[2023-11-10 14:04:35,399] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-11-10 14:04:35,399] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-11-10 14:04:35,400] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-11-10 14:04:35,402] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2023-11-10 14:04:35,402] 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}} [2023-11-10 14:04:35,402] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2023-11-10 14:04:35,596] multiqc [WARNING] MultiQC Version v1.17 now available! [2023-11-10 14:04:35,596] multiqc [INFO ] This is MultiQC v1.9 [2023-11-10 14:04:35,596] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2023-11-10 14:04:35,596] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/c6/a049dc617648c1d18418b9010bf465/merged [2023-11-10 14:04:35,596] multiqc [INFO ] Template : default [2023-11-10 14:04:35,596] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-11-10 14:04:35,596] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/c6/a049dc617648c1d18418b9010bf465/merged [2023-11-10 14:04:35,597] 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 [2023-11-10 14:04:35,597] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-39968217/tmp_mepikop [2023-11-10 14:04:35,744] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJM7CAFX5_n01_liv_Hash_1_fastqc.html [2023-11-10 14:04:35,754] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJM7CAFX5_n01_liv_Hash_1_fastqc.html [2023-11-10 14:04:35,831] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJM7CAFX5_n01_liv_Hash_2_fastqc.html [2023-11-10 14:04:35,842] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJM7CAFX5_n01_liv_Hash_2_fastqc.html [2023-11-10 14:04:35,921] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJM7CAFX5_n01_liv_Hash_3_fastqc.html [2023-11-10 14:04:35,928] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJM7CAFX5_n01_liv_Hash_3_fastqc.html [2023-11-10 14:04:36,001] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJM7CAFX5_n01_liv_RNA_1_fastqc.html [2023-11-10 14:04:36,009] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJM7CAFX5_n01_liv_RNA_1_fastqc.html [2023-11-10 14:04:36,076] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJM7CAFX5_n01_liv_RNA_2_fastqc.html [2023-11-10 14:04:36,083] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJM7CAFX5_n01_liv_RNA_2_fastqc.html [2023-11-10 14:04:36,166] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJM7CAFX5_n01_liv_RNA_3_fastqc.html [2023-11-10 14:04:36,178] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJM7CAFX5_n01_liv_RNA_3_fastqc.html [2023-11-10 14:04:36,251] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJM7CAFX5_n01_schiC_1_fastqc.html [2023-11-10 14:04:36,258] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJM7CAFX5_n01_schiC_1_fastqc.html [2023-11-10 14:04:36,336] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJM7CAFX5_n01_undetermined_fastqc.html [2023-11-10 14:04:36,345] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJM7CAFX5_n01_undetermined_fastqc.html [2023-11-10 14:04:36,423] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJM7CAFX5_n02_liv_Hash_1_fastqc.html [2023-11-10 14:04:36,431] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJM7CAFX5_n02_liv_Hash_1_fastqc.html [2023-11-10 14:04:36,514] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJM7CAFX5_n02_liv_Hash_2_fastqc.html [2023-11-10 14:04:36,521] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJM7CAFX5_n02_liv_Hash_2_fastqc.html [2023-11-10 14:04:36,609] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJM7CAFX5_n02_liv_Hash_3_fastqc.html [2023-11-10 14:04:36,615] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJM7CAFX5_n02_liv_Hash_3_fastqc.html [2023-11-10 14:04:36,697] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJM7CAFX5_n02_liv_RNA_1_fastqc.html [2023-11-10 14:04:36,704] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJM7CAFX5_n02_liv_RNA_1_fastqc.html [2023-11-10 14:04:36,775] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJM7CAFX5_n02_liv_RNA_2_fastqc.html [2023-11-10 14:04:36,782] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJM7CAFX5_n02_liv_RNA_2_fastqc.html [2023-11-10 14:04:36,852] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJM7CAFX5_n02_liv_RNA_3_fastqc.html [2023-11-10 14:04:36,862] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJM7CAFX5_n02_liv_RNA_3_fastqc.html [2023-11-10 14:04:36,931] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJM7CAFX5_n02_schiC_1_fastqc.html [2023-11-10 14:04:36,938] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJM7CAFX5_n02_schiC_1_fastqc.html [2023-11-10 14:04:37,004] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJM7CAFX5_n02_undetermined_fastqc.html [2023-11-10 