[2019-11-08 16:10:40,187] 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 [2019-11-08 16:10:40,187] multiqc [DEBUG ] No MultiQC config found: /home/mk5636/.multiqc_config.yaml [2019-11-08 16:10:40,187] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2019-11-08 16:10:40,203] multiqc [DEBUG ] Loading config settings from: /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml [2019-11-08 16:10:40,203] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2019-11-08 16:10:40,203] multiqc [DEBUG ] Command used: /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/HW7CJAFXY/merged [2019-11-08 16:10:40,204] multiqc [DEBUG ] Could not connect to multiqc.info for version check [2019-11-08 16:10:40,204] multiqc [INFO ] This is MultiQC v1.0.dev0 [2019-11-08 16:10:40,204] multiqc [DEBUG ] Command : /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/HW7CJAFXY/merged [2019-11-08 16:10:40,204] multiqc [DEBUG ] Working dir : /beegfs/mk5636/logs/html/HW7CJAFXY/merged [2019-11-08 16:10:40,204] multiqc [INFO ] Template : default [2019-11-08 16:10:40,204] multiqc [DEBUG ] Running in --force mode, will overwrite any existing reports. [2019-11-08 16:10:40,204] multiqc [INFO ] Searching '/beegfs/mk5636/logs/html/HW7CJAFXY/merged' [2019-11-08 16:10:40,204] 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 [2019-11-08 16:10:40,204] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-5553632/tmp2pG6N_ [2019-11-08 16:10:40,244] multiqc [DEBUG ] Ignoring directory as matched fn_ignore_dirs: /beegfs/mk5636/logs/html/HW7CJAFXY/merged/multiqc_data [2019-11-08 16:10:40,738] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('/beegfs/mk5636/logs/html/HW7CJAFXY/merged',) [2019-11-08 16:10:40,801] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 35 samples (table) [2019-11-08 16:10:40,812] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2019-11-08 16:10:40,814] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2019-11-08 16:10:40,885] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HW7CJAFXY/merged',) [2019-11-08 16:10:40,909] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HW7CJAFXY/merged',) [2019-11-08 16:10:40,918] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2019-11-08 16:10:41,013] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HW7CJAFXY/merged',) [2019-11-08 16:10:44,825] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('/beegfs/mk5636/logs/html/HW7CJAFXY/merged',) [2019-11-08 16:10:44,848] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HW7CJAFXY/merged',) [2019-11-08 16:10:47,600] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HW7CJAFXY/merged',) [2019-11-08 16:10:47,623] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HW7CJAFXY/merged',) [2019-11-08 16:10:47,661] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('/beegfs/mk5636/logs/html/HW7CJAFXY/merged',) [2019-11-08 16:10:48,342] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HW7CJAFXY/merged',) [2019-11-08 16:10:49,030] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HW7CJAFXY/merged',) [2019-11-08 16:10:49,713] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HW7CJAFXY/merged',) [2019-11-08 16:10:50,382] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HW7CJAFXY/merged',) [2019-11-08 16:10:50,404] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HW7CJAFXY/merged',) [2019-11-08 16:10:57,265] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HW7CJAFXY/merged',) [2019-11-08 16:10:57,291] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('/beegfs/mk5636/logs/html/HW7CJAFXY/merged',) [2019-11-08 16:10:57,974] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HW7CJAFXY/merged',) [2019-11-08 16:11:00,002] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HW7CJAFXY/merged',) [2019-11-08 16:11:00,688] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HW7CJAFXY/merged',) [2019-11-08 16:11:00,775] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HW7CJAFXY/merged',) [2019-11-08 16:11:00,797] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('/beegfs/mk5636/logs/html/HW7CJAFXY/merged',) [2019-11-08 16:11:00,835] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('/beegfs/mk5636/logs/html/HW7CJAFXY/merged',) [2019-11-08 16:11:01,502] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HW7CJAFXY/merged',) [2019-11-08 