[2024-12-05 08:37:40,315] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-12-05 08:37:40,315] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-12-05 08:37:40,315] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-12-05 08:37:40,318] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-12-05 08:37:40,318] 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}} [2024-12-05 08:37:40,318] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-12-05 08:37:40,353] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-12-05 08:37:40,354] multiqc [INFO ] This is MultiQC v1.9 [2024-12-05 08:37:40,354] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-12-05 08:37:40,354] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/c9/b2b61d83269aead9213640daf86738/merged [2024-12-05 08:37:40,354] multiqc [INFO ] Template : default [2024-12-05 08:37:40,354] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-12-05 08:37:40,354] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/c9/b2b61d83269aead9213640daf86738/merged [2024-12-05 08:37:40,354] 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 [2024-12-05 08:37:40,354] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-54360870/tmpk3ydtbih [2024-12-05 08:37:40,503] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-12-05 08:37:40,506] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-12-05 08:37:40,506] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-12-05 08:37:40,506] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-12-05 08:37:40,506] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-12-05 08:37:40,506] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-12-05 08:37:40,506] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-12-05 08:37:40,526] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-12-05 08:37:41,537] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJ3NKDRX5_n01_undetermined_fastqc.html [2024-12-05 08:37:41,539] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJ3NKDRX5_n01_undetermined_fastqc.html [2024-12-05 08:37:41,608] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJ3NKDRX5_n01_Sc_NA_Pombe_high_fastqc.html [2024-12-05 08:37:41,610] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJ3NKDRX5_n01_Sc_NA_Pombe_high_fastqc.html [2024-12-05 08:37:41,716] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJ3NKDRX5_n01_Sc_low_Pombe_NA_fastqc.html [2024-12-05 08:37:41,718] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJ3NKDRX5_n01_Sc_low_Pombe_NA_fastqc.html [2024-12-05 08:37:41,776] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJ3NKDRX5_n01_Sc_high_Pombe_NA_fastqc.html [2024-12-05 08:37:41,778] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJ3NKDRX5_n01_Sc_high_Pombe_NA_fastqc.html [2024-12-05 08:37:41,838] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJ3NKDRX5_n01_Sc_low_Pombe_low_fastqc.html [2024-12-05 08:37:41,840] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJ3NKDRX5_n01_Sc_low_Pombe_low_fastqc.html [2024-12-05 08:37:41,898] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJ3NKDRX5_n01_Sc_NA_Pombe_low_fastqc.html [2024-12-05 08:37:41,900] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJ3NKDRX5_n01_Sc_NA_Pombe_low_fastqc.html [2024-12-05 08:37:41,966] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJ3NKDRX5_n01_Sc_low_Pombe_high_fastqc.html [2024-12-05 08:37:41,968] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJ3NKDRX5_n01_Sc_low_Pombe_high_fastqc.html [2024-12-05 08:37:42,612] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-12-05 08:37:42,615] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-12-05 08:37:42,626] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 7 samples (table) [2024-12-05 08:37:42,628] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-12-05 08:37:42,638] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-12-05 08:37:42,645] multiqc [DEBUG ] No samples found: conpair [2024-12-05 08:37:42,652] multiqc [DEBUG ] No samples found: peddy [2024-12-05 08:37:42,659] multiqc [DEBUG ] No samples found: somalier [2024-12-05 08:37:42,666] multiqc [DEBUG ] No samples found: methylQA [2024-12-05 08:37:42,679] multiqc [DEBUG ] No samples found: mosdepth [2024-12-05 08:37:42,685] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-12-05 