[2021-09-14 21:01:21,264] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-09-14 21:01:21,265] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-09-14 21:01:21,265] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-09-14 21:01:21,266] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-09-14 21:01:21,266] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-09-14 21:01:21,266] 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-ANUJL/1 [2021-09-14 21:01:22,859] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-09-14 21:01:22,859] multiqc [INFO ] This is MultiQC v1.9 [2021-09-14 21:01:22,859] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/000000000-ANUJL/1 [2021-09-14 21:01:22,859] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/000000000-ANUJL/1 [2021-09-14 21:01:22,859] multiqc [INFO ] Template : default [2021-09-14 21:01:22,859] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-09-14 21:01:22,859] multiqc [INFO ] Searching : /scratch/gencore/logs/html/000000000-ANUJL/1 [2021-09-14 21:01:22,859] 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 [2021-09-14 21:01:22,859] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-9997306/tmpidfwzeu4 [2021-09-14 21:01:22,963] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-ANUJL_l01_n01_P1_2_fastqc.html [2021-09-14 21:01:22,965] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-ANUJL_l01_n01_P1_2_fastqc.html [2021-09-14 21:01:23,011] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-ANUJL_l01_n02_B1_2_fastqc.html [2021-09-14 21:01:23,013] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-ANUJL_l01_n02_B1_2_fastqc.html [2021-09-14 21:01:23,053] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-ANUJL_l01_n01_B2_3_fastqc.html [2021-09-14 21:01:23,056] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-ANUJL_l01_n01_B2_3_fastqc.html [2021-09-14 21:01:23,224] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-09-14 21:01:23,225] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-09-14 21:01:23,225] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-09-14 21:01:23,225] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-09-14 21:01:23,225] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-09-14 21:01:23,225] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-09-14 21:01:23,225] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-09-14 21:01:23,263] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-09-14 21:01:24,863] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-ANUJL_l01_n01_undetermined_fastqc.html [2021-09-14 21:01:24,865] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-ANUJL_l01_n01_undetermined_fastqc.html [2021-09-14 21:01:24,906] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-ANUJL_l01_n01_B1_3_fastqc.html [2021-09-14 21:01:24,908] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-ANUJL_l01_n01_B1_3_fastqc.html [2021-09-14 21:01:24,949] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-ANUJL_l01_n02_B2_3_fastqc.html [2021-09-14 21:01:24,950] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-ANUJL_l01_n02_B2_3_fastqc.html [2021-09-14 21:01:24,993] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-ANUJL_l01_n01_B1_2_fastqc.html [2021-09-14 21:01:24,995] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-ANUJL_l01_n01_B1_2_fastqc.html [2021-09-14 21:01:25,035] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-ANUJL_l01_n02_P1_3_fastqc.html [2021-09-14 21:01:25,037] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-ANUJL_l01_n02_P1_3_fastqc.html [2021-09-14 21:01:25,080] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-ANUJL_l01_n01_P3_2_fastqc.html [2021-09-14 21:01:25,082] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-ANUJL_l01_n01_P3_2_fastqc.html [2021-09-14 21:01:25,134] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-ANUJL_l01_n01_P1_3_fastqc.html [2021-09-14 21:01:25,136] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-ANUJL_l01_n01_P1_3_fastqc.html [2021-09-14 21:01:25,178] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-ANUJL_l01_n02_B1_3_fastqc.html [2021-09-14 21:01:25,180] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-ANUJL_l01_n02_B1_3_fastqc.html [2021-09-14 21:01:25,223] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-ANUJL_l01_n02_P2_3_fastqc.html [2021-09-14 21:01:25,225] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-ANUJL_l01_n02_P2_3_fastqc.html [2021-09-14 