[2019-01-17 15:08:56,113] 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 [2019-01-17 15:08:56,166] multiqc [DEBUG ] No MultiQC config found: /home/mk5636/.multiqc_config.yaml [2019-01-17 15:08:56,166] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2019-01-17 15:08:56,178] multiqc [DEBUG ] Loading config settings from: /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml [2019-01-17 15:08:56,178] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2019-01-17 15:08:56,178] multiqc [DEBUG ] Command used: /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/HFYHHAFXY/merged [2019-01-17 15:08:56,178] multiqc [DEBUG ] Could not connect to multiqc.info for version check [2019-01-17 15:08:56,178] multiqc [INFO ] This is MultiQC v1.0.dev0 [2019-01-17 15:08:56,178] multiqc [DEBUG ] Command : /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/HFYHHAFXY/merged [2019-01-17 15:08:56,178] multiqc [DEBUG ] Working dir : /beegfs/mk5636/logs/html/HFYHHAFXY/merged [2019-01-17 15:08:56,179] multiqc [INFO ] Template : default [2019-01-17 15:08:56,179] multiqc [DEBUG ] Running in --force mode, will overwrite any existing reports. [2019-01-17 15:08:56,179] multiqc [INFO ] Searching '/beegfs/mk5636/logs/html/HFYHHAFXY/merged' [2019-01-17 15:08:56,179] 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 [2019-01-17 15:08:56,179] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-14566284/tmpKdjcC4 [2019-01-17 15:08:56,242] multiqc [DEBUG ] Ignoring directory as matched fn_ignore_dirs: /beegfs/mk5636/logs/html/HFYHHAFXY/merged/multiqc_data [2019-01-17 15:08:56,333] multiqc [DEBUG ] Ignoring file as too large: undetermined_barcodes.txt [2019-01-17 15:08:56,861] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('/beegfs/mk5636/logs/html/HFYHHAFXY/merged',) [2019-01-17 15:08:56,983] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 107 samples (table) [2019-01-17 15:08:56,995] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2019-01-17 15:08:56,996] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2019-01-17 15:08:57,109] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HFYHHAFXY/merged',) [2019-01-17 15:08:57,144] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HFYHHAFXY/merged',) [2019-01-17 15:08:57,154] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2019-01-17 15:08:57,313] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HFYHHAFXY/merged',) [2019-01-17 15:09:05,101] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('/beegfs/mk5636/logs/html/HFYHHAFXY/merged',) [2019-01-17 15:09:05,136] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HFYHHAFXY/merged',) [2019-01-17 15:09:08,259] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HFYHHAFXY/merged',) [2019-01-17 15:09:08,295] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HFYHHAFXY/merged',) [2019-01-17 15:09:08,356] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('/beegfs/mk5636/logs/html/HFYHHAFXY/merged',) [2019-01-17 15:09:09,171] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HFYHHAFXY/merged',) [2019-01-17 15:09:09,911] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HFYHHAFXY/merged',) [2019-01-17 15:09:10,635] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HFYHHAFXY/merged',) [2019-01-17 15:09:11,362] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HFYHHAFXY/merged',) [2019-01-17 15:09:11,397] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HFYHHAFXY/merged',) [2019-01-17 15:09:19,101] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HFYHHAFXY/merged',) [2019-01-17 15:09:19,138] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('/beegfs/mk5636/logs/html/HFYHHAFXY/merged',) [2019-01-17 15:09:19,932] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HFYHHAFXY/merged',) [2019-01-17 15:09:22,128] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HFYHHAFXY/merged',) [2019-01-17 15:09:22,851] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HFYHHAFXY/merged',) [2019-01-17 15:09:22,991] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HFYHHAFXY/merged',) [2019-01-17 15:09:23,024] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('/beegfs/mk5636/logs/html/HFYHHAFXY/merged',) [2019-01-17 15:09:23,084] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('/beegfs/mk5636/logs/html/HFYHHAFXY/merged',) [2019-01-17 15:09:23,886] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HFYHHAFXY/merged',) [2019-01-17 15:09:28,371] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2019-01-17 15:09:28,433] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HFYHHAFXY/merged',) [2019-01-17 