14:04:37,012] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJM7CAFX5_n02_undetermined_fastqc.html [2023-11-10 14:04:37,084] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-11-10 14:04:37,091] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-11-10 14:04:38,129] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-11-10 14:04:38,133] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-11-10 14:04:38,146] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 8 samples (table) [2023-11-10 14:04:38,147] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-11-10 14:04:38,157] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-11-10 14:04:38,163] multiqc [DEBUG ] No samples found: conpair [2023-11-10 14:04:38,168] multiqc [DEBUG ] No samples found: peddy [2023-11-10 14:04:38,173] multiqc [DEBUG ] No samples found: somalier [2023-11-10 14:04:38,182] multiqc [DEBUG ] No samples found: methylQA [2023-11-10 14:04:38,190] multiqc [DEBUG ] No samples found: mosdepth [2023-11-10 14:04:38,194] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-11-10 14:04:38,198] multiqc [DEBUG ] No samples found: qualimap [2023-11-10 14:04:38,203] multiqc [DEBUG ] No samples found: preseq [2023-11-10 14:04:38,208] multiqc [DEBUG ] No samples found: quast [2023-11-10 14:04:38,213] multiqc [DEBUG ] No samples found: qorts [2023-11-10 14:04:38,220] multiqc [DEBUG ] No samples found: rna_seqc [2023-11-10 14:04:38,224] multiqc [DEBUG ] No samples found: rockhopper [2023-11-10 14:04:38,229] multiqc [DEBUG ] No samples found: rsem [2023-11-10 14:04:38,249] multiqc [DEBUG ] No samples found: rseqc [2023-11-10 14:04:38,253] multiqc [DEBUG ] No samples found: busco [2023-11-10 14:04:38,258] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-11-10 14:04:38,264] multiqc [DEBUG ] No samples found: disambiguate [2023-11-10 14:04:38,271] multiqc [DEBUG ] No samples found: supernova [2023-11-10 14:04:38,299] multiqc [DEBUG ] No samples found: deeptools [2023-11-10 14:04:38,304] multiqc [DEBUG ] No samples found: sargasso [2023-11-10 14:04:38,311] multiqc [DEBUG ] No samples found: verifybamid [2023-11-10 14:04:38,324] multiqc [DEBUG ] No samples found: mirtrace [2023-11-10 14:04:38,334] multiqc [DEBUG ] No samples found: happy [2023-11-10 14:04:38,342] multiqc [DEBUG ] No samples found: mirtop [2023-11-10 14:04:38,359] multiqc [DEBUG ] No samples found: homer [2023-11-10 14:04:38,364] multiqc [DEBUG ] No samples found: macs2 [2023-11-10 14:04:38,368] multiqc [DEBUG ] No samples found: theta2 [2023-11-10 14:04:38,373] multiqc [DEBUG ] No samples found: snpeff [2023-11-10 14:04:38,380] multiqc [DEBUG ] No samples found: gatk [2023-11-10 14:04:38,385] multiqc [DEBUG ] No samples found: htseq [2023-11-10 14:04:38,392] multiqc [DEBUG ] No samples found: bcftools [2023-11-10 14:04:38,397] multiqc [DEBUG ] No samples found: featureCounts [2023-11-10 14:04:38,403] multiqc [DEBUG ] No samples found: fgbio [2023-11-10 14:04:38,418] multiqc [DEBUG ] No samples found: dragen [2023-11-10 14:04:38,424] multiqc [DEBUG ] No samples found: dedup [2023-11-10 14:04:38,430] multiqc [DEBUG ] No samples found: damageprofiler [2023-11-10 14:04:38,455] multiqc [DEBUG ] No samples found: biobambam2 [2023-11-10 14:04:38,460] multiqc [DEBUG ] No samples found: mtnucratio [2023-11-10 14:04:38,463] multiqc [DEBUG ] No samples found: picard [2023-11-10 14:04:38,468] multiqc [DEBUG ] No samples found: prokka [2023-11-10 14:04:38,473] multiqc [DEBUG ] No samples found: samblaster [2023-11-10 14:04:38,483] multiqc [DEBUG ] No samples found: samtools [2023-11-10 14:04:38,487] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-11-10 14:04:38,493] multiqc [DEBUG ] No samples found: bamtools [2023-11-10 14:04:38,497] multiqc [DEBUG ] No samples found: jellyfish [2023-11-10 14:04:38,506] multiqc [DEBUG ] No samples found: vcftools [2023-11-10 14:04:38,512] multiqc [DEBUG ] No samples found: longranger [2023-11-10 14:04:38,516] multiqc [DEBUG ] No samples found: stacks [2023-11-10 14:04:38,521] multiqc [DEBUG ] No samples found: varscan2 [2023-11-10 14:04:38,536] multiqc [DEBUG ] No samples found: bbmap [2023-11-10 14:04:38,551] multiqc [DEBUG ] No samples found: bismark [2023-11-10 14:04:38,556] multiqc [DEBUG ] No samples found: biscuit [2023-11-10 14:04:38,562] multiqc [DEBUG ] No samples found: hicexplorer [2023-11-10 14:04:38,567] multiqc [DEBUG ] No samples found: hicup [2023-11-10 14:04:38,575] multiqc [DEBUG ] No samples found: hicpro [2023-11-10 14:04:38,582] multiqc [DEBUG ] No samples found: salmon [2023-11-10 14:04:38,587] multiqc [DEBUG ] No samples found: kallisto [2023-11-10 14:04:38,592] multiqc [DEBUG ] No samples found: slamdunk [2023-11-10 14:04:38,597] multiqc [DEBUG ] No samples found: star [2023-11-10 14:04:38,603] multiqc [DEBUG ] No samples found: hisat2 [2023-11-10 14:04:38,608] multiqc [DEBUG ] No