16:11:05,571] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2019-11-08 16:11:05,611] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HW7CJAFXY/merged',) [2019-11-08 16:11:05,634] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HW7CJAFXY/merged',) [2019-11-08 16:11:06,315] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HW7CJAFXY/merged',) [2019-11-08 16:11:06,992] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HW7CJAFXY/merged',) [2019-11-08 16:11:07,673] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HW7CJAFXY/merged',) [2019-11-08 16:11:08,357] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('/beegfs/mk5636/logs/html/HW7CJAFXY/merged',) [2019-11-08 16:11:09,027] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HW7CJAFXY/merged',) [2019-11-08 16:11:09,051] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HW7CJAFXY/merged',) [2019-11-08 16:11:16,930] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HW7CJAFXY_n02_SG163_r1_col_B_L_fastqc.zip' - Bad zip file [2019-11-08 16:11:16,930] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-11-08 16:11:24,740] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HW7CJAFXY_n01_SG163_r1_col_B_L_fastqc.zip' - Bad zip file [2019-11-08 16:11:24,740] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-11-08 16:11:26,706] multiqc.modules.fastqc.fastqc [INFO ] Found 136 reports [2019-11-08 16:11:47,152] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HW7CJAFXY/merged',) [2019-11-08 16:11:47,444] multiqc [WARNING] Deleting : multiqc_report.html (-f was specified) [2019-11-08 16:11:47,445] multiqc [INFO ] Report : multiqc_report.html [2019-11-08 16:11:47,445] multiqc [WARNING] Deleting : multiqc_data (-f was specified) [2019-11-08 16:11:47,452] multiqc [INFO ] Data : multiqc_data [2019-11-08 16:11:47,452] multiqc [DEBUG ] Moving data file from '/state/partition1/job-5553632/tmp2pG6N_/multiqc_data/mqc_fastqc_overrepresented_sequencesi_plot_1.txt' to '/beegfs/mk5636/logs/html/HW7CJAFXY/merged/multiqc_data' [2019-11-08 16:11:47,454] multiqc [DEBUG ] Moving data file from '/state/partition1/job-5553632/tmp2pG6N_/multiqc_data/mqc_fastqc_adapter_content_plot_1.txt' to '/beegfs/mk5636/logs/html/HW7CJAFXY/merged/multiqc_data' [2019-11-08 16:11:47,457] multiqc [DEBUG ] Moving data file from '/state/partition1/job-5553632/tmp2pG6N_/multiqc_data/mqc_fastqc_per_base_n_content_plot_1.txt' to '/beegfs/mk5636/logs/html/HW7CJAFXY/merged/multiqc_data' [2019-11-08 16:11:47,459] multiqc [DEBUG ] Moving data file from '/state/partition1/job-5553632/tmp2pG6N_/multiqc_data/mqc_fastqc_sequence_duplication_levels_plot_1.txt' to '/beegfs/mk5636/logs/html/HW7CJAFXY/merged/multiqc_data' [2019-11-08 16:11:47,461] multiqc [DEBUG ] Moving data file from '/state/partition1/job-5553632/tmp2pG6N_/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Counts.txt' to '/beegfs/mk5636/logs/html/HW7CJAFXY/merged/multiqc_data' [2019-11-08 16:11:47,464] multiqc [DEBUG ] Moving data file from '/state/partition1/job-5553632/tmp2pG6N_/multiqc_data/multiqc_fastqc.txt' to '/beegfs/mk5636/logs/html/HW7CJAFXY/merged/multiqc_data' [2019-11-08 16:11:47,466] multiqc [DEBUG ] Moving data file from '/state/partition1/job-5553632/tmp2pG6N_/multiqc_data/multiqc_sources.txt' to '/beegfs/mk5636/logs/html/HW7CJAFXY/merged/multiqc_data' [2019-11-08 16:11:47,468] multiqc [DEBUG ] Moving data file from '/state/partition1/job-5553632/tmp2pG6N_/multiqc_data/multiqc_general_stats.txt' to '/beegfs/mk5636/logs/html/HW7CJAFXY/merged/multiqc_data' [2019-11-08 16:11:47,470] multiqc [DEBUG ] Moving data file from '/state/partition1/job-5553632/tmp2pG6N_/multiqc_data/mqc_fastqc_per_base_sequence_quality_plot_1.txt' to '/beegfs/mk5636/logs/html/HW7CJAFXY/merged/multiqc_data' [2019-11-08 16:11:47,472] multiqc [DEBUG ] Moving data file from '/state/partition1/job-5553632/tmp2pG6N_/multiqc_data/mqc_fastqc_per_sequence_quality_scores_plot_1.txt' to '/beegfs/mk5636/logs/html/HW7CJAFXY/merged/multiqc_data' [2019-11-08 16:11:47,474] multiqc [DEBUG ] Moving data file from '/state/partition1/job-5553632/tmp2pG6N_/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Percentages.txt' to '/beegfs/mk5636/logs/html/HW7CJAFXY/merged/multiqc_data' [2019-11-08 16:11:47,629] multiqc [INFO ] MultiQC complete