[2022-09-10 03:36:24,366] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-09-10 03:36:24,366] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-09-10 03:36:24,366] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-09-10 03:36:24,367] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-09-10 03:36:24,367] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-09-10 03:36:24,368] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/000000000-KBYBL/1 [2022-09-10 03:36:25,195] multiqc [WARNING] MultiQC Version v1.13 now available! [2022-09-10 03:36:25,195] multiqc [INFO ] This is MultiQC v1.9 [2022-09-10 03:36:25,195] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/000000000-KBYBL/1 [2022-09-10 03:36:25,195] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/000000000-KBYBL/1 [2022-09-10 03:36:25,195] multiqc [INFO ] Template : default [2022-09-10 03:36:25,195] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-09-10 03:36:25,195] multiqc [INFO ] Searching : /scratch/gencore/logs/html/000000000-KBYBL/1 [2022-09-10 03:36:25,196] 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 [2022-09-10 03:36:25,196] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-24712673/tmpa0sz4ktr [2022-09-10 03:36:25,308] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KBYBL_l01_n01_ORFSub1_fastqc.html [2022-09-10 03:36:25,311] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KBYBL_l01_n01_ORFSub1_fastqc.html [2022-09-10 03:36:25,373] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-09-10 03:36:25,375] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-09-10 03:36:25,375] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-09-10 03:36:25,375] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-09-10 03:36:25,375] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-09-10 03:36:25,375] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-09-10 03:36:25,375] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-09-10 03:36:25,395] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-09-10 03:36:26,237] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KBYBL_l01_n01_ORFSub4_fastqc.html [2022-09-10 03:36:26,239] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KBYBL_l01_n01_ORFSub4_fastqc.html [2022-09-10 03:36:26,300] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KBYBL_l01_n01_ORFSub5_fastqc.html [2022-09-10 03:36:26,302] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KBYBL_l01_n01_ORFSub5_fastqc.html [2022-09-10 03:36:26,361] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KBYBL_l01_n01_ORFSub3_fastqc.html [2022-09-10 03:36:26,364] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KBYBL_l01_n01_ORFSub3_fastqc.html [2022-09-10 03:36:26,425] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KBYBL_l01_n01_undetermined_fastqc.html [2022-09-10 03:36:26,427] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KBYBL_l01_n01_undetermined_fastqc.html [2022-09-10 03:36:26,475] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KBYBL_l01_n01_ORFSub2_fastqc.html [2022-09-10 03:36:26,477] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KBYBL_l01_n01_ORFSub2_fastqc.html [2022-09-10 03:36:26,538] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KBYBL_l01_n01_GECKOV2B_fastqc.html [2022-09-10 03:36:26,540] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KBYBL_l01_n01_GECKOV2B_fastqc.html [2022-09-10 03:36:26,603] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KBYBL_l01_n01_ORFSub6_fastqc.html [2022-09-10 03:36:26,605] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KBYBL_l01_n01_ORFSub6_fastqc.html [2022-09-10 03:36:26,969] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-09-10 03:36:26,971] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-09-10 