08:37:42,689] multiqc [DEBUG ] No samples found: qualimap [2024-12-05 08:37:42,696] multiqc [DEBUG ] No samples found: preseq [2024-12-05 08:37:42,703] multiqc [DEBUG ] No samples found: quast [2024-12-05 08:37:42,710] multiqc [DEBUG ] No samples found: qorts [2024-12-05 08:37:42,717] multiqc [DEBUG ] No samples found: rna_seqc [2024-12-05 08:37:42,723] multiqc [DEBUG ] No samples found: rockhopper [2024-12-05 08:37:42,729] multiqc [DEBUG ] No samples found: rsem [2024-12-05 08:37:42,751] multiqc [DEBUG ] No samples found: rseqc [2024-12-05 08:37:42,757] multiqc [DEBUG ] No samples found: busco [2024-12-05 08:37:42,763] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-12-05 08:37:42,770] multiqc [DEBUG ] No samples found: disambiguate [2024-12-05 08:37:42,777] multiqc [DEBUG ] No samples found: supernova [2024-12-05 08:37:42,796] multiqc [DEBUG ] No samples found: deeptools [2024-12-05 08:37:42,804] multiqc [DEBUG ] No samples found: sargasso [2024-12-05 08:37:42,811] multiqc [DEBUG ] No samples found: verifybamid [2024-12-05 08:37:42,817] multiqc [DEBUG ] No samples found: mirtrace [2024-12-05 08:37:42,824] multiqc [DEBUG ] No samples found: happy [2024-12-05 08:37:42,830] multiqc [DEBUG ] No samples found: mirtop [2024-12-05 08:37:42,839] multiqc [DEBUG ] No samples found: homer [2024-12-05 08:37:42,845] multiqc [DEBUG ] No samples found: macs2 [2024-12-05 08:37:42,851] multiqc [DEBUG ] No samples found: theta2 [2024-12-05 08:37:42,858] multiqc [DEBUG ] No samples found: snpeff [2024-12-05 08:37:42,867] multiqc [DEBUG ] No samples found: gatk [2024-12-05 08:37:42,873] multiqc [DEBUG ] No samples found: htseq [2024-12-05 08:37:42,881] multiqc [DEBUG ] No samples found: bcftools [2024-12-05 08:37:42,888] multiqc [DEBUG ] No samples found: featureCounts [2024-12-05 08:37:42,897] multiqc [DEBUG ] No samples found: fgbio [2024-12-05 08:37:42,914] multiqc [DEBUG ] No samples found: dragen [2024-12-05 08:37:42,921] multiqc [DEBUG ] No samples found: dedup [2024-12-05 08:37:42,927] multiqc [DEBUG ] No samples found: damageprofiler [2024-12-05 08:37:42,955] multiqc [DEBUG ] No samples found: biobambam2 [2024-12-05 08:37:42,962] multiqc [DEBUG ] No samples found: mtnucratio [2024-12-05 08:37:42,965] multiqc [DEBUG ] No samples found: picard [2024-12-05 08:37:42,971] multiqc [DEBUG ] No samples found: prokka [2024-12-05 08:37:42,977] multiqc [DEBUG ] No samples found: samblaster [2024-12-05 08:37:42,990] multiqc [DEBUG ] No samples found: samtools [2024-12-05 08:37:43,000] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-12-05 08:37:43,008] multiqc [DEBUG ] No samples found: bamtools [2024-12-05 08:37:43,014] multiqc [DEBUG ] No samples found: jellyfish [2024-12-05 08:37:43,026] multiqc [DEBUG ] No samples found: vcftools [2024-12-05 08:37:43,032] multiqc [DEBUG ] No samples found: longranger [2024-12-05 08:37:43,039] multiqc [DEBUG ] No samples found: stacks [2024-12-05 08:37:43,046] multiqc [DEBUG ] No samples found: varscan2 [2024-12-05 08:37:43,066] multiqc [DEBUG ] No samples found: bbmap [2024-12-05 08:37:43,072] multiqc [DEBUG ] No samples found: bismark [2024-12-05 08:37:43,080] multiqc [DEBUG ] No samples found: biscuit [2024-12-05 08:37:43,086] multiqc [DEBUG ] No samples found: hicexplorer [2024-12-05 08:37:43,093] multiqc [DEBUG ] No samples found: hicup [2024-12-05 08:37:43,100] multiqc [DEBUG ] No samples found: hicpro [2024-12-05 08:37:43,105] multiqc [DEBUG ] No samples found: salmon [2024-12-05 08:37:43,112] multiqc [DEBUG ] No samples found: kallisto [2024-12-05 08:37:43,119] multiqc [DEBUG ] No samples found: slamdunk [2024-12-05 08:37:43,125] multiqc [DEBUG ] No samples found: star [2024-12-05 08:37:43,131] multiqc [DEBUG ] No samples found: hisat2 [2024-12-05 08:37:43,138] multiqc [DEBUG ] No samples found: tophat [2024-12-05 08:37:43,144] multiqc [DEBUG ] No samples found: bowtie2 [2024-12-05 08:37:43,151] multiqc [DEBUG ] No samples found: bowtie1 [2024-12-05 08:37:43,157] multiqc [DEBUG ] No samples found: snpsplit [2024-12-05 08:37:43,163] multiqc [DEBUG ] No samples found: kat [2024-12-05 08:37:43,169] multiqc [DEBUG ] No samples found: leehom [2024-12-05 08:37:43,176] multiqc [DEBUG ] No samples found: adapterRemoval [2024-12-05 08:37:43,183] multiqc [DEBUG ] No samples found: