[2021-10-19 06:55:42,086] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-10-19 06:55:42,086] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-10-19 06:55:42,086] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-10-19 06:55:42,087] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-10-19 06:55:42,087] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-10-19 06:55:42,087] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H5HCLBGXK/merged [2021-10-19 06:55:43,573] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-10-19 06:55:43,574] multiqc [INFO ] This is MultiQC v1.9 [2021-10-19 06:55:43,574] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H5HCLBGXK/merged [2021-10-19 06:55:43,574] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H5HCLBGXK/merged [2021-10-19 06:55:43,574] multiqc [INFO ] Template : default [2021-10-19 06:55:43,574] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-10-19 06:55:43,574] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H5HCLBGXK/merged [2021-10-19 06:55:43,574] 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 [2021-10-19 06:55:43,574] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-10979589/tmp6e5jgyrp [2021-10-19 06:55:43,684] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-10-19 06:55:43,686] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-10-19 06:55:43,686] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-10-19 06:55:43,686] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-10-19 06:55:43,686] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-10-19 06:55:43,686] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-10-19 06:55:43,687] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-10-19 06:55:44,223] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5HCLBGXK_n01_chr20cas13hap1_R1_FTP__fastqc.html [2021-10-19 06:55:44,224] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5HCLBGXK_n01_chr20cas13hap1_R1_FTP__fastqc.html [2021-10-19 06:55:44,278] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5HCLBGXK_n01_circHEK_INP_R1__circHEK_INP_R2__circHEK_D7_R1__fastqc.html [2021-10-19 06:55:44,280] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5HCLBGXK_n01_circHEK_INP_R1__circHEK_INP_R2__circHEK_D7_R1__fastqc.html [2021-10-19 06:55:44,339] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5HCLBGXK_n01_lncHAP_INP_R1__lncHAP_INP_R2__lncHAP_D7_R1__fastqc.html [2021-10-19 06:55:44,341] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5HCLBGXK_n01_lncHAP_INP_R1__lncHAP_INP_R2__lncHAP_D7_R1__fastqc.html [2021-10-19 06:55:44,399] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5HCLBGXK_n01_undetermined_fastqc.html [2021-10-19 06:55:44,401] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5HCLBGXK_n01_undetermined_fastqc.html [2021-10-19 06:55:44,448] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5HCLBGXK_n01_circHEK_D7_R2__circHEK_D14_R1__circHEK_D14_R2__fastqc.html [2021-10-19 06:55:44,450] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5HCLBGXK_n01_circHEK_D7_R2__circHEK_D14_R1__circHEK_D14_R2__fastqc.html [2021-10-19 06:55:44,510] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5HCLBGXK_n01_lncHAP_D7_R2__lncHAP_D14_R1__lncHAP_D14_R2__fastqc.html [2021-10-19 06:55:44,511] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5HCLBGXK_n01_lncHAP_D7_R2__lncHAP_D14_R1__lncHAP_D14_R2__fastqc.html [2021-10-19 06:55:44,568] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5HCLBGXK_n01_circHAP_INP_R1__circHAP_INP_R2__circHAP_D7_R1__fastqc.html [2021-10-19 06:55:44,569] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5HCLBGXK_n01_circHAP_INP_R1__circHAP_INP_R2__circHAP_D7_R1__fastqc.html [2021-10-19 06:55:44,628] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5HCLBGXK_n01_eRNA_lib01__fastqc.html [2021-10-19 06:55:44,630] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5HCLBGXK_n01_eRNA_lib01__fastqc.html [2021-10-19 06:55:44,686] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5HCLBGXK_n01_chr20cas13hap1_R1_ETP__fastqc.html [2021-10-19 06:55:44,688] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5HCLBGXK_n01_chr20cas13hap1_R1_ETP__fastqc.html [2021-10-19 06:55:44,742] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5HCLBGXK_n01_circHAP_D7_R2__circHAP_D14_R1__circHAP_D14_R2__fastqc.html [2021-10-19 06:55:44,743] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5HCLBGXK_n01_circHAP_D7_R2__circHAP_D14_R1__circHAP_D14_R2__fastqc.html [2021-10-19 06:55:44,804] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5HCLBGXK_n01_lncHEK_D7_R2__lncHEK_D14_R1__lncHEK_D14_R2__fastqc.html [2021-10-19 06:55:44,805] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5HCLBGXK_n01_lncHEK_D7_R2__lncHEK_D14_R1__lncHEK_D14_R2__fastqc.html [2021-10-19 06:55:44,861] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5HCLBGXK_n01_chr20cas13hap1_R2_FTP__fastqc.html [2021-10-19 06:55:44,863] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5HCLBGXK_n01_chr20cas13hap1_R2_FTP__fastqc.html [2021-10-19 06:55:44,917] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5HCLBGXK_n01_chr20cas13hap1_R2_ETP__fastqc.html [2021-10-19 06:55:44,919] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5HCLBGXK_n01_chr20cas13hap1_R2_ETP__fastqc.html [2021-10-19 06:55:44,972] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5HCLBGXK_n01_lncHEK_INP_R1__lncHEK_INP_R2__lncHEK_D7_R1__fastqc.html [2021-10-19 06:55:44,974] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5HCLBGXK_n01_lncHEK_INP_R1__lncHEK_INP_R2__lncHEK_D7_R1__fastqc.html [2021-10-19 06:55:45,030] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5HCLBGXK_n01_eRNA_lib02__fastqc.html [2021-10-19 06:55:45,032] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5HCLBGXK_n01_eRNA_lib02__fastqc.html [2021-10-19 06:55:45,356] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-10-19 06:55:45,357] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-10-19 06:55:45,370] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 15 samples (table) [2021-10-19 06:55:45,380] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-10-19 06:55:45,381] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-10-19 06:55:45,386] multiqc [DEBUG ] No samples found: conpair [2021-10-19 06:55:45,391] multiqc [DEBUG ] No samples found: peddy [2021-10-19 06:55:45,396] multiqc [DEBUG ] No samples found: somalier [2021-10-19 06:55:45,401] multiqc [DEBUG ] No samples found: methylQA [2021-10-19 06:55:45,409] multiqc [DEBUG ] No samples found: mosdepth [2021-10-19 06:55:45,413] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-10-19 06:55:45,416] multiqc [DEBUG ] No samples found: qualimap [2021-10-19 06:55:45,421] multiqc [DEBUG ] No samples found: preseq [2021-10-19 06:55:45,426] multiqc [DEBUG ] No samples found: quast [2021-10-19 06:55:45,430] multiqc [DEBUG ] No samples found: qorts [2021-10-19 06:55:45,435] multiqc [DEBUG ] No samples found: rna_seqc [2021-10-19 06:55:45,439] multiqc [DEBUG ] No samples found: rockhopper [2021-10-19 06:55:45,444] multiqc [DEBUG ] No samples found: rsem [2021-10-19 06:55:45,453] multiqc [DEBUG ] No samples found: rseqc [2021-10-19 06:55:45,458] multiqc [DEBUG ] No samples found: busco [2021-10-19 06:55:45,462] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-10-19 06:55:45,467] multiqc [DEBUG ] No samples found: disambiguate [2021-10-19 06:55:45,472] multiqc [DEBUG ] No samples found: supernova [2021-10-19 06:55:45,484] multiqc [DEBUG ] No samples found: deeptools [2021-10-19 06:55:45,488] multiqc [DEBUG ] No samples found: sargasso [2021-10-19 06:55:45,493] multiqc [DEBUG ] No samples found: verifybamid [2021-10-19 06:55:45,498] multiqc [DEBUG ] No samples found: mirtrace [2021-10-19 06:55:45,503] multiqc [DEBUG ] No samples found: happy [2021-10-19 06:55:45,508] multiqc [DEBUG ] No samples found: mirtop [2021-10-19 06:55:45,513] multiqc [DEBUG ] No samples found: homer [2021-10-19 06:55:45,518] multiqc [DEBUG ] No samples found: macs2 [2021-10-19 06:55:45,522] multiqc [DEBUG ] No samples found: theta2 [2021-10-19 06:55:45,527] multiqc [DEBUG ] No samples found: snpeff [2021-10-19 06:55:45,534] multiqc [DEBUG ] No samples found: gatk [2021-10-19 06:55:45,538] multiqc [DEBUG ] No samples found: htseq [2021-10-19 06:55:45,544] multiqc [DEBUG ] No samples found: bcftools [2021-10-19 06:55:45,548] multiqc [DEBUG ] No samples found: featureCounts [2021-10-19 06:55:45,558] multiqc [DEBUG ] No samples found: fgbio [2021-10-19 06:55:45,570] multiqc [DEBUG ] No samples found: dragen [2021-10-19 06:55:45,574] multiqc [DEBUG ] No samples found: dedup [2021-10-19 06:55:45,580] multiqc [DEBUG ] No samples found: damageprofiler [2021-10-19 06:55:45,600] multiqc [DEBUG ] No samples found: biobambam2 [2021-10-19 06:55:45,605] multiqc [DEBUG ] No samples found: mtnucratio [2021-10-19 