[2023-01-25 03:08:02,056] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-01-25 03:08:02,056] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-01-25 03:08:02,056] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-01-25 03:08:02,059] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-01-25 03:08:02,059] multiqc [DEBUG ] New config 'report_section_order': {'general_stats': {'order': 1000}, 'demux_report': {'order': 900}, 'demux_report-1': {'order': 900}, 'demux_report-2': {'order': 900}, 'undetermined_barcodes': {'order': 800}, 'run_stats': {'order': 700}, 'fastqc': {'order': 500}} [2023-01-25 03:08:02,060] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H3TCYAFX5/merged [2023-01-25 03:08:02,782] multiqc [WARNING] MultiQC Version v1.14 now available! [2023-01-25 03:08:02,782] multiqc [INFO ] This is MultiQC v1.9 [2023-01-25 03:08:02,782] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H3TCYAFX5/merged [2023-01-25 03:08:02,782] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H3TCYAFX5/merged [2023-01-25 03:08:02,782] multiqc [INFO ] Template : default [2023-01-25 03:08:02,782] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-01-25 03:08:02,782] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H3TCYAFX5/merged [2023-01-25 03:08:02,783] 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 [2023-01-25 03:08:02,783] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-29505301/tmpfv12zxz4 [2023-01-25 03:08:02,895] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3TCYAFX5_2_fastqc.html [2023-01-25 03:08:02,898] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3TCYAFX5_2_fastqc.html [2023-01-25 03:08:02,949] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3TCYAFX5_4_fastqc.html [2023-01-25 03:08:02,951] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3TCYAFX5_4_fastqc.html [2023-01-25 03:08:02,993] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3TCYAFX5_3_fastqc.html [2023-01-25 03:08:02,995] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3TCYAFX5_3_fastqc.html [2023-01-25 03:08:03,038] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3TCYAFX5_1_fastqc.html [2023-01-25 03:08:03,039] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3TCYAFX5_1_fastqc.html [2023-01-25 03:08:03,596] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-01-25 03:08:03,598] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-01-25 03:08:03,603] multiqc.modules.custom_content.custom_content [WARNING] Not able to parse custom data in undetermined_barcodes_mqc.txt [2023-01-25 03:08:03,605] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-01-25 03:08:03,610] multiqc [DEBUG ] No samples found: conpair [2023-01-25 03:08:03,616] multiqc [DEBUG ] No samples found: peddy [2023-01-25 03:08:03,621] multiqc [DEBUG ] No samples found: somalier [2023-01-25 03:08:03,626] multiqc [DEBUG ] No samples found: methylQA [2023-01-25 03:08:03,635] multiqc [DEBUG ] No samples found: mosdepth [2023-01-25 03:08:03,640] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-01-25 03:08:03,644] multiqc [DEBUG ] No samples found: qualimap [2023-01-25 03:08:03,649] multiqc [DEBUG ] No samples found: preseq [2023-01-25 03:08:03,655] multiqc [DEBUG ] No samples found: quast [2023-01-25 03:08:03,661] multiqc [DEBUG ] No samples found: qorts [2023-01-25 03:08:03,666] multiqc [DEBUG ] No samples found: rna_seqc [2023-01-25 03:08:03,672] multiqc [DEBUG ] No samples found: rockhopper [2023-01-25 03:08:03,677] multiqc [DEBUG ] No samples found: rsem [2023-01-25 03:08:03,690] multiqc [DEBUG ] No samples found: rseqc [2023-01-25 