples found: clipandmerge
[2024-07-17 20:07:52,782] multiqc [DEBUG ] No samples found: cutadapt
[2024-07-17 20:07:52,785] multiqc [DEBUG ] No samples found: flexbar
[2024-07-17 20:07:52,788] multiqc [DEBUG ] No samples found: kaiju
[2024-07-17 20:07:52,790] multiqc [DEBUG ] No samples found: kraken
[2024-07-17 20:07:52,793] multiqc [DEBUG ] No samples found: malt
[2024-07-17 20:07:52,796] multiqc [DEBUG ] No samples found: trimmomatic
[2024-07-17 20:07:52,798] multiqc [DEBUG ] No samples found: sickle
[2024-07-17 20:07:52,801] multiqc [DEBUG ] No samples found: skewer
[2024-07-17 20:07:52,804] multiqc [DEBUG ] No samples found: sortmerna
[2024-07-17 20:07:52,806] multiqc [DEBUG ] No samples found: biobloomtools
[2024-07-17 20:07:52,809] multiqc [DEBUG ] No samples found: fastq_screen
[2024-07-17 20:07:52,812] multiqc [DEBUG ] No samples found: afterqc
[2024-07-17 20:07:52,814] multiqc [DEBUG ] No samples found: fastp
[2024-07-17 20:07:52,848] multiqc.modules.fastqc.fastqc [INFO ] Found 3 reports
[2024-07-17 20:07:52,901] multiqc [DEBUG ] No samples found: pycoqc
[2024-07-17 20:07:52,904] multiqc [DEBUG ] No samples found: minionqc
[2024-07-17 20:07:52,907] multiqc [DEBUG ] No samples found: multivcfanalyzer
[2024-07-17 20:07:52,909] multiqc [DEBUG ] No samples found: clusterflow
[2024-07-17 20:07:52,912] multiqc [DEBUG ] No samples found: bcl2fastq
[2024-07-17 20:07:52,915] multiqc [DEBUG ] No samples found: interop
[2024-07-17 20:07:52,917] multiqc [DEBUG ] No samples found: ivar
[2024-07-17 20:07:52,920] multiqc [DEBUG ] No samples found: flash
[2024-07-17 20:07:52,923] multiqc [DEBUG ] No samples found: seqyclean
[2024-07-17 20:07:52,923] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found.
[2024-07-17 20:07:52,923] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found.
[2024-07-17 20:07:52,923] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found.
[2024-07-17 20:07:52,923] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found.
[2024-07-17 20:07:52,923] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found.
[2024-07-17 20:07:52,923] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'.
[2024-07-17 20:07:52,923] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'.
[2024-07-17 20:07:52,923] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'.
[2024-07-17 20:07:52,923] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'.
[2024-07-17 20:07:52,923] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'.
[2024-07-17 20:07:52,923] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'.
[2024-07-17 20:07:52,923] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'.
[2024-07-17 20:07:52,923] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'.
[2024-07-17 20:07:52,923] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'.
[2024-07-17 20:07:52,923] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'.
[2024-07-17 20:07:52,923] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'.
[2024-07-17 20:07:52,923] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'.
[2024-07-17 20:07:52,923] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'.
[2024-07-17 20:07:52,923] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'.
[2024-07-17 20:07:52,928] multiqc [INFO ] Compressing plot data
[2024-07-17 20:07:52,988] multiqc [INFO ] Report : multiqc_report.html
[2024-07-17 20:07:52,988] multiqc [INFO ] Data : multiqc_data
[2024-07-17 20:07:52,988] multiqc [DEBUG ] Moving data file from '/state/partition1/job-48672200/tmp51gxaohf/multiqc_data' to '/vast/gencore/GENEFLOW/work/aa/6e7d24cc674dcdff75afa7aae845ec/1/multiqc_data'
[2024-07-17 20:07:53,151] multiqc [INFO ] MultiQC complete