[2020-01-23 12:07:03,998] 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 [2020-01-23 12:07:04,043] multiqc [DEBUG ] No MultiQC config found: /home/mk5636/.multiqc_config.yaml [2020-01-23 12:07:04,044] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2020-01-23 12:07:04,062] multiqc [DEBUG ] Loading config settings from: /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml [2020-01-23 12:07:04,062] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2020-01-23 12:07:04,062] multiqc [DEBUG ] Command used: /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/HWJ22BGXC/merged [2020-01-23 12:07:04,062] multiqc [DEBUG ] Could not connect to multiqc.info for version check [2020-01-23 12:07:04,062] multiqc [INFO ] This is MultiQC v1.0.dev0 [2020-01-23 12:07:04,062] multiqc [DEBUG ] Command : /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/HWJ22BGXC/merged [2020-01-23 12:07:04,062] multiqc [DEBUG ] Working dir : /beegfs/mk5636/logs/html/HWJ22BGXC/merged [2020-01-23 12:07:04,062] multiqc [INFO ] Template : default [2020-01-23 12:07:04,063] multiqc [DEBUG ] Running in --force mode, will overwrite any existing reports. [2020-01-23 12:07:04,063] multiqc [INFO ] Searching '/beegfs/mk5636/logs/html/HWJ22BGXC/merged' [2020-01-23 12:07:04,063] 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 [2020-01-23 12:07:04,063] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-7019009/tmp03OD68 [2020-01-23 12:07:04,223] multiqc [DEBUG ] Ignoring file as too large: undetermined_barcodes.txt [2020-01-23 12:07:05,467] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('/beegfs/mk5636/logs/html/HWJ22BGXC/merged',) [2020-01-23 12:07:05,636] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 161 samples (table) [2020-01-23 12:07:05,647] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2020-01-23 12:07:05,649] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2020-01-23 12:07:05,804] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HWJ22BGXC/merged',) [2020-01-23 12:07:05,849] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HWJ22BGXC/merged',) [2020-01-23 12:07:05,860] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2020-01-23 12:07:06,082] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HWJ22BGXC/merged',) [2020-01-23 12:07:12,762] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('/beegfs/mk5636/logs/html/HWJ22BGXC/merged',) [2020-01-23 12:07:12,807] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HWJ22BGXC/merged',) [2020-01-23 12:07:17,327] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HWJ22BGXC/merged',) [2020-01-23 12:07:17,372] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HWJ22BGXC/merged',) [2020-01-23 12:07:17,454] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('/beegfs/mk5636/logs/html/HWJ22BGXC/merged',) [2020-01-23 12:07:18,527] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HWJ22BGXC/merged',) [2020-01-23 12:07:19,598] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HWJ22BGXC/merged',) [2020-01-23 12:07:20,675] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HWJ22BGXC/merged',) [2020-01-23 12:07:21,749] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HWJ22BGXC/merged',) [2020-01-23 12:07:21,793] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HWJ22BGXC/merged',) [2020-01-23 12:07:34,443] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HWJ22BGXC/merged',) [2020-01-23 12:07:34,492] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('/beegfs/mk5636/logs/html/HWJ22BGXC/merged',) [2020-01-23 12:07:35,753] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HWJ22BGXC/merged',) [2020-01-23 12:07:39,419] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HWJ22BGXC/merged',) [2020-01-23 12:07:40,478] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HWJ22BGXC/merged',) [2020-01-23 12:07:40,671] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HWJ22BGXC/merged',) [2020-01-23 