03:08:03,695] multiqc [DEBUG ] No samples found: busco [2023-01-25 03:08:03,701] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-01-25 03:08:03,706] multiqc [DEBUG ] No samples found: disambiguate [2023-01-25 03:08:03,712] multiqc [DEBUG ] No samples found: supernova [2023-01-25 03:08:03,731] multiqc [DEBUG ] No samples found: deeptools [2023-01-25 03:08:03,737] multiqc [DEBUG ] No samples found: sargasso [2023-01-25 03:08:03,744] multiqc [DEBUG ] No samples found: verifybamid [2023-01-25 03:08:03,749] multiqc [DEBUG ] No samples found: mirtrace [2023-01-25 03:08:03,755] multiqc [DEBUG ] No samples found: happy [2023-01-25 03:08:03,761] multiqc [DEBUG ] No samples found: mirtop [2023-01-25 03:08:03,769] multiqc [DEBUG ] No samples found: homer [2023-01-25 03:08:03,774] multiqc [DEBUG ] No samples found: macs2 [2023-01-25 03:08:03,779] multiqc [DEBUG ] No samples found: theta2 [2023-01-25 03:08:03,784] multiqc [DEBUG ] No samples found: snpeff [2023-01-25 03:08:03,792] multiqc [DEBUG ] No samples found: gatk [2023-01-25 03:08:03,797] multiqc [DEBUG ] No samples found: htseq [2023-01-25 03:08:03,804] multiqc [DEBUG ] No samples found: bcftools [2023-01-25 03:08:03,810] multiqc [DEBUG ] No samples found: featureCounts [2023-01-25 03:08:03,817] multiqc [DEBUG ] No samples found: fgbio [2023-01-25 03:08:03,834] multiqc [DEBUG ] No samples found: dragen [2023-01-25 03:08:03,839] multiqc [DEBUG ] No samples found: dedup [2023-01-25 03:08:03,845] multiqc [DEBUG ] No samples found: damageprofiler [2023-01-25 03:08:03,872] multiqc [DEBUG ] No samples found: biobambam2 [2023-01-25 03:08:03,879] multiqc [DEBUG ] No samples found: mtnucratio [2023-01-25 03:08:03,881] multiqc [DEBUG ] No samples found: picard [2023-01-25 03:08:03,886] multiqc [DEBUG ] No samples found: prokka [2023-01-25 03:08:03,891] multiqc [DEBUG ] No samples found: samblaster [2023-01-25 03:08:03,904] multiqc [DEBUG ] No samples found: samtools [2023-01-25 03:08:03,909] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-01-25 03:08:03,915] multiqc [DEBUG ] No samples found: bamtools [2023-01-25 03:08:03,920] multiqc [DEBUG ] No samples found: jellyfish [2023-01-25 03:08:03,930] multiqc [DEBUG ] No samples found: vcftools [2023-01-25 03:08:03,936] multiqc [DEBUG ] No samples found: longranger [2023-01-25 03:08:03,942] multiqc [DEBUG ] No samples found: stacks [2023-01-25 03:08:03,947] multiqc [DEBUG ] No samples found: varscan2 [2023-01-25 03:08:03,965] multiqc [DEBUG ] No samples found: bbmap [2023-01-25 03:08:03,970] multiqc [DEBUG ] No samples found: bismark [2023-01-25 03:08:03,976] multiqc [DEBUG ] No samples found: biscuit [2023-01-25 03:08:03,982] multiqc [DEBUG ] No samples found: hicexplorer [2023-01-25 03:08:03,987] multiqc [DEBUG ] No samples found: hicup [2023-01-25 03:08:03,993] multiqc [DEBUG ] No samples found: hicpro [2023-01-25 03:08:03,997] multiqc [DEBUG ] No samples found: salmon [2023-01-25 03:08:04,002] multiqc [DEBUG ] No samples found: kallisto [2023-01-25 03:08:04,008] multiqc [DEBUG ] No samples found: slamdunk [2023-01-25 03:08:04,013] multiqc [DEBUG ] No samples found: star [2023-01-25 03:08:04,018] multiqc [DEBUG ] No samples found: hisat2 [2023-01-25 03:08:04,023] multiqc [DEBUG ] No samples found: tophat [2023-01-25 03:08:04,029] multiqc [DEBUG ] No samples found: bowtie2 [2023-01-25 03:08:04,042] multiqc [DEBUG ] No samples found: bowtie1 [2023-01-25 03:08:04,049] multiqc [DEBUG ] No samples found: snpsplit [2023-01-25 03:08:04,053] multiqc [DEBUG ] No samples found: kat [2023-01-25 03:08:04,058] multiqc [DEBUG ] No samples found: leehom [2023-01-25 