[2023-11-06 15:51:55,107] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-11-06 15:51:55,107] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-11-06 15:51:55,107] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-11-06 15:51:55,110] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-11-06 15:51:55,110] 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}} [2023-11-06 15:51:55,110] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H7YLTDRX3/merged [2023-11-06 15:51:55,298] multiqc [WARNING] MultiQC Version v1.17 now available! [2023-11-06 15:51:55,298] multiqc [INFO ] This is MultiQC v1.9 [2023-11-06 15:51:55,299] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H7YLTDRX3/merged [2023-11-06 15:51:55,299] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H7YLTDRX3/merged [2023-11-06 15:51:55,299] multiqc [INFO ] Template : default [2023-11-06 15:51:55,299] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-11-06 15:51:55,299] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H7YLTDRX3/merged [2023-11-06 15:51:55,299] 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 [2023-11-06 15:51:55,299] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-39674221/tmpndbz3tfb [2023-11-06 15:51:55,462] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7YLTDRX3_n01_WILD_YEAST_WTA_30M_fastqc.html [2023-11-06 15:51:55,465] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7YLTDRX3_n01_WILD_YEAST_WTA_30M_fastqc.html [2023-11-06 15:51:55,512] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-11-06 15:51:55,513] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-11-06 15:51:55,513] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-11-06 15:51:55,513] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-11-06 15:51:55,513] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-11-06 15:51:55,513] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-11-06 15:51:55,513] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-11-06 15:51:55,568] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-11-06 15:51:58,074] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7YLTDRX3_n01_undetermined_fastqc.html [2023-11-06 15:51:58,076] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7YLTDRX3_n01_undetermined_fastqc.html [2023-11-06 15:51:58,169] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7YLTDRX3_n01_WILD_YEAST_PCR_30M_fastqc.html [2023-11-06 15:51:58,171] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7YLTDRX3_n01_WILD_YEAST_PCR_30M_fastqc.html [2023-11-06 15:51:58,238] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7YLTDRX3_n02_undetermined_fastqc.html [2023-11-06 15:51:58,240] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7YLTDRX3_n02_undetermined_fastqc.html [2023-11-06 15:51:58,286] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7YLTDRX3_n02_WILD_YEAST_WTA_0M_fastqc.html [2023-11-06 15:51:58,288] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7YLTDRX3_n02_WILD_YEAST_WTA_0M_fastqc.html [2023-11-06 15:51:58,399] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7YLTDRX3_n02_WILD_YEAST_PCR_0M_fastqc.html [2023-11-06 15:51:58,401] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7YLTDRX3_n02_WILD_YEAST_PCR_0M_fastqc.html [2023-11-06 15:51:58,502] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7YLTDRX3_n01_WILD_YEAST_WTA_0M_fastqc.html [2023-11-06 15:51:58,504] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7YLTDRX3_n01_WILD_YEAST_WTA_0M_fastqc.html [2023-11-06 15:51:58,558] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7YLTDRX3_n01_WILD_YEAST_PCR_0M_fastqc.html [2023-11-06 15:51:58,560] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7YLTDRX3_n01_WILD_YEAST_PCR_0M_fastqc.html [2023-11-06 15:51:58,637] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7YLTDRX3_n02_WILD_YEAST_WTA_30M_fastqc.html [2023-11-06 15:51:58,639] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7YLTDRX3_n02_WILD_YEAST_WTA_30M_fastqc.html [2023-11-06 15:51:58,700] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H7YLTDRX3_n02_WILD_YEAST_PCR_30M_fastqc.html [2023-11-06 15:51:58,702] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H7YLTDRX3_n02_WILD_YEAST_PCR_30M_fastqc.html [2023-11-06 15:51:59,138] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-11-06 15:51:59,140] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-11-06 15:51:59,157] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-11-06 15:51:59,158] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-11-06 