[2024-04-21 09:50:43,857] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-04-21 09:50:43,857] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-04-21 09:50:43,858] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-04-21 09:50:43,860] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-04-21 09:50:43,861] 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}} [2024-04-21 09:50:43,861] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-04-21 09:50:43,892] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-04-21 09:50:43,893] multiqc [INFO ] This is MultiQC v1.9 [2024-04-21 09:50:43,893] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-04-21 09:50:43,893] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/7d/3cdca5a98451079f5294d137cbc57d/4 [2024-04-21 09:50:43,893] multiqc [INFO ] Template : default [2024-04-21 09:50:43,893] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-04-21 09:50:43,893] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/7d/3cdca5a98451079f5294d137cbc57d/4 [2024-04-21 09:50:43,893] 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 [2024-04-21 09:50:43,893] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-45453540/tmpiwpyna02 [2024-04-21 09:50:44,027] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3WG2DSXC_l04_n01_10G_1-12_NEB_fastqc.html [2024-04-21 09:50:44,034] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3WG2DSXC_l04_n01_10G_1-12_NEB_fastqc.html [2024-04-21 09:50:44,109] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 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[DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3WG2DSXC_l04_n02_8G_1-12_NEB_fastqc.html [2024-04-21 09:50:55,090] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3WG2DSXC_l04_n02_8G_1-2_NEB_fastqc.html [2024-04-21 09:50:55,096] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3WG2DSXC_l04_n02_8G_1-2_NEB_fastqc.html [2024-04-21 09:50:55,160] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3WG2DSXC_l04_n02_8G_1-8_NEB_fastqc.html [2024-04-21 09:50:55,167] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3WG2DSXC_l04_n02_8G_1-8_NEB_fastqc.html [2024-04-21 09:50:55,231] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3WG2DSXC_l04_n02_8R_1-12_NEB_fastqc.html [2024-04-21 09:50:55,238] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3WG2DSXC_l04_n02_8R_1-12_NEB_fastqc.html [2024-04-21 09:50:55,302] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3WG2DSXC_l04_n02_8R_1-2_NEB_fastqc.html [2024-04-21 09:50:55,309] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3WG2DSXC_l04_n02_8R_1-2_NEB_fastqc.html [2024-04-21 09:50:55,372] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3WG2DSXC_l04_n02_8R_1-8_NEB_fastqc.html [2024-04-21 09:50:55,379] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3WG2DSXC_l04_n02_8R_1-8_NEB_fastqc.html [2024-04-21 09:50:55,444] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3WG2DSXC_l04_n02_9G_1-12_NEB_fastqc.html [2024-04-21 09:50:55,452] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3WG2DSXC_l04_n02_9G_1-12_NEB_fastqc.html [2024-04-21 09:50:55,519] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3WG2DSXC_l04_n02_9G_1-2_NEB_fastqc.html [2024-04-21 09:50:55,526] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3WG2DSXC_l04_n02_9G_1-2_NEB_fastqc.html [2024-04-21 09:50:55,591] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3WG2DSXC_l04_n02_9G_1-8_NEB_fastqc.html [2024-04-21 09:50:55,598] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3WG2DSXC_l04_n02_9G_1-8_NEB_fastqc.html [2024-04-21 09:50:55,662] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3WG2DSXC_l04_n02_9R_1-12_NEB_fastqc.html [2024-04-21 09:50:55,669] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3WG2DSXC_l04_n02_9R_1-12_NEB_fastqc.html [2024-04-21 09:50:55,734] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3WG2DSXC_l04_n02_9R_1-2_NEB_fastqc.html [2024-04-21 09:50:55,740] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3WG2DSXC_l04_n02_9R_1-2_NEB_fastqc.html [2024-04-21 09:50:55,805] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3WG2DSXC_l04_n02_9R_1-8_NEB_fastqc.html [2024-04-21 09:50:55,812] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3WG2DSXC_l04_n02_9R_1-8_NEB_fastqc.html [2024-04-21 09:50:55,880] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3WG2DSXC_l04_n02_undetermined_fastqc.html [2024-04-21 09:50:55,886] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3WG2DSXC_l04_n02_undetermined_fastqc.html [2024-04-21 09:50:55,946] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-04-21 09:50:55,953] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-04-21 09:50:55,953] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-04-21 09:50:55,953] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-04-21 