[2020-12-05 07:00:05,988] 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 [2020-12-05 07:00:05,989] multiqc [DEBUG ] No MultiQC config found: /home/mk5636/.multiqc_config.yaml [2020-12-05 07:00:05,989] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2020-12-05 07:00:06,016] multiqc [DEBUG ] Loading config settings from: /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml [2020-12-05 07:00:06,017] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2020-12-05 07:00:06,017] multiqc [DEBUG ] Command used: /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/H7KKVBGXH/merged [2020-12-05 07:00:06,017] multiqc [DEBUG ] Could not connect to multiqc.info for version check [2020-12-05 07:00:06,017] multiqc [INFO ] This is MultiQC v1.0.dev0 [2020-12-05 07:00:06,017] multiqc [DEBUG ] Command : /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/H7KKVBGXH/merged [2020-12-05 07:00:06,017] multiqc [DEBUG ] Working dir : /beegfs/mk5636/logs/html/H7KKVBGXH/merged [2020-12-05 07:00:06,018] multiqc [INFO ] Template : default [2020-12-05 07:00:06,018] multiqc [DEBUG ] Running in --force mode, will overwrite any existing reports. [2020-12-05 07:00:06,018] multiqc [INFO ] Searching '/beegfs/mk5636/logs/html/H7KKVBGXH/merged' [2020-12-05 07:00:06,018] 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 [2020-12-05 07:00:06,018] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-14052081/tmpUtuptf [2020-12-05 07:00:09,510] multiqc [DEBUG ] Ignoring file as too large: undetermined_barcodes.txt [2020-12-05 07:00:11,875] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('/beegfs/mk5636/logs/html/H7KKVBGXH/merged',) [2020-12-05 07:00:12,164] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 257 samples (table) [2020-12-05 07:00:12,175] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2020-12-05 07:00:12,177] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2020-12-05 07:00:12,424] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7KKVBGXH/merged',) [2020-12-05 07:00:12,478] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7KKVBGXH/merged',) [2020-12-05 07:00:12,487] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2020-12-05 07:00:12,766] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7KKVBGXH/merged',) [2020-12-05 07:00:33,135] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('/beegfs/mk5636/logs/html/H7KKVBGXH/merged',) [2020-12-05 07:00:33,229] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7KKVBGXH/merged',) [2020-12-05 07:00:42,338] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7KKVBGXH/merged',) [2020-12-05 07:00:42,429] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7KKVBGXH/merged',) [2020-12-05 07:00:42,542] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('/beegfs/mk5636/logs/html/H7KKVBGXH/merged',) [2020-12-05 07:00:44,427] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/H7KKVBGXH/merged',) [2020-12-05 07:00:46,142] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7KKVBGXH/merged',) [2020-12-05 07:00:47,985] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7KKVBGXH/merged',) [2020-12-05 07:00:49,792] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7KKVBGXH/merged',) [2020-12-05 07:00:49,886] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7KKVBGXH/merged',) [2020-12-05 07:01:16,502] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7KKVBGXH/merged',) [2020-12-05 07:01:16,568] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('/beegfs/mk5636/logs/html/H7KKVBGXH/merged',) [2020-12-05 07:01:19,797] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/H7KKVBGXH/merged',) [2020-12-05 07:01:29,327] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7KKVBGXH/merged',) [2020-12-05 07:01:32,501] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7KKVBGXH/merged',) [2020-12-05 07:01:32,789] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7KKVBGXH/merged',) [2020-12-05 