06:55:45,607] multiqc [DEBUG ] No samples found: picard [2021-10-19 06:55:45,611] multiqc [DEBUG ] No samples found: prokka [2021-10-19 06:55:45,615] multiqc [DEBUG ] No samples found: samblaster [2021-10-19 06:55:45,623] multiqc [DEBUG ] No samples found: samtools [2021-10-19 06:55:45,628] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-10-19 06:55:45,632] multiqc [DEBUG ] No samples found: bamtools [2021-10-19 06:55:45,637] multiqc [DEBUG ] No samples found: jellyfish [2021-10-19 06:55:45,643] multiqc [DEBUG ] No samples found: vcftools [2021-10-19 06:55:45,648] multiqc [DEBUG ] No samples found: longranger [2021-10-19 06:55:45,653] multiqc [DEBUG ] No samples found: stacks [2021-10-19 06:55:45,657] multiqc [DEBUG ] No samples found: varscan2 [2021-10-19 06:55:45,669] multiqc [DEBUG ] No samples found: bbmap [2021-10-19 06:55:45,674] multiqc [DEBUG ] No samples found: bismark [2021-10-19 06:55:45,679] multiqc [DEBUG ] No samples found: biscuit [2021-10-19 06:55:45,684] multiqc [DEBUG ] No samples found: hicexplorer [2021-10-19 06:55:45,688] multiqc [DEBUG ] No samples found: hicup [2021-10-19 06:55:45,693] multiqc [DEBUG ] No samples found: hicpro [2021-10-19 06:55:45,697] multiqc [DEBUG ] No samples found: salmon [2021-10-19 06:55:45,702] multiqc [DEBUG ] No samples found: kallisto [2021-10-19 06:55:45,707] multiqc [DEBUG ] No samples found: slamdunk [2021-10-19 06:55:45,711] multiqc [DEBUG ] No samples found: star [2021-10-19 06:55:45,716] multiqc [DEBUG ] No samples found: hisat2 [2021-10-19 06:55:45,720] multiqc [DEBUG ] No samples found: tophat [2021-10-19 06:55:45,724] multiqc [DEBUG ] No samples found: bowtie2 [2021-10-19 06:55:45,729] multiqc [DEBUG ] No samples found: bowtie1 [2021-10-19 06:55:45,733] multiqc [DEBUG ] No samples found: snpsplit [2021-10-19 06:55:45,738] multiqc [DEBUG ] No samples found: kat [2021-10-19 06:55:45,742] multiqc [DEBUG ] No samples found: leehom [2021-10-19 06:55:45,746] multiqc [DEBUG ] No samples found: adapterRemoval [2021-10-19 06:55:45,750] multiqc [DEBUG ] No samples found: clipandmerge [2021-10-19 06:55:45,754] multiqc [DEBUG ] No samples found: cutadapt [2021-10-19 06:55:45,759] multiqc [DEBUG ] No samples found: flexbar [2021-10-19 06:55:45,763] multiqc [DEBUG ] No samples found: kaiju [2021-10-19 06:55:45,768] multiqc [DEBUG ] No samples found: kraken [2021-10-19 06:55:45,773] multiqc [DEBUG ] No samples found: malt [2021-10-19 06:55:45,777] multiqc [DEBUG ] No samples found: trimmomatic [2021-10-19 06:55:45,781] multiqc [DEBUG ] No samples found: sickle [2021-10-19 06:55:45,786] multiqc [DEBUG ] No samples found: skewer [2021-10-19 06:55:45,790] multiqc [DEBUG ] No samples found: sortmerna [2021-10-19 06:55:45,794] multiqc [DEBUG ] No samples found: biobloomtools [2021-10-19 06:55:45,798] multiqc [DEBUG ] No samples found: fastq_screen [2021-10-19 06:55:45,803] multiqc [DEBUG ] No samples found: afterqc [2021-10-19 06:55:45,808] multiqc [DEBUG ] No samples found: fastp [2021-10-19 06:55:46,714] multiqc.modules.fastqc.fastqc [INFO ] Found 15 reports [2021-10-19 06:55:46,844] multiqc [DEBUG ] No samples found: pycoqc [2021-10-19 06:55:46,848] multiqc [DEBUG ] No samples found: minionqc [2021-10-19 06:55:46,853] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-10-19 06:55:46,858] multiqc [DEBUG ] No samples found: clusterflow [2021-10-19 06:55:46,863] multiqc [DEBUG ] No samples found: bcl2fastq [2021-10-19 06:55:46,867] multiqc [DEBUG ] No samples found: interop [2021-10-19 06:55:46,872] multiqc [DEBUG ] No samples found: ivar [2021-10-19 06:55:46,877] multiqc [DEBUG ] No samples found: flash [2021-10-19 06:55:46,881] multiqc [DEBUG ] No samples found: seqyclean [2021-10-19 06:55:46,881] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-10-19 06:55:46,881] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-10-19 06:55:46,881] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-10-19 06:55:46,881] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-10-19 06:55:46,899] multiqc [INFO ] Compressing plot data [2021-10-19 06:55:47,123] multiqc [INFO ] Report : multiqc_report.html [2021-10-19 06:55:47,123] multiqc [INFO ] Data : multiqc_data [2021-10-19 06:55:47,123] multiqc [DEBUG ] Moving data file from '/state/partition1/job-10979589/tmp6e5jgyrp/multiqc_data' to '/scratch/gencore/logs/html/H5HCLBGXK/merged/multiqc_data' [2021-10-19 06:55:47,274] multiqc [INFO ] MultiQC complete