03:36:26,982] multiqc.modules.custom_content.custom_content [INFO ] demux_report-1: Found 8 samples (table) [2022-09-10 03:36:26,983] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-09-10 03:36:26,993] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-09-10 03:36:26,998] multiqc [DEBUG ] No samples found: conpair [2022-09-10 03:36:27,002] multiqc [DEBUG ] No samples found: peddy [2022-09-10 03:36:27,008] multiqc [DEBUG ] No samples found: somalier [2022-09-10 03:36:27,012] multiqc [DEBUG ] No samples found: methylQA [2022-09-10 03:36:27,021] multiqc [DEBUG ] No samples found: mosdepth [2022-09-10 03:36:27,025] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-09-10 03:36:27,029] multiqc [DEBUG ] No samples found: qualimap [2022-09-10 03:36:27,034] multiqc [DEBUG ] No samples found: preseq [2022-09-10 03:36:27,040] multiqc [DEBUG ] No samples found: quast [2022-09-10 03:36:27,045] multiqc [DEBUG ] No samples found: qorts [2022-09-10 03:36:27,050] multiqc [DEBUG ] No samples found: rna_seqc [2022-09-10 03:36:27,055] multiqc [DEBUG ] No samples found: rockhopper [2022-09-10 03:36:27,060] multiqc [DEBUG ] No samples found: rsem [2022-09-10 03:36:27,070] multiqc [DEBUG ] No samples found: rseqc [2022-09-10 03:36:27,074] multiqc [DEBUG ] No samples found: busco [2022-09-10 03:36:27,079] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-09-10 03:36:27,083] multiqc [DEBUG ] No samples found: disambiguate [2022-09-10 03:36:27,088] multiqc [DEBUG ] No samples found: supernova [2022-09-10 03:36:27,101] multiqc [DEBUG ] No samples found: deeptools [2022-09-10 03:36:27,105] multiqc [DEBUG ] No samples found: sargasso [2022-09-10 03:36:27,110] multiqc [DEBUG ] No samples found: verifybamid [2022-09-10 03:36:27,115] multiqc [DEBUG ] No samples found: mirtrace [2022-09-10 03:36:27,119] multiqc [DEBUG ] No samples found: happy [2022-09-10 03:36:27,124] multiqc [DEBUG ] No samples found: mirtop [2022-09-10 03:36:27,130] multiqc [DEBUG ] No samples found: homer [2022-09-10 03:36:27,135] multiqc [DEBUG ] No samples found: macs2 [2022-09-10 03:36:27,139] multiqc [DEBUG ] No samples found: theta2 [2022-09-10 03:36:27,144] multiqc [DEBUG ] No samples found: snpeff [2022-09-10 03:36:27,151] multiqc [DEBUG ] No samples found: gatk [2022-09-10 03:36:27,155] multiqc [DEBUG ] No samples found: htseq [2022-09-10 03:36:27,161] multiqc [DEBUG ] No samples found: bcftools [2022-09-10 03:36:27,165] multiqc [DEBUG ] No samples found: featureCounts [2022-09-10 03:36:27,171] multiqc [DEBUG ] No samples found: fgbio [2022-09-10 03:36:27,184] multiqc [DEBUG ] No samples found: dragen [2022-09-10 03:36:27,189] multiqc [DEBUG ] No samples found: dedup [2022-09-10 03:36:27,194] multiqc [DEBUG ] No samples found: damageprofiler [2022-09-10 03:36:27,217] multiqc [DEBUG ] No samples found: biobambam2 [2022-09-10 03:36:27,221] multiqc [DEBUG ] No samples found: mtnucratio [2022-09-10 03:36:27,223] multiqc [DEBUG ] No samples found: picard [2022-09-10 03:36:27,228] multiqc [DEBUG ] No samples found: prokka [2022-09-10 03:36:27,232] multiqc [DEBUG ] No samples found: samblaster [2022-09-10 03:36:27,240] multiqc [DEBUG ] No samples found: samtools [2022-09-10 03:36:27,245] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-09-10 03:36:27,250] multiqc [DEBUG ] No samples found: bamtools [2022-09-10 03:36:27,254] multiqc [DEBUG ] No samples found: jellyfish [2022-09-10 03:36:27,261] multiqc [DEBUG ] No samples found: vcftools [2022-09-10 03:36:27,266] multiqc [DEBUG ] No samples found: longranger [2022-09-10 03:36:27,270] multiqc [DEBUG ] No samples found: stacks [2022-09-10 03:36:27,275] multiqc [DEBUG ] No samples found: varscan2 [2022-09-10 03:36:27,289] multiqc [DEBUG ] No samples found: bbmap [2022-09-10 03:36:27,294] multiqc [DEBUG ] No samples found: bismark [2022-09-10 03:36:27,299] multiqc [DEBUG ] No samples found: biscuit [2022-09-10 03:36:27,304] multiqc [DEBUG ] No samples found: hicexplorer [2022-09-10 03:36:27,309] multiqc [DEBUG ] No samples found: hicup [2022-09-10 03:36:27,314] multiqc [DEBUG ] No samples found: hicpro [2022-09-10 03:36:27,318] multiqc [DEBUG ] No samples found: salmon [2022-09-10 03:36:27,323] multiqc [DEBUG ] No samples found: kallisto [2022-09-10 03:36:27,328] multiqc [DEBUG ] No samples found: slamdunk [2022-09-10 03:36:27,332] multiqc [DEBUG ] No samples found: star [2022-09-10 03:36:27,337] multiqc [DEBUG ] No samples found: hisat2 [2022-09-10 03:36:27,341] multiqc [DEBUG ] No samples found: tophat [2022-09-10 03:36:27,346] multiqc [DEBUG ] No samples found: bowtie2 [2022-09-10 03:36:27,351] multiqc [DEBUG ] No samples found: bowtie1 [2022-09-10 03:36:27,355] multiqc [DEBUG ] No samples found: snpsplit [2022-09-10 03:36:27,359] multiqc [DEBUG ] No samples found: kat [2022-09-10 03:36:27,363] multiqc [DEBUG ] No samples found: leehom [2022-09-10 03:36:27,368] multiqc [DEBUG ] No samples found: adapterRemoval [2022-09-10 03:36:27,372] multiqc [DEBUG ] No samples found: clipandmerge [2022-09-10 03:36:27,377] multiqc [DEBUG ] No samples found: cutadapt [2022-09-10 03:36:27,381] multiqc [DEBUG ] No samples found: flexbar [2022-09-10 03:36:27,385] multiqc [DEBUG ] No samples found: kaiju [2022-09-10 03:36:27,390] multiqc [DEBUG ] No samples found: kraken [2022-09-10 03:36:27,395] multiqc [DEBUG ] No samples found: malt [2022-09-10 03:36:27,399] multiqc [DEBUG ] No samples found: trimmomatic [2022-09-10 03:36:27,403] multiqc [DEBUG ] No samples found: sickle [2022-09-10 03:36:27,408] multiqc [DEBUG ] No samples found: skewer [2022-09-10 03:36:27,412] multiqc [DEBUG ] No samples found: sortmerna [2022-09-10 03:36:27,416] multiqc [DEBUG ] No samples found: biobloomtools [2022-09-10 03:36:27,422] multiqc [DEBUG ] No samples found: fastq_screen [2022-09-10 03:36:27,426] multiqc [DEBUG ] No samples found: afterqc [2022-09-10 03:36:27,431] multiqc [DEBUG ] No samples found: fastp [2022-09-10 03:36:27,494] multiqc.modules.fastqc.fastqc [INFO ] Found 8 reports [2022-09-10 03:36:27,580] multiqc [DEBUG ] No samples found: pycoqc [2022-09-10 03:36:27,584] multiqc [DEBUG ] No samples found: minionqc [2022-09-10 03:36:27,589] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-09-10 03:36:27,594] multiqc [DEBUG ] No samples found: clusterflow [2022-09-10 03:36:27,599] multiqc [DEBUG ] No samples found: bcl2fastq [2022-09-10 03:36:27,604] multiqc [DEBUG ] No samples found: interop [2022-09-10 03:36:27,609] multiqc [DEBUG ] No samples found: ivar [2022-09-10 03:36:27,614] multiqc [DEBUG ] No samples found: flash [2022-09-10 03:36:27,618] multiqc [DEBUG ] No samples found: seqyclean [2022-09-10 03:36:27,618] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2022-09-10 03:36:27,618] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 1 Demultiplexing Report'. [2022-09-10 03:36:27,618] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2022-09-10 03:36:27,618] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-09-10 03:36:27,618] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-09-10 03:36:27,629] multiqc [INFO ] Compressing plot data [2022-09-10 03:36:27,750] multiqc [INFO ] Report : multiqc_report.html [2022-09-10 03:36:27,750] multiqc [INFO ] Data : multiqc_data [2022-09-10 03:36:27,750] multiqc [DEBUG ] Moving data file from '/state/partition1/job-24712673/tmpa0sz4ktr/multiqc_data' to '/scratch/gencore/logs/html/000000000-KBYBL/1/multiqc_data' [2022-09-10 03:36:27,878] multiqc [INFO ] MultiQC complete