[2020-10-02 09:02:21,316] 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 [2020-10-02 09:02:21,317] multiqc [DEBUG ] No MultiQC config found: /home/mk5636/.multiqc_config.yaml [2020-10-02 09:02:21,317] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2020-10-02 09:02:21,329] multiqc [DEBUG ] Loading config settings from: /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml [2020-10-02 09:02:21,329] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2020-10-02 09:02:21,329] multiqc [DEBUG ] Command used: /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/HTGTLBGXG/merged [2020-10-02 09:02:21,329] multiqc [DEBUG ] Could not connect to multiqc.info for version check [2020-10-02 09:02:21,329] multiqc [INFO ] This is MultiQC v1.0.dev0 [2020-10-02 09:02:21,330] multiqc [DEBUG ] Command : /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/HTGTLBGXG/merged [2020-10-02 09:02:21,330] multiqc [DEBUG ] Working dir : /beegfs/mk5636/logs/html/HTGTLBGXG/merged [2020-10-02 09:02:21,330] multiqc [INFO ] Template : default [2020-10-02 09:02:21,330] multiqc [DEBUG ] Running in --force mode, will overwrite any existing reports. [2020-10-02 09:02:21,330] multiqc [INFO ] Searching '/beegfs/mk5636/logs/html/HTGTLBGXG/merged' [2020-10-02 09:02:21,330] 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 [2020-10-02 09:02:21,330] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-12850945/tmp8ba14J [2020-10-02 09:02:21,668] multiqc [DEBUG ] Ignoring directory as matched fn_ignore_dirs: /beegfs/mk5636/logs/html/HTGTLBGXG/merged/multiqc_data [2020-10-02 09:02:22,177] multiqc [DEBUG ] Ignoring file as too large: undetermined_barcodes.txt [2020-10-02 09:02:23,467] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('/beegfs/mk5636/logs/html/HTGTLBGXG/merged',) [2020-10-02 09:02:23,889] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 385 samples (table) [2020-10-02 09:02:23,899] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2020-10-02 09:02:23,901] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2020-10-02 09:02:24,441] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HTGTLBGXG/merged',) [2020-10-02 09:02:24,576] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HTGTLBGXG/merged',) [2020-10-02 09:02:24,586] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2020-10-02 09:02:25,478] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HTGTLBGXG/merged',) [2020-10-02 09:03:20,454] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('/beegfs/mk5636/logs/html/HTGTLBGXG/merged',) [2020-10-02 09:03:20,611] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HTGTLBGXG/merged',) [2020-10-02 09:03:37,380] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HTGTLBGXG/merged',) [2020-10-02 09:03:37,517] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HTGTLBGXG/merged',) [2020-10-02 09:03:37,781] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('/beegfs/mk5636/logs/html/HTGTLBGXG/merged',) [2020-10-02 09:03:41,883] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HTGTLBGXG/merged',) [2020-10-02 09:03:45,978] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HTGTLBGXG/merged',) [2020-10-02 09:03:50,040] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HTGTLBGXG/merged',) [2020-10-02 09:03:54,055] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HTGTLBGXG/merged',) [2020-10-02 09:03:54,191] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HTGTLBGXG/merged',) [2020-10-02 09:04:35,239] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HTGTLBGXG/merged',) [2020-10-02 09:04:35,378] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('/beegfs/mk5636/logs/html/HTGTLBGXG/merged',) [2020-10-02 09:04:39,414] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HTGTLBGXG/merged',) [2020-10-02 09:04:51,671] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HTGTLBGXG/merged',) [2020-10-02 09:04:55,741] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HTGTLBGXG/merged',) [2020-10-02 09:04:56,400] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HTGTLBGXG/merged',) [2020-10-02 09:04:56,538] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('/beegfs/mk5636/logs/html/HTGTLBGXG/merged',) [2020-10-02 09:04:56,803] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('/beegfs/mk5636/logs/html/HTGTLBGXG/merged',) [2020-10-02 09:05:00,816] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HTGTLBGXG/merged',) [2020-10-02 09:05:25,265] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2020-10-02 