[2021-03-26 03:48:48,302] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-03-26 03:48:48,302] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-03-26 03:48:48,302] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-03-26 03:48:48,303] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-03-26 03:48:48,303] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-03-26 03:48:48,303] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HV3J5BGXG/merged [2021-03-26 03:48:49,664] multiqc [WARNING] MultiQC Version v1.10 now available! [2021-03-26 03:48:49,664] multiqc [INFO ] This is MultiQC v1.9 [2021-03-26 03:48:49,665] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HV3J5BGXG/merged [2021-03-26 03:48:49,665] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HV3J5BGXG/merged [2021-03-26 03:48:49,665] multiqc [INFO ] Template : default [2021-03-26 03:48:49,665] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-03-26 03:48:49,665] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HV3J5BGXG/merged [2021-03-26 03:48:49,665] 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 [2021-03-26 03:48:49,665] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-4231077/tmppxwm3rdb [2021-03-26 03:48:49,766] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HV3J5BGXG_n01_AKM224_fastqc.html [2021-03-26 03:48:49,768] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HV3J5BGXG_n01_AKM224_fastqc.html [2021-03-26 03:48:49,811] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HV3J5BGXG_n01_undetermined_fastqc.html [2021-03-26 03:48:49,813] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HV3J5BGXG_n01_undetermined_fastqc.html [2021-03-26 03:48:49,850] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-03-26 03:48:49,851] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-03-26 03:48:49,962] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HV3J5BGXG_n01_AKM223_fastqc.html [2021-03-26 03:48:49,963] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HV3J5BGXG_n01_AKM223_fastqc.html [2021-03-26 03:48:50,001] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HV3J5BGXG_n01_AKM213_fastqc.html [2021-03-26 03:48:50,003] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HV3J5BGXG_n01_AKM213_fastqc.html [2021-03-26 03:48:50,041] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HV3J5BGXG_n01_AKM207_fastqc.html [2021-03-26 03:48:50,042] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HV3J5BGXG_n01_AKM207_fastqc.html [2021-03-26 03:48:50,082] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HV3J5BGXG_n01_AKM214_fastqc.html [2021-03-26 03:48:50,084] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HV3J5BGXG_n01_AKM214_fastqc.html [2021-03-26 03:48:50,122] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HV3J5BGXG_n01_AKM208_fastqc.html [2021-03-26 03:48:50,124] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HV3J5BGXG_n01_AKM208_fastqc.html [2021-03-26 03:48:50,165] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HV3J5BGXG_n01_AKM219_fastqc.html [2021-03-26 03:48:50,167] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HV3J5BGXG_n01_AKM219_fastqc.html [2021-03-26 03:48:50,205] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HV3J5BGXG_n01_AKM221_fastqc.html [2021-03-26 03:48:50,207] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HV3J5BGXG_n01_AKM221_fastqc.html [2021-03-26 03:48:50,246] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HV3J5BGXG_n01_AKM220_fastqc.html [2021-03-26 03:48:50,247] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HV3J5BGXG_n01_AKM220_fastqc.html [2021-03-26 03:48:50,286] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HV3J5BGXG_n01_AKM205_fastqc.html [2021-03-26 03:48:50,288] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HV3J5BGXG_n01_AKM205_fastqc.html [2021-03-26 03:48:50,327] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HV3J5BGXG_n01_AKM222_fastqc.html [2021-03-26 03:48:50,328] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HV3J5BGXG_n01_AKM222_fastqc.html [2021-03-26 03:48:50,366] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HV3J5BGXG_n01_AKM204_fastqc.html [2021-03-26 03:48:50,368] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HV3J5BGXG_n01_AKM204_fastqc.html [2021-03-26 03:48:50,411] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HV3J5BGXG_n01_AKM212_fastqc.html [2021-03-26 03:48:50,413] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HV3J5BGXG_n01_AKM212_fastqc.html [2021-03-26 03:48:50,450] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HV3J5BGXG_n01_AKM206_fastqc.html [2021-03-26 03:48:50,452] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HV3J5BGXG_n01_AKM206_fastqc.html [2021-03-26 