[2021-05-08 04:07:27,184] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-05-08 04:07:27,184] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-05-08 04:07:27,184] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-05-08 04:07:27,185] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-05-08 04:07:27,185] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-05-08 04:07:27,185] 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-JG8VC/1 [2021-05-08 04:07:28,581] multiqc [WARNING] MultiQC Version v1.10.1 now available! [2021-05-08 04:07:28,582] multiqc [INFO ] This is MultiQC v1.9 [2021-05-08 04:07:28,582] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/000000000-JG8VC/1 [2021-05-08 04:07:28,582] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/000000000-JG8VC/1 [2021-05-08 04:07:28,582] multiqc [INFO ] Template : default [2021-05-08 04:07:28,582] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-05-08 04:07:28,582] multiqc [INFO ] Searching : /scratch/gencore/logs/html/000000000-JG8VC/1 [2021-05-08 04:07:28,582] 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 [2021-05-08 04:07:28,582] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-6576346/tmp0heq57vt [2021-05-08 04:07:28,684] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-05-08 04:07:28,687] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-05-08 04:07:28,687] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-05-08 04:07:28,687] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-05-08 04:07:28,687] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-05-08 04:07:28,687] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-05-08 04:07:28,687] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-05-08 04:07:28,699] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-05-08 04:07:29,202] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JG8VC_l01_n02_CNV-RNAseq-1728-1_fastqc.html [2021-05-08 04:07:29,203] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JG8VC_l01_n02_CNV-RNAseq-1728-1_fastqc.html [2021-05-08 04:07:29,242] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JG8VC_l01_n01_CNV-RNAseq-1734-2_fastqc.html [2021-05-08 04:07:29,244] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JG8VC_l01_n01_CNV-RNAseq-1734-2_fastqc.html [2021-05-08 04:07:29,282] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JG8VC_l01_n01_CNV-RNAseq-1733-3_fastqc.html [2021-05-08 04:07:29,284] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JG8VC_l01_n01_CNV-RNAseq-1733-3_fastqc.html [2021-05-08 04:07:29,321] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JG8VC_l01_n02_CNV-RNAseq-1734-2_fastqc.html [2021-05-08 04:07:29,322] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JG8VC_l01_n02_CNV-RNAseq-1734-2_fastqc.html [2021-05-08 04:07:29,362] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JG8VC_l01_n02_CNV-RNAseq-1731-1_fastqc.html [2021-05-08 04:07:29,364] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JG8VC_l01_n02_CNV-RNAseq-1731-1_fastqc.html [2021-05-08 04:07:29,403] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JG8VC_l01_n01_CNV-RNAseq-1728-1_fastqc.html [2021-05-08 04:07:29,405] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JG8VC_l01_n01_CNV-RNAseq-1728-1_fastqc.html [2021-05-08 04:07:29,444] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JG8VC_l01_n01_undetermined_fastqc.html [2021-05-08 04:07:29,445] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JG8VC_l01_n01_undetermined_fastqc.html [2021-05-08 04:07:29,484] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JG8VC_l01_n02_CNV-RNAseq-1733-3_fastqc.html [2021-05-08 04:07:29,486] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JG8VC_l01_n02_CNV-RNAseq-1733-3_fastqc.html [2021-05-08 04:07:29,525] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JG8VC_l01_n01_CNV-RNAseq-1731-1_fastqc.html [2021-05-08 04:07:29,527] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JG8VC_l01_n01_CNV-RNAseq-1731-1_fastqc.html [2021-05-08 04:07:29,564] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JG8VC_l01_n02_undetermined_fastqc.html [2021-05-08 04:07:29,566] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JG8VC_l01_n02_undetermined_fastqc.html [2021-05-08 04:07:29,888] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-05-08 04:07:29,891] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-05-08 04:07:29,906] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-05-08 04:07:29,909] multiqc.modules.custom_content.custom_content [INFO ] demux_report-1: Found 5 samples (table) [2021-05-08 04:07:29,911] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-05-08 04:07:29,915] multiqc [DEBUG ] No samples found: conpair [2021-05-08 04:07:29,919] multiqc [DEBUG ] No samples found: peddy [2021-05-08 04:07:29,924] multiqc [DEBUG ] No samples found: somalier [2021-05-08 04:07:29,928] multiqc [DEBUG ] No samples found: methylQA [2021-05-08 04:07:29,935] multiqc [DEBUG ] No samples found: mosdepth [2021-05-08 04:07:29,939] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-05-08 04:07:29,942] multiqc [DEBUG ] No samples found: qualimap [2021-05-08 04:07:29,947] multiqc [DEBUG ] No samples found: preseq [2021-05-08 04:07:29,951] multiqc [DEBUG ] No samples found: quast [2021-05-08 04:07:29,956] multiqc [DEBUG ] No samples found: qorts [2021-05-08 04:07:29,960] multiqc [DEBUG ] No samples found: rna_seqc [2021-05-08 04:07:29,965] multiqc [DEBUG ] No samples found: rockhopper [2021-05-08 04:07:29,969] multiqc [DEBUG ] No samples found: rsem [2021-05-08 04:07:29,977] multiqc [DEBUG ] No samples found: rseqc [2021-05-08 04:07:29,981] multiqc [DEBUG ] No samples found: busco [2021-05-08 04:07:29,986] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-05-08 04:07:29,989] multiqc [DEBUG ] No samples found: disambiguate [2021-05-08 04:07:29,994] multiqc [DEBUG ] No samples found: supernova [2021-05-08 04:07:30,004] multiqc [DEBUG ] No samples found: deeptools [2021-05-08 04:07:30,009] multiqc [DEBUG ] No samples found: sargasso [2021-05-08 04:07:30,013] multiqc [DEBUG ] No samples found: verifybamid [2021-05-08 04:07:30,018] multiqc [DEBUG ] No samples found: mirtrace [2021-05-08 04:07:30,022] multiqc [DEBUG ] No samples found: happy [2021-05-08 04:07:30,026] multiqc [DEBUG ] No samples found: mirtop [2021-05-08 04:07:30,032] multiqc [DEBUG ] No samples found: homer [2021-05-08 04:07:30,037] multiqc [DEBUG ] No samples found: macs2 [2021-05-08 04:07:30,040] multiqc [DEBUG ] No samples found: theta2 [2021-05-08 04:07:30,045] multiqc [DEBUG ] No samples found: snpeff [2021-05-08 04:07:30,051] multiqc [DEBUG ] No samples found: gatk [2021-05-08 04:07:30,055] multiqc [DEBUG ] No samples found: htseq [2021-05-08 04:07:30,060] multiqc [DEBUG ] No samples found: bcftools [2021-05-08 04:07:30,066] multiqc [DEBUG ] No samples found: featureCounts [2021-05-08 04:07:30,071] multiqc [DEBUG ] No samples found: fgbio [2021-05-08 04:07:30,082] multiqc [DEBUG ] No samples found: dragen [2021-05-08 04:07:30,086] multiqc [DEBUG ] No samples found: dedup [2021-05-08 04:07:30,091] multiqc [DEBUG ] No samples found: damageprofiler [2021-05-08 04:07:30,121] multiqc [DEBUG ] No samples found: biobambam2 [2021-05-08 04:07:30,125] multiqc [DEBUG ] No samples found: mtnucratio [2021-05-08 04:07:30,128] multiqc [DEBUG ] No samples found: picard [2021-05-08 04:07:30,132] multiqc [DEBUG ] No samples found: prokka [2021-05-08 04:07:30,136] multiqc [DEBUG ] No samples found: samblaster [2021-05-08 04:07:30,143] multiqc [DEBUG ] No samples found: samtools [2021-05-08 04:07:30,150] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-05-08 04:07:30,154] multiqc [DEBUG ] No samples found: bamtools [2021-05-08 04:07:30,158] multiqc [DEBUG ] No samples found: jellyfish [2021-05-08 04:07:30,164] multiqc [DEBUG ] No samples found: vcftools [2021-05-08 04:07:30,168] multiqc [DEBUG ] No