09:05:25,532] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HTGTLBGXG/merged',) [2020-10-02 09:05:25,666] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HTGTLBGXG/merged',) [2020-10-02 09:05:29,733] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HTGTLBGXG/merged',) [2020-10-02 09:05:33,680] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HTGTLBGXG/merged',) [2020-10-02 09:05:37,712] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HTGTLBGXG/merged',) [2020-10-02 09:05:42,801] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('/beegfs/mk5636/logs/html/HTGTLBGXG/merged',) [2020-10-02 09:05:46,830] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HTGTLBGXG/merged',) [2020-10-02 09:05:46,966] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HTGTLBGXG/merged',) [2020-10-02 09:05:48,369] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HTGTLBGXG_n02_S1_R1_E02_FD_fastqc.zip' - Bad zip file [2020-10-02 09:05:48,369] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2020-10-02 09:05:52,766] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HTGTLBGXG_n01_S1_R1_E02_FD_fastqc.zip' - Bad zip file [2020-10-02 09:05:52,766] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2020-10-02 09:05:58,451] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HTGTLBGXG_n02_S2_R1_D06_FD_fastqc.zip' - Bad zip file [2020-10-02 09:05:58,451] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2020-10-02 09:06:01,555] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HTGTLBGXG_n01_S2_R1_A02_FD_fastqc.zip' - Bad zip file [2020-10-02 09:06:01,555] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2020-10-02 09:06:04,850] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HTGTLBGXG_n02_S1_R1_G02_FD_fastqc.zip' - Bad zip file [2020-10-02 09:06:04,850] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2020-10-02 09:06:10,104] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HTGTLBGXG_n02_S1_R1_A02_FD_fastqc.zip' - Bad zip file [2020-10-02 09:06:10,104] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2020-10-02 09:06:21,813] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HTGTLBGXG_n01_S2_R1_E02_FD_fastqc.zip' - Bad zip file [2020-10-02 09:06:21,813] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2020-10-02 09:06:24,152] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HTGTLBGXG_n02_S2_R1_G02_FD_fastqc.zip' - Bad zip file [2020-10-02 09:06:24,153] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2020-10-02 09:06:27,950] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HTGTLBGXG_n02_S1_R1_D02_FD_fastqc.zip' - Bad zip file [2020-10-02 09:06:27,950] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2020-10-02 09:06:34,575] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HTGTLBGXG_n02_S2_R1_C02_FD_fastqc.zip' - Bad zip file [2020-10-02 09:06:34,576] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2020-10-02 09:06:37,836] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HTGTLBGXG_n02_S2_R1_E02_FD_fastqc.zip' - Bad zip file [2020-10-02 09:06:37,836] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2020-10-02 09:06:49,467] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HTGTLBGXG_n02_S1_R1_H02_FD_fastqc.zip' - Bad zip file [2020-10-02 09:06:49,467] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2020-10-02 09:06:52,293] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HTGTLBGXG_n01_S2_R1_G02_FD_fastqc.zip' - Bad zip file [2020-10-02 09:06:52,293] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2020-10-02 09:07:27,478] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HTGTLBGXG_n01_S2_R1_C02_FD_fastqc.zip' - Bad zip file [2020-10-02 09:07:27,478] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2020-10-02 09:07:59,566] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HTGTLBGXG_n02_S1_R1_F02_FD_fastqc.zip' - Bad zip file [2020-10-02 09:07:59,566] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2020-10-02 09:08:06,484] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HTGTLBGXG_n01_S1_R1_A02_FD_fastqc.zip' - Bad zip file [2020-10-02 09:08:06,484] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2020-10-02 09:08:06,733] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HTGTLBGXG_n01_S1_R1_H02_FD_fastqc.zip' - Bad zip file [2020-10-02 09:08:06,733] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2020-10-02 09:08:19,671] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HTGTLBGXG_n01_S1_R1_G02_FD_fastqc.zip' - Bad zip file [2020-10-02 09:08:19,671] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2020-10-02 