[2020-03-16 20:53:21,581] 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 [2020-03-16 20:53:21,617] multiqc [DEBUG ] No MultiQC config found: /home/mk5636/.multiqc_config.yaml [2020-03-16 20:53:21,617] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2020-03-16 20:53:21,624] multiqc [DEBUG ] Loading config settings from: /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml [2020-03-16 20:53:21,625] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2020-03-16 20:53:21,625] multiqc [DEBUG ] Command used: /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/HKVH7DRXX/merged [2020-03-16 20:53:21,625] multiqc [DEBUG ] Could not connect to multiqc.info for version check [2020-03-16 20:53:21,625] multiqc [INFO ] This is MultiQC v1.0.dev0 [2020-03-16 20:53:21,625] multiqc [DEBUG ] Command : /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/HKVH7DRXX/merged [2020-03-16 20:53:21,625] multiqc [DEBUG ] Working dir : /beegfs/mk5636/logs/html/HKVH7DRXX/merged [2020-03-16 20:53:21,625] multiqc [INFO ] Template : default [2020-03-16 20:53:21,626] multiqc [DEBUG ] Running in --force mode, will overwrite any existing reports. [2020-03-16 20:53:21,626] multiqc [INFO ] Searching '/beegfs/mk5636/logs/html/HKVH7DRXX/merged' [2020-03-16 20:53:21,626] 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 [2020-03-16 20:53:21,626] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-8285613/tmpf7RtI7 [2020-03-16 20:53:21,694] multiqc [DEBUG ] Ignoring directory as matched fn_ignore_dirs: /beegfs/mk5636/logs/html/HKVH7DRXX/merged/multiqc_data [2020-03-16 20:53:21,769] multiqc [DEBUG ] Ignoring file as too large: undetermined_barcodes.txt [2020-03-16 20:53:22,493] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('/beegfs/mk5636/logs/html/HKVH7DRXX/merged',) [2020-03-16 20:53:22,666] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 71 samples (table) [2020-03-16 20:53:22,679] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2020-03-16 20:53:22,682] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2020-03-16 20:53:22,816] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HKVH7DRXX/merged',) [2020-03-16 20:53:22,852] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HKVH7DRXX/merged',) [2020-03-16 20:53:22,861] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2020-03-16 20:53:23,031] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HKVH7DRXX/merged',) [2020-03-16 20:53:32,765] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('/beegfs/mk5636/logs/html/HKVH7DRXX/merged',) [2020-03-16 20:53:32,796] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HKVH7DRXX/merged',) [2020-03-16 20:53:35,930] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HKVH7DRXX/merged',) [2020-03-16 20:53:35,960] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HKVH7DRXX/merged',) [2020-03-16 20:53:36,013] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('/beegfs/mk5636/logs/html/HKVH7DRXX/merged',) [2020-03-16 20:53:36,779] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HKVH7DRXX/merged',) [2020-03-16 20:53:37,552] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HKVH7DRXX/merged',) [2020-03-16 20:53:38,315] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HKVH7DRXX/merged',) [2020-03-16 20:53:39,075] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HKVH7DRXX/merged',) [2020-03-16 20:53:39,106] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HKVH7DRXX/merged',) [2020-03-16 20:53:46,699] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HKVH7DRXX/merged',) [2020-03-16 20:53:46,732] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('/beegfs/mk5636/logs/html/HKVH7DRXX/merged',) [2020-03-16 20:53:47,491] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HKVH7DRXX/merged',) [2020-03-16 20:53:49,795] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HKVH7DRXX/merged',) [2020-03-16 20:53:50,556] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HKVH7DRXX/merged',) [2020-03-16 20:53:50,679] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HKVH7DRXX/merged',) [2020-03-16 20:53:50,709] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('/beegfs/mk5636/logs/html/HKVH7DRXX/merged',) [2020-03-16 20:53:50,763] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('/beegfs/mk5636/logs/html/HKVH7DRXX/merged',) [2020-03-16 