07:01:32,842] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('/beegfs/mk5636/logs/html/H7KKVBGXH/merged',) [2020-12-05 07:01:32,943] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('/beegfs/mk5636/logs/html/H7KKVBGXH/merged',) [2020-12-05 07:01:36,044] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7KKVBGXH/merged',) [2020-12-05 07:01:54,990] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2020-12-05 07:01:55,098] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7KKVBGXH/merged',) [2020-12-05 07:01:55,154] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7KKVBGXH/merged',) [2020-12-05 07:01:58,375] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7KKVBGXH/merged',) [2020-12-05 07:02:01,446] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7KKVBGXH/merged',) [2020-12-05 07:02:03,974] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7KKVBGXH/merged',) [2020-12-05 07:02:06,335] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('/beegfs/mk5636/logs/html/H7KKVBGXH/merged',) [2020-12-05 07:02:09,496] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/H7KKVBGXH/merged',) [2020-12-05 07:02:09,570] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7KKVBGXH/merged',) [2020-12-05 07:04:28,974] multiqc.modules.fastqc.fastqc [INFO ] Found 514 reports [2020-12-05 07:05:51,348] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H7KKVBGXH/merged',) [2020-12-05 07:05:51,352] multiqc.plots.table [DEBUG ] Plotting beeswarm instead of table, 514 samples [2020-12-05 07:05:51,372] multiqc [INFO ] Report : multiqc_report.html [2020-12-05 07:05:51,380] multiqc [INFO ] Data : multiqc_data [2020-12-05 07:05:51,380] multiqc [DEBUG ] Moving data file from '/state/partition1/job-14052081/tmpUtuptf/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Counts.txt' to '/beegfs/mk5636/logs/html/H7KKVBGXH/merged/multiqc_data' [2020-12-05 07:05:51,406] multiqc [DEBUG ] Moving data file from '/state/partition1/job-14052081/tmpUtuptf/multiqc_data/mqc_fastqc_per_base_sequence_quality_plot_1.txt' to '/beegfs/mk5636/logs/html/H7KKVBGXH/merged/multiqc_data' [2020-12-05 07:05:51,423] multiqc [DEBUG ] Moving data file from '/state/partition1/job-14052081/tmpUtuptf/multiqc_data/multiqc_fastqc.txt' to '/beegfs/mk5636/logs/html/H7KKVBGXH/merged/multiqc_data' [2020-12-05 07:05:51,452] multiqc [DEBUG ] Moving data file from '/state/partition1/job-14052081/tmpUtuptf/multiqc_data/mqc_fastqc_per_base_n_content_plot_1.txt' to '/beegfs/mk5636/logs/html/H7KKVBGXH/merged/multiqc_data' [2020-12-05 07:05:51,470] multiqc [DEBUG ] Moving data file from '/state/partition1/job-14052081/tmpUtuptf/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Percentages.txt' to '/beegfs/mk5636/logs/html/H7KKVBGXH/merged/multiqc_data' [2020-12-05 07:05:51,485] multiqc [DEBUG ] Moving data file from '/state/partition1/job-14052081/tmpUtuptf/multiqc_data/mqc_fastqc_adapter_content_plot_1.txt' to '/beegfs/mk5636/logs/html/H7KKVBGXH/merged/multiqc_data' [2020-12-05 07:05:51,504] multiqc [DEBUG ] Moving data file from '/state/partition1/job-14052081/tmpUtuptf/multiqc_data/mqc_fastqc_sequence_duplication_levels_plot_1.txt' to '/beegfs/mk5636/logs/html/H7KKVBGXH/merged/multiqc_data' [2020-12-05 07:05:51,539] multiqc [DEBUG ] Moving data file from '/state/partition1/job-14052081/tmpUtuptf/multiqc_data/mqc_fastqc_per_sequence_quality_scores_plot_1.txt' to '/beegfs/mk5636/logs/html/H7KKVBGXH/merged/multiqc_data' [2020-12-05 07:05:51,565] multiqc [DEBUG ] Moving data file from '/state/partition1/job-14052081/tmpUtuptf/multiqc_data/mqc_fastqc_overrepresented_sequencesi_plot_1.txt' to '/beegfs/mk5636/logs/html/H7KKVBGXH/merged/multiqc_data' [2020-12-05 07:05:51,590] multiqc [DEBUG ] Moving data file from '/state/partition1/job-14052081/tmpUtuptf/multiqc_data/multiqc_sources.txt' to '/beegfs/mk5636/logs/html/H7KKVBGXH/merged/multiqc_data' [2020-12-05 07:05:51,839] multiqc [INFO ] MultiQC complete