15:51:59,161] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 5 samples (table) [2023-11-06 15:51:59,166] multiqc [DEBUG ] No samples found: conpair [2023-11-06 15:51:59,171] multiqc [DEBUG ] No samples found: peddy [2023-11-06 15:51:59,177] multiqc [DEBUG ] No samples found: somalier [2023-11-06 15:51:59,182] multiqc [DEBUG ] No samples found: methylQA [2023-11-06 15:51:59,191] multiqc [DEBUG ] No samples found: mosdepth [2023-11-06 15:51:59,196] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-11-06 15:51:59,199] multiqc [DEBUG ] No samples found: qualimap [2023-11-06 15:51:59,204] multiqc [DEBUG ] No samples found: preseq [2023-11-06 15:51:59,209] multiqc [DEBUG ] No samples found: quast [2023-11-06 15:51:59,214] multiqc [DEBUG ] No samples found: qorts [2023-11-06 15:51:59,219] multiqc [DEBUG ] No samples found: rna_seqc [2023-11-06 15:51:59,223] multiqc [DEBUG ] No samples found: rockhopper [2023-11-06 15:51:59,228] multiqc [DEBUG ] No samples found: rsem [2023-11-06 15:51:59,237] multiqc [DEBUG ] No samples found: rseqc [2023-11-06 15:51:59,241] multiqc [DEBUG ] No samples found: busco [2023-11-06 15:51:59,246] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-11-06 15:51:59,250] multiqc [DEBUG ] No samples found: disambiguate [2023-11-06 15:51:59,256] multiqc [DEBUG ] No samples found: supernova [2023-11-06 15:51:59,268] multiqc [DEBUG ] No samples found: deeptools [2023-11-06 15:51:59,273] multiqc [DEBUG ] No samples found: sargasso [2023-11-06 15:51:59,278] multiqc [DEBUG ] No samples found: verifybamid [2023-11-06 15:51:59,283] multiqc [DEBUG ] No samples found: mirtrace [2023-11-06 15:51:59,288] multiqc [DEBUG ] No samples found: happy [2023-11-06 15:51:59,293] multiqc [DEBUG ] No samples found: mirtop [2023-11-06 15:51:59,299] multiqc [DEBUG ] No samples found: homer [2023-11-06 15:51:59,304] multiqc [DEBUG ] No samples found: macs2 [2023-11-06 15:51:59,308] multiqc [DEBUG ] No samples found: theta2 [2023-11-06 15:51:59,313] multiqc [DEBUG ] No samples found: snpeff [2023-11-06 15:51:59,320] multiqc [DEBUG ] No samples found: gatk [2023-11-06 15:51:59,324] multiqc [DEBUG ] No samples found: htseq [2023-11-06 15:51:59,330] multiqc [DEBUG ] No samples found: bcftools [2023-11-06 15:51:59,334] multiqc [DEBUG ] No samples found: featureCounts [2023-11-06 15:51:59,341] multiqc [DEBUG ] No samples found: fgbio [2023-11-06 15:51:59,353] multiqc [DEBUG ] No samples found: dragen [2023-11-06 15:51:59,358] multiqc [DEBUG ] No samples found: dedup [2023-11-06 15:51:59,363] multiqc [DEBUG ] No samples found: damageprofiler [2023-11-06 15:51:59,385] multiqc [DEBUG ] No samples found: biobambam2 [2023-11-06 15:51:59,391] multiqc [DEBUG ] No samples found: mtnucratio [2023-11-06 15:51:59,394] multiqc [DEBUG ] No samples found: picard [2023-11-06 15:51:59,398] multiqc [DEBUG ] No samples found: prokka [2023-11-06 15:51:59,403] multiqc [DEBUG ] No samples found: samblaster [2023-11-06 15:51:59,412] multiqc [DEBUG ] No samples found: samtools [2023-11-06 15:51:59,418] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-11-06 15:51:59,423] multiqc [DEBUG ] No samples found: bamtools [2023-11-06 15:51:59,428] multiqc [DEBUG ] No samples found: jellyfish [2023-11-06 15:51:59,436] multiqc [DEBUG ] No samples found: vcftools [2023-11-06 15:51:59,441] multiqc [DEBUG ] No samples found: longranger [2023-11-06 15:51:59,446] multiqc [DEBUG ] No samples found: stacks [2023-11-06 15:51:59,451] multiqc [DEBUG ] No samples found: varscan2 [2023-11-06 15:51:59,464] multiqc [DEBUG ] No samples found: bbmap [2023-11-06 15:51:59,469] multiqc [DEBUG ] No samples found: bismark [2023-11-06 15:51:59,474] multiqc [DEBUG ] No samples found: biscuit [2023-11-06 15:51:59,479] multiqc [DEBUG ] No samples found: hicexplorer [2023-11-06 15:51:59,484] multiqc [DEBUG ] No samples found: hicup [2023-11-06 15:51:59,489] multiqc [DEBUG ] No samples found: hicpro [2023-11-06 15:51:59,494] multiqc [DEBUG ] No samples found: salmon [2023-11-06 15:51:59,499] multiqc [DEBUG ] No samples found: kallisto [2023-11-06 15:51:59,504] multiqc [DEBUG ] No samples found: slamdunk [2023-11-06 15:51:59,509] multiqc [DEBUG ] No samples found: star [2023-11-06 15:51:59,514] multiqc [DEBUG ] No samples found: hisat2 [2023-11-06 15:51:59,519] multiqc [DEBUG ] No samples found: tophat [2023-11-06 15:51:59,524] multiqc [DEBUG ] No samples found: bowtie2 [2023-11-06 15:51:59,529] multiqc [DEBUG ] No samples found: bowtie1 [2023-11-06 15:51:59,534] multiqc [DEBUG ] No samples found: snpsplit [2023-11-06 