21:01:25,268] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-ANUJL_l01_n02_B3_2_fastqc.html [2021-09-14 21:01:25,270] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-ANUJL_l01_n02_B3_2_fastqc.html [2021-09-14 21:01:25,313] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-ANUJL_l01_n01_B3_2_fastqc.html [2021-09-14 21:01:25,315] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-ANUJL_l01_n01_B3_2_fastqc.html [2021-09-14 21:01:25,357] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-ANUJL_l01_n02_P1_2_fastqc.html [2021-09-14 21:01:25,359] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-ANUJL_l01_n02_P1_2_fastqc.html [2021-09-14 21:01:25,403] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-ANUJL_l01_n02_undetermined_fastqc.html [2021-09-14 21:01:25,405] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-ANUJL_l01_n02_undetermined_fastqc.html [2021-09-14 21:01:25,450] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-ANUJL_l01_n02_P3_2_fastqc.html [2021-09-14 21:01:25,452] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-ANUJL_l01_n02_P3_2_fastqc.html [2021-09-14 21:01:25,504] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-ANUJL_l01_n01_P2_3_fastqc.html [2021-09-14 21:01:25,506] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-ANUJL_l01_n01_P2_3_fastqc.html [2021-09-14 21:01:25,977] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-09-14 21:01:25,978] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-09-14 21:01:25,985] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-09-14 21:01:25,990] multiqc.modules.custom_content.custom_content [INFO ] demux_report-1: Found 9 samples (table) [2021-09-14 21:01:26,000] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-09-14 21:01:26,006] multiqc [DEBUG ] No samples found: conpair [2021-09-14 21:01:26,011] multiqc [DEBUG ] No samples found: peddy [2021-09-14 21:01:26,015] multiqc [DEBUG ] No samples found: somalier [2021-09-14 21:01:26,019] multiqc [DEBUG ] No samples found: methylQA [2021-09-14 21:01:26,031] multiqc [DEBUG ] No samples found: mosdepth [2021-09-14 21:01:26,035] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-09-14 21:01:26,039] multiqc [DEBUG ] No samples found: qualimap [2021-09-14 21:01:26,044] multiqc [DEBUG ] No samples found: preseq [2021-09-14 21:01:26,048] multiqc [DEBUG ] No samples found: quast [2021-09-14 21:01:26,053] multiqc [DEBUG ] No samples found: qorts [2021-09-14 21:01:26,058] multiqc [DEBUG ] No samples found: rna_seqc [2021-09-14 21:01:26,062] multiqc [DEBUG ] No samples found: rockhopper [2021-09-14 21:01:26,067] multiqc [DEBUG ] No samples found: rsem [2021-09-14 21:01:26,078] multiqc [DEBUG ] No samples found: rseqc [2021-09-14 21:01:26,082] multiqc [DEBUG ] No samples found: busco [2021-09-14 21:01:26,088] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-09-14 21:01:26,092] multiqc [DEBUG ] No samples found: disambiguate [2021-09-14 21:01:26,098] multiqc [DEBUG ] No samples found: supernova [2021-09-14 21:01:26,110] multiqc [DEBUG ] No samples found: deeptools [2021-09-14 21:01:26,115] multiqc [DEBUG ] No samples found: sargasso [2021-09-14 21:01:26,120] multiqc [DEBUG ] No samples found: verifybamid [2021-09-14 21:01:26,124] multiqc [DEBUG ] No samples found: mirtrace [2021-09-14 21:01:26,129] multiqc [DEBUG ] No samples found: happy [2021-09-14 21:01:26,134] multiqc [DEBUG ] No samples found: mirtop [2021-09-14 21:01:26,141] multiqc [DEBUG ] No samples found: homer [2021-09-14 21:01:26,146] multiqc [DEBUG ] No samples found: macs2 [2021-09-14 21:01:26,150] multiqc [DEBUG ] No samples found: theta2 [2021-09-14 21:01:26,155] multiqc [DEBUG ] No samples found: snpeff [2021-09-14 21:01:26,161] multiqc [DEBUG ] No samples found: gatk [2021-09-14 21:01:26,166] multiqc [DEBUG ] No samples found: htseq [2021-09-14 21:01:26,171] multiqc [DEBUG ] No samples found: bcftools [2021-09-14 21:01:26,175] multiqc [DEBUG ] No samples found: featureCounts [2021-09-14 21:01:26,182] multiqc [DEBUG ] No samples found: fgbio [2021-09-14 21:01:26,194] multiqc [DEBUG ] No samples found: dragen [2021-09-14 21:01:26,199] multiqc [DEBUG ] No samples found: dedup [2021-09-14 21:01:26,203] multiqc [DEBUG ] No samples found: damageprofiler [2021-09-14 21:01:26,223] multiqc [DEBUG ] No samples found: biobambam2 [2021-09-14 21:01:26,226] multiqc [DEBUG ] No samples found: mtnucratio [2021-09-14 21:01:26,229] multiqc [DEBUG ] No samples found: picard [2021-09-14 