03:08:04,063] multiqc [DEBUG ] No samples found: adapterRemoval [2023-01-25 03:08:04,068] multiqc [DEBUG ] No samples found: clipandmerge [2023-01-25 03:08:04,073] multiqc [DEBUG ] No samples found: cutadapt [2023-01-25 03:08:04,077] multiqc [DEBUG ] No samples found: flexbar [2023-01-25 03:08:04,083] multiqc [DEBUG ] No samples found: kaiju [2023-01-25 03:08:04,088] multiqc [DEBUG ] No samples found: kraken [2023-01-25 03:08:04,093] multiqc [DEBUG ] No samples found: malt [2023-01-25 03:08:04,098] multiqc [DEBUG ] No samples found: trimmomatic [2023-01-25 03:08:04,102] multiqc [DEBUG ] No samples found: sickle [2023-01-25 03:08:04,108] multiqc [DEBUG ] No samples found: skewer [2023-01-25 03:08:04,112] multiqc [DEBUG ] No samples found: sortmerna [2023-01-25 03:08:04,117] multiqc [DEBUG ] No samples found: biobloomtools [2023-01-25 03:08:04,122] multiqc [DEBUG ] No samples found: fastq_screen [2023-01-25 03:08:04,127] multiqc [DEBUG ] No samples found: afterqc [2023-01-25 03:08:04,132] multiqc [DEBUG ] No samples found: fastp [2023-01-25 03:08:04,193] multiqc.modules.fastqc.fastqc [INFO ] Found 4 reports [2023-01-25 03:08:04,246] multiqc [DEBUG ] No samples found: pycoqc [2023-01-25 03:08:04,251] multiqc [DEBUG ] No samples found: minionqc [2023-01-25 03:08:04,256] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-01-25 03:08:04,261] multiqc [DEBUG ] No samples found: clusterflow [2023-01-25 03:08:04,266] multiqc [DEBUG ] No samples found: bcl2fastq [2023-01-25 03:08:04,272] multiqc [DEBUG ] No samples found: interop [2023-01-25 03:08:04,277] multiqc [DEBUG ] No samples found: ivar [2023-01-25 03:08:04,282] multiqc [DEBUG ] No samples found: flash [2023-01-25 03:08:04,287] multiqc [DEBUG ] No samples found: seqyclean [2023-01-25 03:08:04,288] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-01-25 03:08:04,288] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2023-01-25 03:08:04,288] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-01-25 03:08:04,288] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-01-25 03:08:04,288] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found. [2023-01-25 03:08:04,288] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-01-25 03:08:04,288] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-01-25 03:08:04,288] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-01-25 03:08:04,288] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-01-25 03:08:04,288] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-01-25 03:08:04,288] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-01-25 03:08:04,288] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-01-25 03:08:04,288] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-01-25 03:08:04,288] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-01-25 03:08:04,288] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-01-25 03:08:04,288] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-01-25 03:08:04,288] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-01-25 03:08:04,288] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-01-25 03:08:04,288] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-01-25 03:08:04,295] multiqc [INFO ] Compressing plot data [2023-01-25 03:08:04,360] multiqc [INFO ] Report : multiqc_report.html [2023-01-25 03:08:04,360] multiqc [INFO ] Data : multiqc_data [2023-01-25 03:08:04,360] multiqc [DEBUG ] Moving data file from '/state/partition1/job-29505301/tmpfv12zxz4/multiqc_data' to '/scratch/gencore/logs/html/H3TCYAFX5/merged/multiqc_data' [2023-01-25 03:08:04,504] multiqc [INFO ] MultiQC complete