03:48:50,492] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HV3J5BGXG_n01_AKM217_fastqc.html [2021-03-26 03:48:50,493] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HV3J5BGXG_n01_AKM217_fastqc.html [2021-03-26 03:48:50,531] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HV3J5BGXG_n01_AKM218_fastqc.html [2021-03-26 03:48:50,532] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HV3J5BGXG_n01_AKM218_fastqc.html [2021-03-26 03:48:50,572] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HV3J5BGXG_n01_AKM225_fastqc.html [2021-03-26 03:48:50,574] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HV3J5BGXG_n01_AKM225_fastqc.html [2021-03-26 03:48:50,614] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HV3J5BGXG_n01_AKM227_fastqc.html [2021-03-26 03:48:50,616] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HV3J5BGXG_n01_AKM227_fastqc.html [2021-03-26 03:48:50,656] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HV3J5BGXG_n01_AKM226_fastqc.html [2021-03-26 03:48:50,658] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HV3J5BGXG_n01_AKM226_fastqc.html [2021-03-26 03:48:50,699] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HV3J5BGXG_n01_AKM209_fastqc.html [2021-03-26 03:48:50,700] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HV3J5BGXG_n01_AKM209_fastqc.html [2021-03-26 03:48:50,741] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HV3J5BGXG_n01_AKM228_fastqc.html [2021-03-26 03:48:50,743] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HV3J5BGXG_n01_AKM228_fastqc.html [2021-03-26 03:48:50,783] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HV3J5BGXG_n01_AKM216_fastqc.html [2021-03-26 03:48:50,785] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HV3J5BGXG_n01_AKM216_fastqc.html [2021-03-26 03:48:50,823] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HV3J5BGXG_n01_AKM215_fastqc.html [2021-03-26 03:48:50,825] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HV3J5BGXG_n01_AKM215_fastqc.html [2021-03-26 03:48:51,130] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-03-26 03:48:51,132] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-03-26 03:48:51,139] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-03-26 03:48:51,151] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 24 samples (table) [2021-03-26 03:48:51,160] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-03-26 03:48:51,169] multiqc [DEBUG ] No samples found: conpair [2021-03-26 03:48:51,177] multiqc [DEBUG ] No samples found: peddy [2021-03-26 03:48:51,182] multiqc [DEBUG ] No samples found: somalier [2021-03-26 03:48:51,190] multiqc [DEBUG ] No samples found: methylQA [2021-03-26 03:48:51,199] multiqc [DEBUG ] No samples found: mosdepth [2021-03-26 03:48:51,205] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-03-26 03:48:51,208] multiqc [DEBUG ] No samples found: qualimap [2021-03-26 03:48:51,215] multiqc [DEBUG ] No samples found: preseq [2021-03-26 03:48:51,221] multiqc [DEBUG ] No samples found: quast [2021-03-26 03:48:51,228] multiqc [DEBUG ] No samples found: qorts [2021-03-26 03:48:51,234] multiqc [DEBUG ] No samples found: rna_seqc [2021-03-26 03:48:51,242] multiqc [DEBUG ] No samples found: rockhopper [2021-03-26 03:48:51,247] multiqc [DEBUG ] No samples found: rsem [2021-03-26 03:48:51,258] multiqc [DEBUG ] No samples found: rseqc [2021-03-26 03:48:51,263] multiqc [DEBUG ] No samples found: busco [2021-03-26 03:48:51,270] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-03-26 03:48:51,276] multiqc [DEBUG ] No samples found: disambiguate [2021-03-26 03:48:51,284] multiqc [DEBUG ] No samples found: supernova [2021-03-26 03:48:51,297] multiqc [DEBUG ] No samples found: deeptools [2021-03-26 03:48:51,303] multiqc [DEBUG ] No samples found: sargasso [2021-03-26 03:48:51,310] multiqc [DEBUG ] No samples found: verifybamid [2021-03-26 03:48:51,315] multiqc [DEBUG ] No samples found: mirtrace [2021-03-26 03:48:51,320] multiqc [DEBUG ] No samples found: happy [2021-03-26 03:48:51,325] multiqc [DEBUG ] No samples found: mirtop [2021-03-26 03:48:51,333] multiqc [DEBUG ] No samples found: homer [2021-03-26 03:48:51,340] multiqc [DEBUG ] No samples found: macs2 [2021-03-26 03:48:51,348] multiqc [DEBUG ] No samples found: theta2 [2021-03-26 03:48:51,354] multiqc [DEBUG ] No samples found: snpeff [2021-03-26 03:48:51,363] multiqc [DEBUG ] No samples found: gatk [2021-03-26 03:48:51,370] multiqc [DEBUG ] No samples found: htseq [2021-03-26 03:48:51,378] multiqc [DEBUG ] No samples found: bcftools [2021-03-26 03:48:51,385] multiqc [DEBUG ] No samples found: featureCounts [2021-03-26 03:48:51,392] multiqc [DEBUG ] No samples found: fgbio [2021-03-26 03:48:51,408] multiqc [DEBUG ] No samples found: dragen [2021-03-26 03:48:51,415] multiqc [DEBUG ] No samples found: dedup [2021-03-26 03:48:51,422] multiqc [DEBUG ] No samples found: damageprofiler [2021-03-26 03:48:51,448] multiqc [DEBUG ] No samples found: biobambam2 [2021-03-26 03:48:51,453] multiqc [DEBUG ] No samples found: mtnucratio [2021-03-26 03:48:51,455] multiqc [DEBUG ] No samples found: picard [2021-03-26 03:48:51,462] multiqc [DEBUG ] No samples found: prokka [2021-03-26 03:48:51,467] multiqc [DEBUG ] No samples found: samblaster [2021-03-26 03:48:51,477] multiqc [DEBUG ] No samples found: samtools [2021-03-26 03:48:51,482] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-03-26 03:48:51,490] multiqc [DEBUG ] No samples found: bamtools [2021-03-26 03:48:51,497] multiqc [DEBUG ] No samples found: jellyfish [2021-03-26 03:48:51,503] multiqc [DEBUG ] No samples found: vcftools [2021-03-26 03:48:51,508] multiqc [DEBUG ] No samples found: longranger [2021-03-26 03:48:51,514] multiqc [DEBUG ] No samples found: stacks [2021-03-26 03:48:51,520] multiqc [DEBUG ] No samples found: varscan2 [2021-03-26 03:48:51,537] multiqc [DEBUG ] No samples found: bbmap [2021-03-26 03:48:51,543] multiqc [DEBUG ] No samples found: bismark [2021-03-26 03:48:51,549] multiqc [DEBUG ] No samples found: biscuit [2021-03-26 03:48:51,555] multiqc [DEBUG ] No samples found: hicexplorer [2021-03-26 03:48:51,561] multiqc [DEBUG ] No samples found: hicup [2021-03-26 03:48:51,568] multiqc [DEBUG ] No samples found: hicpro [2021-03-26 03:48:51,576] multiqc [DEBUG ] No samples found: salmon [2021-03-26 03:48:51,583] multiqc [DEBUG ] No samples found: kallisto [2021-03-26 03:48:51,588] multiqc [DEBUG ] No samples found: slamdunk [2021-03-26 03:48:51,594] multiqc [DEBUG ] No samples found: star [2021-03-26 03:48:51,601] multiqc [DEBUG ] No samples found: hisat2 [2021-03-26 03:48:51,609] multiqc [DEBUG ] No samples found: tophat [2021-03-26 03:48:51,615] multiqc [DEBUG ] No samples found: bowtie2 [2021-03-26 03:48:51,622] multiqc [DEBUG ] No samples found: bowtie1 [2021-03-26 03:48:51,629] multiqc [DEBUG ] No samples found: snpsplit [2021-03-26 03:48:51,635] multiqc [DEBUG ] No samples found: kat [2021-03-26 03:48:51,641] multiqc [DEBUG ] No samples found: leehom [2021-03-26 03:48:51,647] multiqc [DEBUG ] No samples found: adapterRemoval [2021-03-26 03:48:51,653] multiqc [DEBUG ] No samples found: clipandmerge [2021-03-26 03:48:51,661] multiqc [DEBUG ] No samples found: cutadapt [2021-03-26 03:48:51,667] multiqc [DEBUG ] No samples found: flexbar [2021-03-26 03:48:51,674] multiqc [DEBUG ] No samples found: kaiju [2021-03-26 03:48:51,681] multiqc [DEBUG ] No samples found: kraken [2021-03-26 03:48:51,686] multiqc [DEBUG ] No samples found: malt [2021-03-26 03:48:51,693] multiqc [DEBUG ] No samples found: trimmomatic [2021-03-26 03:48:51,700] multiqc [DEBUG ] No samples found: sickle [2021-03-26 03:48:51,705] multiqc [DEBUG ] No samples found: skewer [2021-03-26 03:48:51,712] multiqc [DEBUG ] No samples found: sortmerna [2021-03-26 03:48:51,718] multiqc [DEBUG ] No samples found: biobloomtools [2021-03-26 03:48:51,726] multiqc [DEBUG ] No samples found: fastq_screen [2021-03-26 03:48:51,731] multiqc [DEBUG ] No samples found: afterqc [2021-03-26 03:48:51,737] multiqc [DEBUG ] No samples found: fastp [2021-03-26 03:48:53,362] multiqc.modules.fastqc.fastqc [INFO ] Found 24 reports [2021-03-26 03:48:53,873] multiqc [DEBUG ] No samples found: pycoqc [2021-03-26 03:48:53,879] multiqc [DEBUG ] No samples found: minionqc [2021-03-26 03:48:53,886] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-03-26 03:48:53,894] multiqc [DEBUG ] No samples found: clusterflow [2021-03-26 03:48:53,903] multiqc [DEBUG ] No samples found: bcl2fastq [2021-03-26 03:48:53,909] multiqc [DEBUG ] No samples found: interop [2021-03-26 03:48:53,915] multiqc [DEBUG ] No samples found: ivar [2021-03-26 03:48:53,920] multiqc [DEBUG ] No samples found: flash [2021-03-26 03:48:53,926] multiqc [DEBUG ] No samples found: seqyclean [2021-03-26 03:48:53,926] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-03-26 03:48:53,926] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-03-26 03:48:53,926] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-03-26 03:48:53,926] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-03-26 03:48:53,955] multiqc [INFO ] Compressing plot data [2021-03-26 03:48:54,386] multiqc [INFO ] Report : multiqc_report.html [2021-03-26 03:48:54,386] multiqc [INFO ] Data : multiqc_data [2021-03-26 03:48:54,386] multiqc [DEBUG ] Moving data file from '/state/partition1/job-4231077/tmppxwm3rdb/multiqc_data' to '/scratch/gencore/logs/html/HV3J5BGXG/merged/multiqc_data' [2021-03-26 03:49:20,132] multiqc [INFO ] MultiQC complete