[2019-09-12 15:51:48,532] 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 [2019-09-12 15:51:48,532] multiqc [DEBUG ] No MultiQC config found: /home/mk5636/.multiqc_config.yaml [2019-09-12 15:51:48,533] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2019-09-12 15:51:48,555] multiqc [DEBUG ] Loading config settings from: /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml [2019-09-12 15:51:48,555] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2019-09-12 15:51:48,555] multiqc [DEBUG ] Command used: /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/HMJVKBGX7/merged [2019-09-12 15:51:48,555] multiqc [DEBUG ] Could not connect to multiqc.info for version check [2019-09-12 15:51:48,555] multiqc [INFO ] This is MultiQC v1.0.dev0 [2019-09-12 15:51:48,555] multiqc [DEBUG ] Command : /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/HMJVKBGX7/merged [2019-09-12 15:51:48,555] multiqc [DEBUG ] Working dir : /beegfs/mk5636/logs/html/HMJVKBGX7/merged [2019-09-12 15:51:48,555] multiqc [INFO ] Template : default [2019-09-12 15:51:48,556] multiqc [DEBUG ] Running in --force mode, will overwrite any existing reports. [2019-09-12 15:51:48,556] multiqc [INFO ] Searching '/beegfs/mk5636/logs/html/HMJVKBGX7/merged' [2019-09-12 15:51:48,556] 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 [2019-09-12 15:51:48,556] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-4247432/tmpiiJxHH [2019-09-12 15:51:49,250] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('/beegfs/mk5636/logs/html/HMJVKBGX7/merged',) [2019-09-12 15:51:49,350] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 95 samples (table) [2019-09-12 15:51:49,360] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2019-09-12 15:51:49,361] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2019-09-12 15:51:49,445] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMJVKBGX7/merged',) [2019-09-12 15:51:49,471] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMJVKBGX7/merged',) [2019-09-12 15:51:49,480] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2019-09-12 15:51:49,595] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMJVKBGX7/merged',) [2019-09-12 15:51:56,086] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('/beegfs/mk5636/logs/html/HMJVKBGX7/merged',) [2019-09-12 15:51:56,111] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMJVKBGX7/merged',) [2019-09-12 15:51:59,543] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMJVKBGX7/merged',) [2019-09-12 15:51:59,564] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMJVKBGX7/merged',) [2019-09-12 15:51:59,600] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('/beegfs/mk5636/logs/html/HMJVKBGX7/merged',) [2019-09-12 15:52:00,286] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HMJVKBGX7/merged',) [2019-09-12 15:52:01,086] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMJVKBGX7/merged',) [2019-09-12 15:52:01,764] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMJVKBGX7/merged',) [2019-09-12 15:52:02,501] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMJVKBGX7/merged',) [2019-09-12 15:52:02,523] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMJVKBGX7/merged',) [2019-09-12 15:52:10,629] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMJVKBGX7/merged',) [2019-09-12 15:52:10,654] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('/beegfs/mk5636/logs/html/HMJVKBGX7/merged',) [2019-09-12 15:52:11,440] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HMJVKBGX7/merged',) [2019-09-12 15:52:13,525] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMJVKBGX7/merged',) [2019-09-12 15:52:14,230] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMJVKBGX7/merged',) [2019-09-12 15:52:14,315] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMJVKBGX7/merged',) [2019-09-12 15:52:14,344] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('/beegfs/mk5636/logs/html/HMJVKBGX7/merged',) [2019-09-12 