clipandmerge [2024-12-05 08:37:43,189] multiqc [DEBUG ] No samples found: cutadapt [2024-12-05 08:37:43,196] multiqc [DEBUG ] No samples found: flexbar [2024-12-05 08:37:43,202] multiqc [DEBUG ] No samples found: kaiju [2024-12-05 08:37:43,214] multiqc [DEBUG ] No samples found: kraken [2024-12-05 08:37:43,227] multiqc [DEBUG ] No samples found: malt [2024-12-05 08:37:43,233] multiqc [DEBUG ] No samples found: trimmomatic [2024-12-05 08:37:43,240] multiqc [DEBUG ] No samples found: sickle [2024-12-05 08:37:43,246] multiqc [DEBUG ] No samples found: skewer [2024-12-05 08:37:43,251] multiqc [DEBUG ] No samples found: sortmerna [2024-12-05 08:37:43,258] multiqc [DEBUG ] No samples found: biobloomtools [2024-12-05 08:37:43,264] multiqc [DEBUG ] No samples found: fastq_screen [2024-12-05 08:37:43,270] multiqc [DEBUG ] No samples found: afterqc [2024-12-05 08:37:43,277] multiqc [DEBUG ] No samples found: fastp [2024-12-05 08:37:43,900] multiqc.modules.fastqc.fastqc [INFO ] Found 7 reports [2024-12-05 08:37:44,022] multiqc [DEBUG ] No samples found: pycoqc [2024-12-05 08:37:44,028] multiqc [DEBUG ] No samples found: minionqc [2024-12-05 08:37:44,034] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-12-05 08:37:44,040] multiqc [DEBUG ] No samples found: clusterflow [2024-12-05 08:37:44,047] multiqc [DEBUG ] No samples found: bcl2fastq [2024-12-05 08:37:44,053] multiqc [DEBUG ] No samples found: interop [2024-12-05 08:37:44,059] multiqc [DEBUG ] No samples found: ivar [2024-12-05 08:37:44,065] multiqc [DEBUG ] No samples found: flash [2024-12-05 08:37:44,072] multiqc [DEBUG ] No samples found: seqyclean [2024-12-05 08:37:44,072] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-12-05 08:37:44,072] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-12-05 08:37:44,072] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-12-05 08:37:44,072] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-12-05 08:37:44,072] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-12-05 08:37:44,072] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-12-05 08:37:44,072] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-12-05 08:37:44,072] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-12-05 08:37:44,072] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-12-05 08:37:44,072] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-12-05 08:37:44,072] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-12-05 08:37:44,072] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-12-05 08:37:44,072] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-12-05 08:37:44,072] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-12-05 08:37:44,072] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-12-05 08:37:44,072] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-12-05 08:37:44,072] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-12-05 08:37:44,072] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-12-05 08:37:44,072] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-12-05 08:37:44,072] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-12-05 08:37:44,072] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-12-05 08:37:44,072] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-12-05 08:37:44,072] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-12-05 08:37:44,072] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-12-05 08:37:44,072] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-12-05 08:37:44,073] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-12-05 08:37:44,073] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-12-05 08:37:44,073] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-12-05 08:37:44,073] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-12-05 08:37:44,073] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-12-05 08:37:44,082] multiqc [INFO ] Compressing plot data [2024-12-05 08:37:44,232] multiqc [INFO ] Report : multiqc_report.html [2024-12-05 08:37:44,233] multiqc [INFO ] Data : multiqc_data [2024-12-05 08:37:44,233] multiqc [DEBUG ] Moving data file from '/state/partition1/job-54360870/tmpk3ydtbih/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/c9/b2b61d83269aead9213640daf86738/merged/multiqc_data' [2024-12-05 08:37:44,417] multiqc [INFO ] MultiQC complete