21:01:26,233] multiqc [DEBUG ] No samples found: prokka [2021-09-14 21:01:26,238] multiqc [DEBUG ] No samples found: samblaster [2021-09-14 21:01:26,245] multiqc [DEBUG ] No samples found: samtools [2021-09-14 21:01:26,249] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-09-14 21:01:26,254] multiqc [DEBUG ] No samples found: bamtools [2021-09-14 21:01:26,259] multiqc [DEBUG ] No samples found: jellyfish [2021-09-14 21:01:26,266] multiqc [DEBUG ] No samples found: vcftools [2021-09-14 21:01:26,270] multiqc [DEBUG ] No samples found: longranger [2021-09-14 21:01:26,275] multiqc [DEBUG ] No samples found: stacks [2021-09-14 21:01:26,279] multiqc [DEBUG ] No samples found: varscan2 [2021-09-14 21:01:26,291] multiqc [DEBUG ] No samples found: bbmap [2021-09-14 21:01:26,296] multiqc [DEBUG ] No samples found: bismark [2021-09-14 21:01:26,301] multiqc [DEBUG ] No samples found: biscuit [2021-09-14 21:01:26,305] multiqc [DEBUG ] No samples found: hicexplorer [2021-09-14 21:01:26,310] multiqc [DEBUG ] No samples found: hicup [2021-09-14 21:01:26,315] multiqc [DEBUG ] No samples found: hicpro [2021-09-14 21:01:26,319] multiqc [DEBUG ] No samples found: salmon [2021-09-14 21:01:26,324] multiqc [DEBUG ] No samples found: kallisto [2021-09-14 21:01:26,328] multiqc [DEBUG ] No samples found: slamdunk [2021-09-14 21:01:26,333] multiqc [DEBUG ] No samples found: star [2021-09-14 21:01:26,338] multiqc [DEBUG ] No samples found: hisat2 [2021-09-14 21:01:26,343] multiqc [DEBUG ] No samples found: tophat [2021-09-14 21:01:26,347] multiqc [DEBUG ] No samples found: bowtie2 [2021-09-14 21:01:26,351] multiqc [DEBUG ] No samples found: bowtie1 [2021-09-14 21:01:26,356] multiqc [DEBUG ] No samples found: snpsplit [2021-09-14 21:01:26,361] multiqc [DEBUG ] No samples found: kat [2021-09-14 21:01:26,365] multiqc [DEBUG ] No samples found: leehom [2021-09-14 21:01:26,370] multiqc [DEBUG ] No samples found: adapterRemoval [2021-09-14 21:01:26,374] multiqc [DEBUG ] No samples found: clipandmerge [2021-09-14 21:01:26,379] multiqc [DEBUG ] No samples found: cutadapt [2021-09-14 21:01:26,383] multiqc [DEBUG ] No samples found: flexbar [2021-09-14 21:01:26,388] multiqc [DEBUG ] No samples found: kaiju [2021-09-14 21:01:26,392] multiqc [DEBUG ] No samples found: kraken [2021-09-14 21:01:26,397] multiqc [DEBUG ] No samples found: malt [2021-09-14 21:01:26,402] multiqc [DEBUG ] No samples found: trimmomatic [2021-09-14 21:01:26,407] multiqc [DEBUG ] No samples found: sickle [2021-09-14 21:01:26,411] multiqc [DEBUG ] No samples found: skewer [2021-09-14 21:01:26,415] multiqc [DEBUG ] No samples found: sortmerna [2021-09-14 21:01:26,419] multiqc [DEBUG ] No samples found: biobloomtools [2021-09-14 21:01:26,424] multiqc [DEBUG ] No samples found: fastq_screen [2021-09-14 21:01:26,429] multiqc [DEBUG ] No samples found: afterqc [2021-09-14 21:01:26,433] multiqc [DEBUG ] No samples found: fastp [2021-09-14 21:01:26,620] multiqc.modules.fastqc.fastqc [INFO ] Found 18 reports [2021-09-14 21:01:26,936] multiqc [DEBUG ] No samples found: pycoqc [2021-09-14 21:01:26,941] multiqc [DEBUG ] No samples found: minionqc [2021-09-14 21:01:26,945] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-09-14 21:01:26,950] multiqc [DEBUG ] No samples found: clusterflow [2021-09-14 21:01:26,954] multiqc [DEBUG ] No samples found: bcl2fastq [2021-09-14 21:01:26,958] multiqc [DEBUG ] No samples found: interop [2021-09-14 21:01:26,963] multiqc [DEBUG ] No samples found: ivar [2021-09-14 21:01:26,967] multiqc [DEBUG ] No samples found: flash [2021-09-14 21:01:26,971] multiqc [DEBUG ] No samples found: seqyclean [2021-09-14 21:01:26,971] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2021-09-14 21:01:26,971] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2021-09-14 21:01:26,971] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 1 Demultiplexing Report'. [2021-09-14 21:01:26,972] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-09-14 21:01:26,972] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-09-14 21:01:26,993] multiqc [INFO ] Compressing plot data [2021-09-14 21:01:27,319] multiqc [INFO ] Report : multiqc_report.html [2021-09-14 21:01:27,319] multiqc [INFO ] Data : multiqc_data [2021-09-14 21:01:27,319] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9997306/tmpidfwzeu4/multiqc_data' to '/scratch/gencore/logs/html/000000000-ANUJL/1/multiqc_data' [2021-09-14 21:01:27,439] multiqc [INFO ] MultiQC complete