[2020-12-02 08:47:31,771] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/20170330/intel/lib/python2.7/site-packages/multiqc-1.0.dev0-py2.7.egg/multiqc_config.yaml [2020-12-02 08:47:31,772] multiqc [DEBUG ] No MultiQC config found: /home/mk5636/.multiqc_config.yaml [2020-12-02 08:47:31,772] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2020-12-02 08:47:31,785] multiqc [DEBUG ] Loading config settings from: /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml [2020-12-02 08:47:31,785] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2020-12-02 08:47:31,786] multiqc [DEBUG ] Command used: /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/HTW7MBGXG/merged [2020-12-02 08:47:31,786] multiqc [DEBUG ] Could not connect to multiqc.info for version check [2020-12-02 08:47:31,786] multiqc [INFO ] This is MultiQC v1.0.dev0 [2020-12-02 08:47:31,786] multiqc [DEBUG ] Command : /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/HTW7MBGXG/merged [2020-12-02 08:47:31,786] multiqc [DEBUG ] Working dir : /beegfs/mk5636/logs/html/HTW7MBGXG/merged [2020-12-02 08:47:31,786] multiqc [INFO ] Template : default [2020-12-02 08:47:31,786] multiqc [DEBUG ] Running in --force mode, will overwrite any existing reports. [2020-12-02 08:47:31,786] multiqc [INFO ] Searching '/beegfs/mk5636/logs/html/HTW7MBGXG/merged' [2020-12-02 08:47:31,786] multiqc [DEBUG ] Analysing modules: rna_seqc, custom_content, peddy, methylQA, qualimap, preseq, quast, rseqc, busco, goleft_indexcov, snpeff, gatk, htseq, bcftools, featureCounts, picard, prokka, samblaster, samtools, bamtools, bismark, hicup, salmon, kallisto, slamdunk, star, tophat, bowtie2, bowtie1, cutadapt, trimmomatic, skewer, fastq_screen, fastqc, clusterflow [2020-12-02 08:47:31,786] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-14009463/tmpEmIk2I [2020-12-02 08:47:31,822] multiqc [DEBUG ] Ignoring file as too large: undetermined_barcodes.txt [2020-12-02 08:47:32,370] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('/beegfs/mk5636/logs/html/HTW7MBGXG/merged',) [2020-12-02 08:47:32,429] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 64 samples (table) [2020-12-02 08:47:32,436] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2020-12-02 08:47:32,437] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2020-12-02 08:47:32,463] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HTW7MBGXG/merged',) [2020-12-02 08:47:32,474] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HTW7MBGXG/merged',) [2020-12-02 08:47:32,482] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2020-12-02 08:47:32,512] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HTW7MBGXG/merged',) [2020-12-02 08:47:34,636] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('/beegfs/mk5636/logs/html/HTW7MBGXG/merged',) [2020-12-02 08:47:34,648] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HTW7MBGXG/merged',) [2020-12-02 08:47:35,755] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HTW7MBGXG/merged',) [2020-12-02 08:47:35,767] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HTW7MBGXG/merged',) [2020-12-02 08:47:35,783] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('/beegfs/mk5636/logs/html/HTW7MBGXG/merged',) [2020-12-02 08:47:36,059] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HTW7MBGXG/merged',) [2020-12-02 08:47:36,336] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HTW7MBGXG/merged',) [2020-12-02 08:47:36,608] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HTW7MBGXG/merged',) [2020-12-02 08:47:36,881] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HTW7MBGXG/merged',) [2020-12-02 08:47:36,892] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HTW7MBGXG/merged',) [2020-12-02 08:47:39,618] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HTW7MBGXG/merged',) [2020-12-02 08:47:39,632] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('/beegfs/mk5636/logs/html/HTW7MBGXG/merged',) [2020-12-02 08:47:39,907] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HTW7MBGXG/merged',) [2020-12-02 08:47:40,721] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HTW7MBGXG/merged',) [2020-12-02 08:47:40,993] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HTW7MBGXG/merged',) [2020-12-02 08:47:41,025] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HTW7MBGXG/merged',) [2020-12-02 08:47:41,036] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('/beegfs/mk5636/logs/html/HTW7MBGXG/merged',) [2020-12-02 08:47:41,052] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('/beegfs/mk5636/logs/html/HTW7MBGXG/merged',) [2020-12-02 08:47:41,322] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HTW7MBGXG/merged',) [2020-12-02 08:47:42,932] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2020-12-02 08:47:42,948] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HTW7MBGXG/merged',) [2020-12-02 08:47:42,959] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HTW7MBGXG/merged',) [2020-12-02 08:47:43,231] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HTW7MBGXG/merged',) [2020-12-02 08:47:43,503] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HTW7MBGXG/merged',) [2020-12-02 08:47:43,779] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HTW7MBGXG/merged',) [2020-12-02 08:47:44,054] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('/beegfs/mk5636/logs/html/HTW7MBGXG/merged',) [2020-12-02 08:47:44,326] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HTW7MBGXG/merged',) [2020-12-02 08:47:44,337] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HTW7MBGXG/merged',) [2020-12-02 08:48:00,164] multiqc.modules.fastqc.fastqc [INFO ] Found 64 reports [2020-12-02 08:48:04,154] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HTW7MBGXG/merged',) [2020-12-02 08:48:04,212] multiqc [INFO ] Report : multiqc_report.html [2020-12-02 08:48:04,213] multiqc [INFO ] Data : multiqc_data [2020-12-02 08:48:04,213] multiqc [DEBUG ] Moving data file from '/state/partition1/job-14009463/tmpEmIk2I/multiqc_data/multiqc_fastqc.txt' to '/beegfs/mk5636/logs/html/HTW7MBGXG/merged/multiqc_data' [2020-12-02 08:48:04,216] multiqc [DEBUG ] Moving data file from '/state/partition1/job-14009463/tmpEmIk2I/multiqc_data/multiqc_general_stats.txt' to '/beegfs/mk5636/logs/html/HTW7MBGXG/merged/multiqc_data' [2020-12-02 08:48:04,218] multiqc [DEBUG ] Moving data file from '/state/partition1/job-14009463/tmpEmIk2I/multiqc_data/multiqc_sources.txt' to '/beegfs/mk5636/logs/html/HTW7MBGXG/merged/multiqc_data' [2020-12-02 08:48:04,358] multiqc [INFO ] MultiQC complete