[2021-08-11 02:18:09,976] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-08-11 02:18:09,977] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-08-11 02:18:09,977] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-08-11 02:18:09,978] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-08-11 02:18:09,978] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-08-11 02:18:09,978] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HLT3MBGXJ/merged [2021-08-11 02:18:11,653] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-08-11 02:18:11,653] multiqc [INFO ] This is MultiQC v1.9 [2021-08-11 02:18:11,653] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HLT3MBGXJ/merged [2021-08-11 02:18:11,653] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HLT3MBGXJ/merged [2021-08-11 02:18:11,653] multiqc [INFO ] Template : default [2021-08-11 02:18:11,653] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-08-11 02:18:11,653] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HLT3MBGXJ/merged [2021-08-11 02:18:11,654] 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 [2021-08-11 02:18:11,654] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-9305230/tmpwtispl_c [2021-08-11 02:18:11,782] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-08-11 02:18:11,785] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-08-11 02:18:12,205] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLT3MBGXJ_n01_ATAC_Tcell_S_2_fastqc.html [2021-08-11 02:18:12,207] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLT3MBGXJ_n01_ATAC_Tcell_S_2_fastqc.html [2021-08-11 02:18:12,250] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLT3MBGXJ_n01_ATAC_Tcell_S_4_fastqc.html [2021-08-11 02:18:12,252] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLT3MBGXJ_n01_ATAC_Tcell_S_4_fastqc.html [2021-08-11 02:18:12,295] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLT3MBGXJ_n01_ATAC_Tcell_S_1_fastqc.html [2021-08-11 02:18:12,297] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLT3MBGXJ_n01_ATAC_Tcell_S_1_fastqc.html [2021-08-11 02:18:12,341] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLT3MBGXJ_n01_ATAC_Tcell_S_5_fastqc.html [2021-08-11 02:18:12,343] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLT3MBGXJ_n01_ATAC_Tcell_S_5_fastqc.html [2021-08-11 02:18:12,438] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLT3MBGXJ_n01_undetermined_fastqc.html [2021-08-11 02:18:12,440] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLT3MBGXJ_n01_undetermined_fastqc.html [2021-08-11 02:18:13,027] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-08-11 02:18:13,029] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-08-11 02:18:13,038] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-08-11 02:18:13,048] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-08-11 02:18:13,051] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 5 samples (table) [2021-08-11 02:18:13,056] multiqc [DEBUG ] No samples found: conpair [2021-08-11 02:18:13,064] multiqc [DEBUG ] No samples found: peddy [2021-08-11 02:18:13,070] multiqc [DEBUG ] No samples found: somalier [2021-08-11 02:18:13,075] multiqc [DEBUG ] No samples found: methylQA [2021-08-11 02:18:13,084] multiqc [DEBUG ] No samples found: mosdepth [2021-08-11 02:18:13,088] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-08-11 02:18:13,093] multiqc [DEBUG ] No samples found: qualimap [2021-08-11 02:18:13,098] multiqc [DEBUG ] No samples found: preseq [2021-08-11 02:18:13,103] multiqc [DEBUG ] No samples found: quast [2021-08-11 02:18:13,109] multiqc [DEBUG ] No samples found: qorts [2021-08-11 02:18:13,114] multiqc [DEBUG ] No samples found: rna_seqc [2021-08-11 02:18:13,121] multiqc [DEBUG ] No samples found: rockhopper [2021-08-11 02:18:13,128] multiqc [DEBUG ] No samples found: rsem [2021-08-11 02:18:13,140] multiqc [DEBUG ] No samples found: rseqc [2021-08-11 02:18:13,145] multiqc [DEBUG ] No samples found: busco [2021-08-11 02:18:13,151] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-08-11 02:18:13,156] multiqc [DEBUG ] No samples found: disambiguate [2021-08-11 02:18:13,162] multiqc [DEBUG ] No samples found: supernova [2021-08-11 02:18:13,177] multiqc [DEBUG ] No samples found: deeptools [2021-08-11 02:18:13,184] multiqc [DEBUG ] No samples found: sargasso [2021-08-11 02:18:13,190] multiqc [DEBUG ] No samples found: verifybamid [2021-08-11 02:18:13,196] multiqc [DEBUG ] No samples found: mirtrace [2021-08-11 02:18:13,202] multiqc [DEBUG ] No samples found: happy [2021-08-11 02:18:13,207] multiqc [DEBUG ] No samples found: mirtop [2021-08-11 02:18:13,217] multiqc [DEBUG ] No samples found: homer [2021-08-11 02:18:13,222] multiqc [DEBUG ] No samples found: macs2 [2021-08-11 02:18:13,226] multiqc [DEBUG ] No samples found: theta2 [2021-08-11 02:18:13,231] multiqc [DEBUG ] No samples found: snpeff [2021-08-11 02:18:13,241] multiqc [DEBUG ] No samples found: gatk [2021-08-11 02:18:13,247] multiqc [DEBUG ] No samples found: htseq [2021-08-11 02:18:13,253] multiqc [DEBUG ] No samples found: bcftools [2021-08-11 02:18:13,258] multiqc [DEBUG ] No samples found: featureCounts [2021-08-11 02:18:13,265] multiqc [DEBUG ] No samples found: fgbio [2021-08-11 02:18:13,280] multiqc [DEBUG ] No samples found: dragen [2021-08-11 02:18:13,285] multiqc [DEBUG ] No samples found: dedup [2021-08-11 02:18:13,290] multiqc [DEBUG ] No samples found: damageprofiler [2021-08-11 02:18:13,315] multiqc [DEBUG ] No samples found: biobambam2 [2021-08-11 02:18:13,321] multiqc [DEBUG ] No samples found: mtnucratio [2021-08-11 02:18:13,323] multiqc [DEBUG ] No samples found: picard [2021-08-11 02:18:13,328] multiqc [DEBUG ] No samples found: prokka [2021-08-11 02:18:13,333] multiqc [DEBUG ] No samples found: samblaster [2021-08-11 02:18:13,342] multiqc [DEBUG ] No samples found: samtools [2021-08-11 02:18:13,347] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-08-11 02:18:13,353] multiqc [DEBUG ] No samples found: bamtools [2021-08-11 02:18:13,358] multiqc [DEBUG ] No samples found: jellyfish [2021-08-11 02:18:13,365] multiqc [DEBUG ] No samples found: vcftools [2021-08-11 02:18:13,371] multiqc [DEBUG ] No samples found: longranger [2021-08-11 02:18:13,376] multiqc [DEBUG ] No samples found: stacks [2021-08-11 02:18:13,381] multiqc [DEBUG ] No samples found: varscan2 [2021-08-11 02:18:13,396] multiqc [DEBUG ] No samples found: bbmap [2021-08-11 02:18:13,402] multiqc [DEBUG ] No samples found: bismark [2021-08-11 02:18:13,407] multiqc [DEBUG ] No samples found: biscuit [2021-08-11 02:18:13,413] multiqc [DEBUG ] No samples found: hicexplorer [2021-08-11 02:18:13,418] multiqc [DEBUG ] No samples found: hicup [2021-08-11 02:18:13,423] multiqc [DEBUG ] No samples found: hicpro [2021-08-11 02:18:13,427] multiqc [DEBUG ] No samples found: salmon [2021-08-11 02:18:13,434] multiqc [DEBUG ] No samples found: kallisto [2021-08-11 02:18:13,439] multiqc [DEBUG ] No samples found: slamdunk [2021-08-11 02:18:13,444] multiqc [DEBUG ] No samples found: star [2021-08-11 02:18:13,449] multiqc [DEBUG ] No samples found: hisat2 [2021-08-11 02:18:13,454] multiqc [DEBUG ] No samples found: tophat [2021-08-11 02:18:13,460] multiqc [DEBUG ] No samples found: bowtie2 [2021-08-11 02:18:13,466] multiqc [DEBUG ] No samples found: bowtie1 [2021-08-11 02:18:13,471] multiqc [DEBUG ] No samples found: snpsplit [2021-08-11 02:18:13,476] multiqc [DEBUG ] No samples found: kat [2021-08-11 02:18:13,480] multiqc [DEBUG ] No samples found: leehom [2021-08-11 02:18:13,485] multiqc [DEBUG ] No samples found: adapterRemoval [2021-08-11 02:18:13,490] multiqc [DEBUG ] No samples found: clipandmerge [2021-08-11 02:18:13,494] multiqc [DEBUG ] No samples found: cutadapt [2021-08-11 02:18:13,499] multiqc [DEBUG ] No samples found: flexbar [2021-08-11 02:18:13,506] multiqc [DEBUG ] No samples found: kaiju [2021-08-11 02:18:13,512] multiqc [DEBUG ] No samples found: kraken [2021-08-11 02:18:13,520] multiqc [DEBUG ] No samples found: malt [2021-08-11 02:18:13,525] multiqc [DEBUG ] No samples found: trimmomatic [2021-08-11 02:18:13,531] multiqc [DEBUG ] No samples found: sickle [2021-08-11 02:18:13,536] multiqc [DEBUG ] No samples found: skewer [2021-08-11 02:18:13,541] multiqc [DEBUG ] No samples found: sortmerna [2021-08-11 02:18:13,545] multiqc [DEBUG ] No samples found: biobloomtools [2021-08-11 02:18:13,551] multiqc [DEBUG ] No samples found: fastq_screen [2021-08-11 02:18:13,556] multiqc [DEBUG ] No samples found: afterqc [2021-08-11 02:18:13,561] multiqc [DEBUG ] No samples found: fastp [2021-08-11 02:18:13,948] multiqc.modules.fastqc.fastqc [INFO ] Found 5 reports [2021-08-11 02:18:14,077] multiqc [DEBUG ] No samples found: pycoqc [2021-08-11 02:18:14,082] multiqc [DEBUG ] No samples found: minionqc [2021-08-11 02:18:14,087] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-08-11 02:18:14,093] multiqc [DEBUG ] No samples found: clusterflow [2021-08-11 02:18:14,098] multiqc [DEBUG ] No samples found: bcl2fastq [2021-08-11 02:18:14,104] multiqc [DEBUG ] No samples found: interop [2021-08-11 02:18:14,110] multiqc [DEBUG ] No samples found: ivar [2021-08-11 02:18:14,115] multiqc [DEBUG ] No samples found: flash [2021-08-11 02:18:14,121] multiqc [DEBUG ] No samples found: seqyclean [2021-08-11 02:18:14,121] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-08-11 02:18:14,121] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-08-11 02:18:14,121] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-08-11 02:18:14,121] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-08-11 02:18:14,128] multiqc [INFO ] Compressing plot data [2021-08-11 02:18:14,234] multiqc [INFO ] Report : multiqc_report.html [2021-08-11 02:18:14,235] multiqc [INFO ] Data : multiqc_data [2021-08-11 02:18:14,235] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9305230/tmpwtispl_c/multiqc_data' to '/scratch/gencore/logs/html/HLT3MBGXJ/merged/multiqc_data' [2021-08-11 02:18:14,373] multiqc [INFO ] MultiQC complete