15:09:28,468] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HFYHHAFXY/merged',) [2019-01-17 15:09:29,273] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HFYHHAFXY/merged',) [2019-01-17 15:09:30,048] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HFYHHAFXY/merged',) [2019-01-17 15:09:30,773] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HFYHHAFXY/merged',) [2019-01-17 15:09:31,542] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('/beegfs/mk5636/logs/html/HFYHHAFXY/merged',) [2019-01-17 15:09:32,259] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HFYHHAFXY/merged',) [2019-01-17 15:09:32,294] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HFYHHAFXY/merged',) [2019-01-17 15:09:40,556] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HFYHHAFXY_n02_ColSPL9_pool19011C_B_e_fastqc.zip' - Bad zip file [2019-01-17 15:09:40,556] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-01-17 15:09:42,785] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HFYHHAFXY_n02_ColSPL9_pool19011B_B_e_fastqc.zip' - Bad zip file [2019-01-17 15:09:42,785] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-01-17 15:09:55,245] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HFYHHAFXY_n01_ColSPL9_pool19011C_B_e_fastqc.zip' - Bad zip file [2019-01-17 15:09:55,245] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-01-17 15:09:57,039] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HFYHHAFXY_n01_ColSPL9_pool19011B_B_e_fastqc.zip' - Bad zip file [2019-01-17 15:09:57,039] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-01-17 15:10:08,457] multiqc.modules.fastqc.fastqc [INFO ] Found 238 reports [2019-01-17 15:10:43,786] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HFYHHAFXY/merged',) [2019-01-17 15:10:44,132] multiqc [WARNING] Deleting : multiqc_report.html (-f was specified) [2019-01-17 15:10:44,134] multiqc [INFO ] Report : multiqc_report.html [2019-01-17 15:10:44,134] multiqc [WARNING] Deleting : multiqc_data (-f was specified) [2019-01-17 15:10:44,142] multiqc [INFO ] Data : multiqc_data [2019-01-17 15:10:44,142] multiqc [DEBUG ] Moving data file from '/state/partition1/job-14566284/tmpKdjcC4/multiqc_data/multiqc_sources.txt' to '/beegfs/mk5636/logs/html/HFYHHAFXY/merged/multiqc_data' [2019-01-17 15:10:44,144] multiqc [DEBUG ] Moving data file from '/state/partition1/job-14566284/tmpKdjcC4/multiqc_data/mqc_fastqc_overrepresented_sequencesi_plot_1.txt' to '/beegfs/mk5636/logs/html/HFYHHAFXY/merged/multiqc_data' [2019-01-17 15:10:44,147] multiqc [DEBUG ] Moving data file from '/state/partition1/job-14566284/tmpKdjcC4/multiqc_data/mqc_fastqc_per_sequence_quality_scores_plot_1.txt' to '/beegfs/mk5636/logs/html/HFYHHAFXY/merged/multiqc_data' [2019-01-17 15:10:44,149] multiqc [DEBUG ] Moving data file from '/state/partition1/job-14566284/tmpKdjcC4/multiqc_data/mqc_fastqc_per_base_sequence_quality_plot_1.txt' to '/beegfs/mk5636/logs/html/HFYHHAFXY/merged/multiqc_data' [2019-01-17 15:10:44,152] multiqc [DEBUG ] Moving data file from '/state/partition1/job-14566284/tmpKdjcC4/multiqc_data/multiqc_fastqc.txt' to '/beegfs/mk5636/logs/html/HFYHHAFXY/merged/multiqc_data' [2019-01-17 15:10:44,155] multiqc [DEBUG ] Moving data file from '/state/partition1/job-14566284/tmpKdjcC4/multiqc_data/mqc_fastqc_sequence_duplication_levels_plot_1.txt' to '/beegfs/mk5636/logs/html/HFYHHAFXY/merged/multiqc_data' [2019-01-17 15:10:44,158] multiqc [DEBUG ] Moving data file from '/state/partition1/job-14566284/tmpKdjcC4/multiqc_data/mqc_fastqc_per_base_n_content_plot_1.txt' to '/beegfs/mk5636/logs/html/HFYHHAFXY/merged/multiqc_data' [2019-01-17 15:10:44,161] multiqc [DEBUG ] Moving data file from '/state/partition1/job-14566284/tmpKdjcC4/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Counts.txt' to '/beegfs/mk5636/logs/html/HFYHHAFXY/merged/multiqc_data' [2019-01-17 15:10:44,164] multiqc [DEBUG ] Moving data file from '/state/partition1/job-14566284/tmpKdjcC4/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Percentages.txt' to '/beegfs/mk5636/logs/html/HFYHHAFXY/merged/multiqc_data' [2019-01-17 15:10:44,166] multiqc [DEBUG ] Moving data file from '/state/partition1/job-14566284/tmpKdjcC4/multiqc_data/mqc_fastqc_adapter_content_plot_1.txt' to '/beegfs/mk5636/logs/html/HFYHHAFXY/merged/multiqc_data' [2019-01-17 15:10:44,169] multiqc [DEBUG ] Moving data file from '/state/partition1/job-14566284/tmpKdjcC4/multiqc_data/multiqc_general_stats.txt' to '/beegfs/mk5636/logs/html/HFYHHAFXY/merged/multiqc_data' [2019-01-17 15:10:44,346] multiqc [INFO ] MultiQC complete