09:08:22,785] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HTGTLBGXG_n02_S2_R1_F02_FD_fastqc.zip' - Bad zip file [2020-10-02 09:08:22,785] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2020-10-02 09:08:30,798] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HTGTLBGXG_n01_S1_R1_F02_FD_fastqc.zip' - Bad zip file [2020-10-02 09:08:30,798] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2020-10-02 09:08:47,732] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HTGTLBGXG_n01_S1_R1_D02_FD_fastqc.zip' - Bad zip file [2020-10-02 09:08:47,732] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2020-10-02 09:08:56,085] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HTGTLBGXG_n02_S2_R1_A02_FD_fastqc.zip' - Bad zip file [2020-10-02 09:08:56,085] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2020-10-02 09:09:10,606] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HTGTLBGXG_n01_S2_R1_F02_FD_fastqc.zip' - Bad zip file [2020-10-02 09:09:10,606] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2020-10-02 09:09:23,270] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HTGTLBGXG_n01_S2_R1_D06_FD_fastqc.zip' - Bad zip file [2020-10-02 09:09:23,271] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2020-10-02 09:09:23,313] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HTGTLBGXG_n01_S1_R1_C02_FD_fastqc.zip' - Bad zip file [2020-10-02 09:09:23,313] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2020-10-02 09:09:50,076] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HTGTLBGXG_n02_S1_R1_C02_FD_fastqc.zip' - Bad zip file [2020-10-02 09:09:50,076] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2020-10-02 09:09:54,090] multiqc.modules.fastqc.fastqc [INFO ] Found 1512 reports [2020-10-02 09:13:53,195] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HTGTLBGXG/merged',) [2020-10-02 09:13:53,206] multiqc.plots.table [DEBUG ] Plotting beeswarm instead of table, 1512 samples [2020-10-02 09:13:53,231] multiqc [WARNING] Deleting : multiqc_report.html (-f was specified) [2020-10-02 09:13:53,236] multiqc [INFO ] Report : multiqc_report.html [2020-10-02 09:13:53,237] multiqc [WARNING] Deleting : multiqc_data (-f was specified) [2020-10-02 09:13:53,469] multiqc [INFO ] Data : multiqc_data [2020-10-02 09:13:53,469] multiqc [DEBUG ] Moving data file from '/state/partition1/job-12850945/tmp8ba14J/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Percentages.txt' to '/beegfs/mk5636/logs/html/HTGTLBGXG/merged/multiqc_data' [2020-10-02 09:13:53,632] multiqc [DEBUG ] Moving data file from '/state/partition1/job-12850945/tmp8ba14J/multiqc_data/mqc_fastqc_sequence_duplication_levels_plot_1.txt' to '/beegfs/mk5636/logs/html/HTGTLBGXG/merged/multiqc_data' [2020-10-02 09:13:53,731] multiqc [DEBUG ] Moving data file from '/state/partition1/job-12850945/tmp8ba14J/multiqc_data/multiqc_sources.txt' to '/beegfs/mk5636/logs/html/HTGTLBGXG/merged/multiqc_data' [2020-10-02 09:13:53,739] multiqc [DEBUG ] Moving data file from '/state/partition1/job-12850945/tmp8ba14J/multiqc_data/mqc_fastqc_overrepresented_sequencesi_plot_1.txt' to '/beegfs/mk5636/logs/html/HTGTLBGXG/merged/multiqc_data' [2020-10-02 09:13:53,807] multiqc [DEBUG ] Moving data file from '/state/partition1/job-12850945/tmp8ba14J/multiqc_data/mqc_fastqc_per_base_sequence_quality_plot_1.txt' to '/beegfs/mk5636/logs/html/HTGTLBGXG/merged/multiqc_data' [2020-10-02 09:13:53,863] multiqc [DEBUG ] Moving data file from '/state/partition1/job-12850945/tmp8ba14J/multiqc_data/mqc_fastqc_per_sequence_quality_scores_plot_1.txt' to '/beegfs/mk5636/logs/html/HTGTLBGXG/merged/multiqc_data' [2020-10-02 09:13:53,881] multiqc [DEBUG ] Moving data file from '/state/partition1/job-12850945/tmp8ba14J/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Counts.txt' to '/beegfs/mk5636/logs/html/HTGTLBGXG/merged/multiqc_data' [2020-10-02 09:13:53,899] multiqc [DEBUG ] Moving data file from '/state/partition1/job-12850945/tmp8ba14J/multiqc_data/mqc_fastqc_adapter_content_plot_1.txt' to '/beegfs/mk5636/logs/html/HTGTLBGXG/merged/multiqc_data' [2020-10-02 09:13:53,905] multiqc [DEBUG ] Moving data file from '/state/partition1/job-12850945/tmp8ba14J/multiqc_data/multiqc_fastqc.txt' to '/beegfs/mk5636/logs/html/HTGTLBGXG/merged/multiqc_data' [2020-10-02 09:13:53,925] multiqc [DEBUG ] Moving data file from '/state/partition1/job-12850945/tmp8ba14J/multiqc_data/mqc_fastqc_per_base_n_content_plot_1.txt' to '/beegfs/mk5636/logs/html/HTGTLBGXG/merged/multiqc_data' [2020-10-02 09:13:54,242] multiqc [INFO ] MultiQC complete