samples found: tophat [2023-11-10 14:04:38,612] multiqc [DEBUG ] No samples found: bowtie2 [2023-11-10 14:04:38,617] multiqc [DEBUG ] No samples found: bowtie1 [2023-11-10 14:04:38,622] multiqc [DEBUG ] No samples found: snpsplit [2023-11-10 14:04:38,627] multiqc [DEBUG ] No samples found: kat [2023-11-10 14:04:38,632] multiqc [DEBUG ] No samples found: leehom [2023-11-10 14:04:38,637] multiqc [DEBUG ] No samples found: adapterRemoval [2023-11-10 14:04:38,642] multiqc [DEBUG ] No samples found: clipandmerge [2023-11-10 14:04:38,647] multiqc [DEBUG ] No samples found: cutadapt [2023-11-10 14:04:38,652] multiqc [DEBUG ] No samples found: flexbar [2023-11-10 14:04:38,657] multiqc [DEBUG ] No samples found: kaiju [2023-11-10 14:04:38,666] multiqc [DEBUG ] No samples found: kraken [2023-11-10 14:04:38,671] multiqc [DEBUG ] No samples found: malt [2023-11-10 14:04:38,676] multiqc [DEBUG ] No samples found: trimmomatic [2023-11-10 14:04:38,681] multiqc [DEBUG ] No samples found: sickle [2023-11-10 14:04:38,688] multiqc [DEBUG ] No samples found: skewer [2023-11-10 14:04:38,692] multiqc [DEBUG ] No samples found: sortmerna [2023-11-10 14:04:38,697] multiqc [DEBUG ] No samples found: biobloomtools [2023-11-10 14:04:38,702] multiqc [DEBUG ] No samples found: fastq_screen [2023-11-10 14:04:38,708] multiqc [DEBUG ] No samples found: afterqc [2023-11-10 14:04:38,713] multiqc [DEBUG ] No samples found: fastp [2023-11-10 14:04:39,105] multiqc.modules.fastqc.fastqc [INFO ] Found 16 reports [2023-11-10 14:04:39,262] multiqc [DEBUG ] No samples found: pycoqc [2023-11-10 14:04:39,268] multiqc [DEBUG ] No samples found: minionqc [2023-11-10 14:04:39,274] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-11-10 14:04:39,279] multiqc [DEBUG ] No samples found: clusterflow [2023-11-10 14:04:39,285] multiqc [DEBUG ] No samples found: bcl2fastq [2023-11-10 14:04:39,290] multiqc [DEBUG ] No samples found: interop [2023-11-10 14:04:39,296] multiqc [DEBUG ] No samples found: ivar [2023-11-10 14:04:39,301] multiqc [DEBUG ] No samples found: flash [2023-11-10 14:04:39,307] multiqc [DEBUG ] No samples found: seqyclean [2023-11-10 14:04:39,307] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-11-10 14:04:39,307] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-11-10 14:04:39,307] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-11-10 14:04:39,307] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2023-11-10 14:04:39,307] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2023-11-10 14:04:39,307] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2023-11-10 14:04:39,307] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2023-11-10 14:04:39,307] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2023-11-10 14:04:39,307] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2023-11-10 14:04:39,307] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-11-10 14:04:39,307] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-11-10 14:04:39,307] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-11-10 14:04:39,307] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-11-10 14:04:39,307] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-11-10 14:04:39,307] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-11-10 14:04:39,307] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-11-10 14:04:39,307] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-11-10 14:04:39,307] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-11-10 14:04:39,307] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-11-10 14:04:39,307] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-11-10 14:04:39,307] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-11-10 14:04:39,307] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-11-10 14:04:39,307] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-11-10 14:04:39,307] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-11-10 14:04:39,307] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-11-10 14:04:39,308] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-11-10 14:04:39,308] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-11-10 14:04:39,308] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-11-10 14:04:39,308] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-11-10 14:04:39,308] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-11-10 14:04:39,328] multiqc [INFO ] Compressing plot data [2023-11-10 14:04:39,580] multiqc [INFO ] Report : multiqc_report.html [2023-11-10 14:04:39,580] multiqc [INFO ] Data : multiqc_data [2023-11-10 14:04:39,580] multiqc [DEBUG ] Moving data file from '/state/partition1/job-39968217/tmp_mepikop/multiqc_data' to '/vast/gencore/GENEFLOW/work/c6/a049dc617648c1d18418b9010bf465/merged/multiqc_data' [2023-11-10 14:04:39,754] multiqc [INFO ] MultiQC complete