09:50:55,953] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-04-21 09:50:55,953] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-04-21 09:50:55,953] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-04-21 09:50:55,978] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-04-21 09:50:57,448] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-04-21 09:50:57,450] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-04-21 09:50:57,496] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 82 samples (table) [2024-04-21 09:50:57,498] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-04-21 09:50:57,507] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-04-21 09:50:57,512] multiqc [DEBUG ] No samples found: conpair [2024-04-21 09:50:57,517] multiqc [DEBUG ] No samples found: peddy [2024-04-21 09:50:57,522] multiqc [DEBUG ] No samples found: somalier [2024-04-21 09:50:57,526] multiqc [DEBUG ] No samples found: methylQA [2024-04-21 09:50:57,534] multiqc [DEBUG ] No samples found: mosdepth [2024-04-21 09:50:57,538] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-04-21 09:50:57,542] multiqc [DEBUG ] No samples found: qualimap [2024-04-21 09:50:57,547] multiqc [DEBUG ] No samples found: preseq [2024-04-21 09:50:57,551] multiqc [DEBUG ] No samples found: quast [2024-04-21 09:50:57,556] multiqc [DEBUG ] No samples found: qorts [2024-04-21 09:50:57,561] multiqc [DEBUG ] No samples found: rna_seqc [2024-04-21 09:50:57,565] multiqc [DEBUG ] No samples found: rockhopper [2024-04-21 09:50:57,570] multiqc [DEBUG ] No samples found: rsem [2024-04-21 09:50:57,581] multiqc [DEBUG ] No samples found: rseqc [2024-04-21 09:50:57,585] multiqc [DEBUG ] No samples found: busco [2024-04-21 09:50:57,590] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-04-21 09:50:57,594] multiqc [DEBUG ] No samples found: disambiguate [2024-04-21 09:50:57,599] multiqc [DEBUG ] No samples found: supernova [2024-04-21 09:50:57,613] multiqc [DEBUG ] No samples found: deeptools [2024-04-21 09:50:57,618] multiqc [DEBUG ] No samples found: sargasso [2024-04-21 09:50:57,623] multiqc [DEBUG ] No samples found: verifybamid [2024-04-21 09:50:57,628] multiqc [DEBUG ] No samples found: mirtrace [2024-04-21 09:50:57,633] multiqc [DEBUG ] No samples found: happy [2024-04-21 09:50:57,638] multiqc [DEBUG ] No samples found: mirtop [2024-04-21 09:50:57,645] multiqc [DEBUG ] No samples found: homer [2024-04-21 09:50:57,650] multiqc [DEBUG ] No samples found: macs2 [2024-04-21 09:50:57,654] multiqc [DEBUG ] No samples found: theta2 [2024-04-21 09:50:57,659] multiqc [DEBUG ] No samples found: snpeff [2024-04-21 09:50:57,667] multiqc [DEBUG ] No samples found: gatk [2024-04-21 09:50:57,671] multiqc [DEBUG ] No samples found: htseq [2024-04-21 09:50:57,677] multiqc [DEBUG ] No samples found: bcftools [2024-04-21 09:50:57,682] multiqc [DEBUG ] No samples found: featureCounts [2024-04-21 09:50:57,688] multiqc [DEBUG ] No samples found: fgbio [2024-04-21 09:50:57,702] multiqc [DEBUG ] No samples found: dragen [2024-04-21 09:50:57,707] multiqc [DEBUG ] No samples found: dedup [2024-04-21 09:50:57,711] multiqc [DEBUG ] No samples found: damageprofiler [2024-04-21 09:50:57,734] multiqc [DEBUG ] No samples found: biobambam2 [2024-04-21 09:50:57,738] multiqc [DEBUG ] No samples found: mtnucratio [2024-04-21 09:50:57,741] multiqc [DEBUG ] No samples found: picard [2024-04-21 09:50:57,745] multiqc [DEBUG ] No samples found: prokka [2024-04-21 09:50:57,749] multiqc [DEBUG ] No samples found: samblaster [2024-04-21 09:50:57,759] multiqc [DEBUG ] No samples found: samtools [2024-04-21 09:50:57,764] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-04-21 09:50:57,768] multiqc [DEBUG ] No samples found: bamtools [2024-04-21 09:50:57,773] multiqc [DEBUG ] No samples found: jellyfish [2024-04-21 09:50:57,781] multiqc [DEBUG ] No samples found: vcftools [2024-04-21 09:50:57,786] multiqc [DEBUG ] No samples found: longranger [2024-04-21 09:50:57,790] multiqc [DEBUG ] No samples found: stacks [2024-04-21 09:50:57,795] multiqc [DEBUG ] No samples found: varscan2 [2024-04-21 09:50:57,808] multiqc [DEBUG ] No samples found: bbmap [2024-04-21 09:50:57,813] multiqc [DEBUG ] No samples found: bismark [2024-04-21 09:50:57,818] multiqc [DEBUG ] No samples found: biscuit [2024-04-21 09:50:57,823] multiqc [DEBUG ] No samples found: hicexplorer [2024-04-21 09:50:57,828] multiqc [DEBUG ] No samples found: hicup [2024-04-21 09:50:57,832] multiqc [DEBUG ] No samples found: hicpro [2024-04-21 09:50:57,837] multiqc [DEBUG ] No samples found: salmon [2024-04-21 09:50:57,841] multiqc [DEBUG ] No samples found: kallisto [2024-04-21 09:50:57,846] multiqc [DEBUG ] No samples found: slamdunk [2024-04-21 09:50:57,851] multiqc [DEBUG ] No samples found: star [2024-04-21 09:50:57,855] multiqc [DEBUG ] No samples found: hisat2 [2024-04-21 09:50:57,860] multiqc [DEBUG ] No samples found: tophat [2024-04-21 09:50:57,864] multiqc [DEBUG ] No samples found: bowtie2 [2024-04-21 09:50:57,869] multiqc [DEBUG ] No samples found: bowtie1 [2024-04-21 09:50:57,873] multiqc [DEBUG ] No samples found: snpsplit [2024-04-21 09:50:57,878] multiqc [DEBUG ] No samples found: kat [2024-04-21 09:50:57,882] multiqc [DEBUG ] No samples found: leehom [2024-04-21 09:50:57,887] multiqc [DEBUG ] No samples found: adapterRemoval [2024-04-21 09:50:57,891] multiqc [DEBUG ] No samples found: clipandmerge [2024-04-21 09:50:57,896] multiqc [DEBUG ] No samples found: cutadapt [2024-04-21 09:50:57,900] multiqc [DEBUG ] No samples found: flexbar [2024-04-21 09:50:57,905] multiqc [DEBUG ] No samples found: kaiju [2024-04-21 09:50:57,909] multiqc [DEBUG ] No samples found: kraken [2024-04-21 09:50:57,914] multiqc [DEBUG ] No samples found: malt [2024-04-21 09:50:57,918] multiqc [DEBUG ] No samples found: trimmomatic [2024-04-21 09:50:57,923] multiqc [DEBUG ] No samples found: sickle [2024-04-21 09:50:57,927] multiqc [DEBUG ] No samples found: skewer [2024-04-21 09:50:57,932] multiqc [DEBUG ] No samples found: sortmerna [2024-04-21 09:50:57,936] multiqc [DEBUG ] No samples found: biobloomtools [2024-04-21 09:50:57,941] multiqc [DEBUG ] No samples found: fastq_screen [2024-04-21 09:50:57,945] multiqc [DEBUG ] No samples found: afterqc [2024-04-21 09:50:57,950] multiqc [DEBUG ] No samples found: fastp [2024-04-21 09:51:29,348] multiqc.modules.fastqc.fastqc [INFO ] Found 164 reports [2024-04-21 09:51:49,203] multiqc [DEBUG ] No samples found: pycoqc [2024-04-21 09:51:49,207] multiqc [DEBUG ] No samples found: minionqc [2024-04-21 09:51:49,212] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-04-21 09:51:49,216] multiqc [DEBUG ] No samples found: clusterflow [2024-04-21 09:51:49,221] multiqc [DEBUG ] No samples found: bcl2fastq [2024-04-21 09:51:49,226] multiqc [DEBUG ] No samples found: interop [2024-04-21 09:51:49,230] multiqc [DEBUG ] No samples found: ivar [2024-04-21 09:51:49,235] multiqc [DEBUG ] No samples found: flash [2024-04-21 09:51:49,239] multiqc [DEBUG ] No samples found: seqyclean [2024-04-21 09:51:49,239] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-04-21 09:51:49,239] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-04-21 09:51:49,239] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-04-21 09:51:49,239] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-04-21 09:51:49,239] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-04-21 09:51:49,239] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-04-21 09:51:49,239] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-04-21 09:51:49,239] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-04-21 09:51:49,239] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-04-21 09:51:49,239] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-04-21 09:51:49,239] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-04-21 09:51:49,239] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-04-21 09:51:49,239] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-04-21 09:51:49,240] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-04-21 09:51:49,240] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-04-21 09:51:49,240] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-04-21 09:51:49,240] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-04-21 09:51:49,240] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-04-21 09:51:49,240] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-04-21 09:51:49,240] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-04-21 09:51:49,240] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-04-21 09:51:49,240] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-04-21 09:51:49,240] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-04-21 09:51:49,240] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-04-21 09:51:49,240] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-04-21 09:51:49,240] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-04-21 09:51:49,240] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-04-21 09:51:49,240] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-04-21 09:51:49,240] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-04-21 09:51:49,240] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-04-21 09:51:49,430] multiqc [INFO ] Compressing plot data [2024-04-21 09:51:49,527] multiqc [INFO ] Report : multiqc_report.html [2024-04-21 09:51:49,527] multiqc [INFO ] Data : multiqc_data [2024-04-21 09:51:49,527] multiqc [DEBUG ] Moving data file from '/state/partition1/job-45453540/tmpiwpyna02/multiqc_data' to '/vast/gencore/GENEFLOW/work/7d/3cdca5a98451079f5294d137cbc57d/4/multiqc_data' [2024-04-21 09:51:49,756] multiqc [INFO ] MultiQC complete