12:07:40,716] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('/beegfs/mk5636/logs/html/HWJ22BGXC/merged',) [2020-01-23 12:07:40,797] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('/beegfs/mk5636/logs/html/HWJ22BGXC/merged',) [2020-01-23 12:07:41,856] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HWJ22BGXC/merged',) [2020-01-23 12:07:49,130] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2020-01-23 12:07:49,213] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HWJ22BGXC/merged',) [2020-01-23 12:07:49,258] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HWJ22BGXC/merged',) [2020-01-23 12:07:50,315] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HWJ22BGXC/merged',) [2020-01-23 12:07:51,370] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HWJ22BGXC/merged',) [2020-01-23 12:07:52,431] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HWJ22BGXC/merged',) [2020-01-23 12:07:53,500] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('/beegfs/mk5636/logs/html/HWJ22BGXC/merged',) [2020-01-23 12:07:54,551] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HWJ22BGXC/merged',) [2020-01-23 12:07:54,595] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HWJ22BGXC/merged',) [2020-01-23 12:09:54,843] multiqc.modules.fastqc.fastqc [INFO ] Found 322 reports [2020-01-23 12:10:59,031] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HWJ22BGXC/merged',) [2020-01-23 12:10:59,492] multiqc [INFO ] Report : multiqc_report.html [2020-01-23 12:10:59,493] multiqc [INFO ] Data : multiqc_data [2020-01-23 12:10:59,494] multiqc [DEBUG ] Moving data file from '/state/partition1/job-7019009/tmp03OD68/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Counts.txt' to '/beegfs/mk5636/logs/html/HWJ22BGXC/merged/multiqc_data' [2020-01-23 12:10:59,496] multiqc [DEBUG ] Moving data file from '/state/partition1/job-7019009/tmp03OD68/multiqc_data/multiqc_general_stats.txt' to '/beegfs/mk5636/logs/html/HWJ22BGXC/merged/multiqc_data' [2020-01-23 12:10:59,499] multiqc [DEBUG ] Moving data file from '/state/partition1/job-7019009/tmp03OD68/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Percentages.txt' to '/beegfs/mk5636/logs/html/HWJ22BGXC/merged/multiqc_data' [2020-01-23 12:10:59,501] multiqc [DEBUG ] Moving data file from '/state/partition1/job-7019009/tmp03OD68/multiqc_data/mqc_fastqc_overrepresented_sequencesi_plot_1.txt' to '/beegfs/mk5636/logs/html/HWJ22BGXC/merged/multiqc_data' [2020-01-23 12:10:59,504] multiqc [DEBUG ] Moving data file from '/state/partition1/job-7019009/tmp03OD68/multiqc_data/multiqc_fastqc.txt' to '/beegfs/mk5636/logs/html/HWJ22BGXC/merged/multiqc_data' [2020-01-23 12:10:59,506] multiqc [DEBUG ] Moving data file from '/state/partition1/job-7019009/tmp03OD68/multiqc_data/multiqc_sources.txt' to '/beegfs/mk5636/logs/html/HWJ22BGXC/merged/multiqc_data' [2020-01-23 12:10:59,508] multiqc [DEBUG ] Moving data file from '/state/partition1/job-7019009/tmp03OD68/multiqc_data/mqc_fastqc_sequence_duplication_levels_plot_1.txt' to '/beegfs/mk5636/logs/html/HWJ22BGXC/merged/multiqc_data' [2020-01-23 12:10:59,512] multiqc [DEBUG ] Moving data file from '/state/partition1/job-7019009/tmp03OD68/multiqc_data/mqc_fastqc_per_base_n_content_plot_1.txt' to '/beegfs/mk5636/logs/html/HWJ22BGXC/merged/multiqc_data' [2020-01-23 12:10:59,514] multiqc [DEBUG ] Moving data file from '/state/partition1/job-7019009/tmp03OD68/multiqc_data/mqc_fastqc_adapter_content_plot_1.txt' to '/beegfs/mk5636/logs/html/HWJ22BGXC/merged/multiqc_data' [2020-01-23 12:10:59,517] multiqc [DEBUG ] Moving data file from '/state/partition1/job-7019009/tmp03OD68/multiqc_data/mqc_fastqc_per_base_sequence_quality_plot_1.txt' to '/beegfs/mk5636/logs/html/HWJ22BGXC/merged/multiqc_data' [2020-01-23 12:10:59,519] multiqc [DEBUG ] Moving data file from '/state/partition1/job-7019009/tmp03OD68/multiqc_data/mqc_fastqc_per_sequence_quality_scores_plot_1.txt' to '/beegfs/mk5636/logs/html/HWJ22BGXC/merged/multiqc_data' [2020-01-23 12:10:59,689] multiqc [INFO ] MultiQC complete