samples found: longranger [2021-05-08 04:07:30,173] multiqc [DEBUG ] No samples found: stacks [2021-05-08 04:07:30,177] multiqc [DEBUG ] No samples found: varscan2 [2021-05-08 04:07:30,188] multiqc [DEBUG ] No samples found: bbmap [2021-05-08 04:07:30,192] multiqc [DEBUG ] No samples found: bismark [2021-05-08 04:07:30,197] multiqc [DEBUG ] No samples found: biscuit [2021-05-08 04:07:30,202] multiqc [DEBUG ] No samples found: hicexplorer [2021-05-08 04:07:30,206] multiqc [DEBUG ] No samples found: hicup [2021-05-08 04:07:30,210] multiqc [DEBUG ] No samples found: hicpro [2021-05-08 04:07:30,214] multiqc [DEBUG ] No samples found: salmon [2021-05-08 04:07:30,219] multiqc [DEBUG ] No samples found: kallisto [2021-05-08 04:07:30,223] multiqc [DEBUG ] No samples found: slamdunk [2021-05-08 04:07:30,227] multiqc [DEBUG ] No samples found: star [2021-05-08 04:07:30,231] multiqc [DEBUG ] No samples found: hisat2 [2021-05-08 04:07:30,235] multiqc [DEBUG ] No samples found: tophat [2021-05-08 04:07:30,240] multiqc [DEBUG ] No samples found: bowtie2 [2021-05-08 04:07:30,244] multiqc [DEBUG ] No samples found: bowtie1 [2021-05-08 04:07:30,248] multiqc [DEBUG ] No samples found: snpsplit [2021-05-08 04:07:30,252] multiqc [DEBUG ] No samples found: kat [2021-05-08 04:07:30,256] multiqc [DEBUG ] No samples found: leehom [2021-05-08 04:07:30,260] multiqc [DEBUG ] No samples found: adapterRemoval [2021-05-08 04:07:30,264] multiqc [DEBUG ] No samples found: clipandmerge [2021-05-08 04:07:30,268] multiqc [DEBUG ] No samples found: cutadapt [2021-05-08 04:07:30,272] multiqc [DEBUG ] No samples found: flexbar [2021-05-08 04:07:30,276] multiqc [DEBUG ] No samples found: kaiju [2021-05-08 04:07:30,281] multiqc [DEBUG ] No samples found: kraken [2021-05-08 04:07:30,285] multiqc [DEBUG ] No samples found: malt [2021-05-08 04:07:30,289] multiqc [DEBUG ] No samples found: trimmomatic [2021-05-08 04:07:30,293] multiqc [DEBUG ] No samples found: sickle [2021-05-08 04:07:30,297] multiqc [DEBUG ] No samples found: skewer [2021-05-08 04:07:30,301] multiqc [DEBUG ] No samples found: sortmerna [2021-05-08 04:07:30,304] multiqc [DEBUG ] No samples found: biobloomtools [2021-05-08 04:07:30,309] multiqc [DEBUG ] No samples found: fastq_screen [2021-05-08 04:07:30,313] multiqc [DEBUG ] No samples found: afterqc [2021-05-08 04:07:30,319] multiqc [DEBUG ] No samples found: fastp [2021-05-08 04:07:30,414] multiqc.modules.fastqc.fastqc [INFO ] Found 10 reports [2021-05-08 04:07:30,631] multiqc [DEBUG ] No samples found: pycoqc [2021-05-08 04:07:30,635] multiqc [DEBUG ] No samples found: minionqc [2021-05-08 04:07:30,639] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-05-08 04:07:30,643] multiqc [DEBUG ] No samples found: clusterflow [2021-05-08 04:07:30,648] multiqc [DEBUG ] No samples found: bcl2fastq [2021-05-08 04:07:30,652] multiqc [DEBUG ] No samples found: interop [2021-05-08 04:07:30,656] multiqc [DEBUG ] No samples found: ivar [2021-05-08 04:07:30,661] multiqc [DEBUG ] No samples found: flash [2021-05-08 04:07:30,664] multiqc [DEBUG ] No samples found: seqyclean [2021-05-08 04:07:30,665] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2021-05-08 04:07:30,665] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-05-08 04:07:30,665] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 1 Demultiplexing Report'. [2021-05-08 04:07:30,665] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2021-05-08 04:07:30,665] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-05-08 04:07:30,677] multiqc [INFO ] Compressing plot data [2021-05-08 04:07:30,862] multiqc [INFO ] Report : multiqc_report.html [2021-05-08 04:07:30,862] multiqc [INFO ] Data : multiqc_data [2021-05-08 04:07:30,863] multiqc [DEBUG ] Moving data file from '/state/partition1/job-6576346/tmp0heq57vt/multiqc_data' to '/scratch/gencore/logs/html/000000000-JG8VC/1/multiqc_data' [2021-05-08 04:07:30,976] multiqc [INFO ] MultiQC complete