15:51:59,538] multiqc [DEBUG ] No samples found: kat [2023-11-06 15:51:59,543] multiqc [DEBUG ] No samples found: leehom [2023-11-06 15:51:59,548] multiqc [DEBUG ] No samples found: adapterRemoval [2023-11-06 15:51:59,553] multiqc [DEBUG ] No samples found: clipandmerge [2023-11-06 15:51:59,557] multiqc [DEBUG ] No samples found: cutadapt [2023-11-06 15:51:59,562] multiqc [DEBUG ] No samples found: flexbar [2023-11-06 15:51:59,567] multiqc [DEBUG ] No samples found: kaiju [2023-11-06 15:51:59,572] multiqc [DEBUG ] No samples found: kraken [2023-11-06 15:51:59,577] multiqc [DEBUG ] No samples found: malt [2023-11-06 15:51:59,582] multiqc [DEBUG ] No samples found: trimmomatic [2023-11-06 15:51:59,588] multiqc [DEBUG ] No samples found: sickle [2023-11-06 15:51:59,593] multiqc [DEBUG ] No samples found: skewer [2023-11-06 15:51:59,597] multiqc [DEBUG ] No samples found: sortmerna [2023-11-06 15:51:59,602] multiqc [DEBUG ] No samples found: biobloomtools [2023-11-06 15:51:59,607] multiqc [DEBUG ] No samples found: fastq_screen [2023-11-06 15:51:59,612] multiqc [DEBUG ] No samples found: afterqc [2023-11-06 15:51:59,617] multiqc [DEBUG ] No samples found: fastp [2023-11-06 15:52:00,334] multiqc.modules.fastqc.fastqc [INFO ] Found 10 reports [2023-11-06 15:52:00,428] multiqc [DEBUG ] No samples found: pycoqc [2023-11-06 15:52:00,433] multiqc [DEBUG ] No samples found: minionqc [2023-11-06 15:52:00,438] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-11-06 15:52:00,443] multiqc [DEBUG ] No samples found: clusterflow [2023-11-06 15:52:00,448] multiqc [DEBUG ] No samples found: bcl2fastq [2023-11-06 15:52:00,453] multiqc [DEBUG ] No samples found: interop [2023-11-06 15:52:00,458] multiqc [DEBUG ] No samples found: ivar [2023-11-06 15:52:00,463] multiqc [DEBUG ] No samples found: flash [2023-11-06 15:52:00,468] multiqc [DEBUG ] No samples found: seqyclean [2023-11-06 15:52:00,468] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-11-06 15:52:00,468] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-11-06 15:52:00,468] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-11-06 15:52:00,468] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2023-11-06 15:52:00,468] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2023-11-06 15:52:00,468] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2023-11-06 15:52:00,468] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2023-11-06 15:52:00,468] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2023-11-06 15:52:00,468] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2023-11-06 15:52:00,468] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-11-06 15:52:00,468] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-11-06 15:52:00,468] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-11-06 15:52:00,468] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-11-06 15:52:00,468] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-11-06 15:52:00,468] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-11-06 15:52:00,468] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-11-06 15:52:00,468] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-11-06 15:52:00,468] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-11-06 15:52:00,468] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-11-06 15:52:00,469] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-11-06 15:52:00,469] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-11-06 15:52:00,469] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-11-06 15:52:00,469] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-11-06 15:52:00,469] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-11-06 15:52:00,469] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-11-06 15:52:00,469] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-11-06 15:52:00,469] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-11-06 15:52:00,469] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-11-06 15:52:00,469] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-11-06 15:52:00,469] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-11-06 15:52:00,482] multiqc [INFO ] Compressing plot data [2023-11-06 15:52:00,646] multiqc [INFO ] Report : multiqc_report.html [2023-11-06 15:52:00,646] multiqc [INFO ] Data : multiqc_data [2023-11-06 15:52:00,646] multiqc [DEBUG ] Moving data file from '/state/partition1/job-39674221/tmpndbz3tfb/multiqc_data' to '/scratch/gencore/logs/html/H7YLTDRX3/merged/multiqc_data' [2023-11-06 15:52:00,812] multiqc [INFO ] MultiQC complete