15:52:14,390] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('/beegfs/mk5636/logs/html/HMJVKBGX7/merged',) [2019-09-12 15:52:15,155] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMJVKBGX7/merged',) [2019-09-12 15:52:20,129] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2019-09-12 15:52:20,167] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMJVKBGX7/merged',) [2019-09-12 15:52:20,211] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMJVKBGX7/merged',) [2019-09-12 15:52:20,996] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMJVKBGX7/merged',) [2019-09-12 15:52:21,726] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMJVKBGX7/merged',) [2019-09-12 15:52:22,418] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMJVKBGX7/merged',) [2019-09-12 15:52:23,153] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('/beegfs/mk5636/logs/html/HMJVKBGX7/merged',) [2019-09-12 15:52:23,888] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HMJVKBGX7/merged',) [2019-09-12 15:52:23,910] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMJVKBGX7/merged',) [2019-09-12 15:53:12,439] multiqc.modules.fastqc.fastqc [INFO ] Found 190 reports [2019-09-12 15:53:32,253] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMJVKBGX7/merged',) [2019-09-12 15:53:32,464] multiqc [INFO ] Report : multiqc_report.html [2019-09-12 15:53:32,465] multiqc [INFO ] Data : multiqc_data [2019-09-12 15:53:32,465] multiqc [DEBUG ] Moving data file from '/state/partition1/job-4247432/tmpiiJxHH/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Counts.txt' to '/beegfs/mk5636/logs/html/HMJVKBGX7/merged/multiqc_data' [2019-09-12 15:53:32,468] multiqc [DEBUG ] Moving data file from '/state/partition1/job-4247432/tmpiiJxHH/multiqc_data/multiqc_general_stats.txt' to '/beegfs/mk5636/logs/html/HMJVKBGX7/merged/multiqc_data' [2019-09-12 15:53:32,472] multiqc [DEBUG ] Moving data file from '/state/partition1/job-4247432/tmpiiJxHH/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Percentages.txt' to '/beegfs/mk5636/logs/html/HMJVKBGX7/merged/multiqc_data' [2019-09-12 15:53:32,475] multiqc [DEBUG ] Moving data file from '/state/partition1/job-4247432/tmpiiJxHH/multiqc_data/mqc_fastqc_sequence_duplication_levels_plot_1.txt' to '/beegfs/mk5636/logs/html/HMJVKBGX7/merged/multiqc_data' [2019-09-12 15:53:32,481] multiqc [DEBUG ] Moving data file from '/state/partition1/job-4247432/tmpiiJxHH/multiqc_data/mqc_fastqc_overrepresented_sequencesi_plot_1.txt' to '/beegfs/mk5636/logs/html/HMJVKBGX7/merged/multiqc_data' [2019-09-12 15:53:32,484] multiqc [DEBUG ] Moving data file from '/state/partition1/job-4247432/tmpiiJxHH/multiqc_data/mqc_fastqc_per_base_n_content_plot_1.txt' to '/beegfs/mk5636/logs/html/HMJVKBGX7/merged/multiqc_data' [2019-09-12 15:53:32,486] multiqc [DEBUG ] Moving data file from '/state/partition1/job-4247432/tmpiiJxHH/multiqc_data/mqc_fastqc_adapter_content_plot_1.txt' to '/beegfs/mk5636/logs/html/HMJVKBGX7/merged/multiqc_data' [2019-09-12 15:53:32,489] multiqc [DEBUG ] Moving data file from '/state/partition1/job-4247432/tmpiiJxHH/multiqc_data/mqc_fastqc_per_sequence_quality_scores_plot_1.txt' to '/beegfs/mk5636/logs/html/HMJVKBGX7/merged/multiqc_data' [2019-09-12 15:53:32,494] multiqc [DEBUG ] Moving data file from '/state/partition1/job-4247432/tmpiiJxHH/multiqc_data/multiqc_sources.txt' to '/beegfs/mk5636/logs/html/HMJVKBGX7/merged/multiqc_data' [2019-09-12 15:53:32,496] multiqc [DEBUG ] Moving data file from '/state/partition1/job-4247432/tmpiiJxHH/multiqc_data/mqc_fastqc_per_base_sequence_quality_plot_1.txt' to '/beegfs/mk5636/logs/html/HMJVKBGX7/merged/multiqc_data' [2019-09-12 15:53:32,502] multiqc [DEBUG ] Moving data file from '/state/partition1/job-4247432/tmpiiJxHH/multiqc_data/multiqc_fastqc.txt' to '/beegfs/mk5636/logs/html/HMJVKBGX7/merged/multiqc_data' [2019-09-12 15:53:32,686] multiqc [INFO ] MultiQC complete