20:53:51,526] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HKVH7DRXX/merged',) [2020-03-16 20:53:56,103] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2020-03-16 20:53:56,156] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HKVH7DRXX/merged',) [2020-03-16 20:53:56,187] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HKVH7DRXX/merged',) [2020-03-16 20:53:57,001] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HKVH7DRXX/merged',) [2020-03-16 20:53:57,766] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HKVH7DRXX/merged',) [2020-03-16 20:53:58,529] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HKVH7DRXX/merged',) [2020-03-16 20:53:59,302] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('/beegfs/mk5636/logs/html/HKVH7DRXX/merged',) [2020-03-16 20:54:00,053] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HKVH7DRXX/merged',) [2020-03-16 20:54:00,082] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HKVH7DRXX/merged',) [2020-03-16 20:54:03,293] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HKVH7DRXX_n02_dpr46_fastqc.zip' - Bad zip file [2020-03-16 20:54:03,293] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2020-03-16 20:54:08,315] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HKVH7DRXX_n01_dpr46_fastqc.zip' - Bad zip file [2020-03-16 20:54:08,316] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2020-03-16 20:54:18,441] multiqc.modules.fastqc.fastqc [INFO ] Found 280 reports [2020-03-16 20:54:37,148] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HKVH7DRXX/merged',) [2020-03-16 20:54:37,456] multiqc [WARNING] Deleting : multiqc_report.html (-f was specified) [2020-03-16 20:54:37,459] multiqc [INFO ] Report : multiqc_report.html [2020-03-16 20:54:37,459] multiqc [WARNING] Deleting : multiqc_data (-f was specified) [2020-03-16 20:54:37,688] multiqc [INFO ] Data : multiqc_data [2020-03-16 20:54:37,688] multiqc [DEBUG ] Moving data file from '/state/partition1/job-8285613/tmpf7RtI7/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Counts.txt' to '/beegfs/mk5636/logs/html/HKVH7DRXX/merged/multiqc_data' [2020-03-16 20:54:37,692] multiqc [DEBUG ] Moving data file from '/state/partition1/job-8285613/tmpf7RtI7/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Percentages.txt' to '/beegfs/mk5636/logs/html/HKVH7DRXX/merged/multiqc_data' [2020-03-16 20:54:37,694] multiqc [DEBUG ] Moving data file from '/state/partition1/job-8285613/tmpf7RtI7/multiqc_data/mqc_fastqc_adapter_content_plot_1.txt' to '/beegfs/mk5636/logs/html/HKVH7DRXX/merged/multiqc_data' [2020-03-16 20:54:37,697] multiqc [DEBUG ] Moving data file from '/state/partition1/job-8285613/tmpf7RtI7/multiqc_data/mqc_fastqc_per_base_sequence_quality_plot_1.txt' to '/beegfs/mk5636/logs/html/HKVH7DRXX/merged/multiqc_data' [2020-03-16 20:54:37,700] multiqc [DEBUG ] Moving data file from '/state/partition1/job-8285613/tmpf7RtI7/multiqc_data/mqc_fastqc_per_sequence_quality_scores_plot_1.txt' to '/beegfs/mk5636/logs/html/HKVH7DRXX/merged/multiqc_data' [2020-03-16 20:54:37,702] multiqc [DEBUG ] Moving data file from '/state/partition1/job-8285613/tmpf7RtI7/multiqc_data/multiqc_sources.txt' to '/beegfs/mk5636/logs/html/HKVH7DRXX/merged/multiqc_data' [2020-03-16 20:54:37,705] multiqc [DEBUG ] Moving data file from '/state/partition1/job-8285613/tmpf7RtI7/multiqc_data/mqc_fastqc_per_base_n_content_plot_1.txt' to '/beegfs/mk5636/logs/html/HKVH7DRXX/merged/multiqc_data' [2020-03-16 20:54:37,707] multiqc [DEBUG ] Moving data file from '/state/partition1/job-8285613/tmpf7RtI7/multiqc_data/multiqc_general_stats.txt' to '/beegfs/mk5636/logs/html/HKVH7DRXX/merged/multiqc_data' [2020-03-16 20:54:37,709] multiqc [DEBUG ] Moving data file from '/state/partition1/job-8285613/tmpf7RtI7/multiqc_data/mqc_fastqc_overrepresented_sequencesi_plot_1.txt' to '/beegfs/mk5636/logs/html/HKVH7DRXX/merged/multiqc_data' [2020-03-16 20:54:37,712] multiqc [DEBUG ] Moving data file from '/state/partition1/job-8285613/tmpf7RtI7/multiqc_data/mqc_fastqc_sequence_duplication_levels_plot_1.txt' to '/beegfs/mk5636/logs/html/HKVH7DRXX/merged/multiqc_data' [2020-03-16 20:54:37,715] multiqc [DEBUG ] Moving data file from '/state/partition1/job-8285613/tmpf7RtI7/multiqc_data/multiqc_fastqc.txt' to '/beegfs/mk5636/logs/html/HKVH7DRXX/merged/multiqc_data' [2020-03-16 20:54:37,906] multiqc [INFO ] MultiQC complete