[2020-01-28 01:50:48,642] 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 [2020-01-28 01:50:48,643] multiqc [DEBUG ] No MultiQC config found: /home/mk5636/.multiqc_config.yaml [2020-01-28 01:50:48,643] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2020-01-28 01:50:48,644] multiqc [DEBUG ] Loading config settings from: /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml [2020-01-28 01:50:48,644] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2020-01-28 01:50:48,644] multiqc [DEBUG ] Command used: /share/apps/multiqc/20170330/intel/bin/multiqc . -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/HJMJ5DRXX/merged [2020-01-28 01:50:48,644] multiqc [DEBUG ] Could not connect to multiqc.info for version check [2020-01-28 01:50:48,645] multiqc [INFO ] This is MultiQC v1.0.dev0 [2020-01-28 01:50:48,645] multiqc [DEBUG ] Command : /share/apps/multiqc/20170330/intel/bin/multiqc . -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/HJMJ5DRXX/merged [2020-01-28 01:50:48,645] multiqc [DEBUG ] Working dir : /beegfs/mk5636/logs/html/HJMJ5DRXX/merged [2020-01-28 01:50:48,645] multiqc [INFO ] Template : default [2020-01-28 01:50:48,645] multiqc [INFO ] Searching '.' [2020-01-28 01:50:48,645] multiqc [INFO ] Searching '/beegfs/mk5636/logs/html/HJMJ5DRXX/merged' [2020-01-28 01:50:48,645] 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 [2020-01-28 01:50:48,646] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-7106275/tmpz5BRX3 [2020-01-28 01:50:49,011] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('.', '/beegfs/mk5636/logs/html/HJMJ5DRXX/merged') [2020-01-28 01:50:49,073] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 48 samples (table) [2020-01-28 01:50:49,082] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2020-01-28 01:50:49,084] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2020-01-28 01:50:49,124] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('.', '/beegfs/mk5636/logs/html/HJMJ5DRXX/merged') [2020-01-28 01:50:49,139] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('.', '/beegfs/mk5636/logs/html/HJMJ5DRXX/merged') [2020-01-28 01:50:49,146] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2020-01-28 01:50:49,198] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('.', '/beegfs/mk5636/logs/html/HJMJ5DRXX/merged') [2020-01-28 01:50:49,723] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('.', '/beegfs/mk5636/logs/html/HJMJ5DRXX/merged') [2020-01-28 01:50:49,738] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('.', '/beegfs/mk5636/logs/html/HJMJ5DRXX/merged') [2020-01-28 01:50:51,358] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('.', '/beegfs/mk5636/logs/html/HJMJ5DRXX/merged') [2020-01-28 01:50:51,374] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('.', '/beegfs/mk5636/logs/html/HJMJ5DRXX/merged') [2020-01-28 01:50:51,396] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('.', '/beegfs/mk5636/logs/html/HJMJ5DRXX/merged') [2020-01-28 01:50:51,792] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('.', '/beegfs/mk5636/logs/html/HJMJ5DRXX/merged') [2020-01-28 01:50:52,178] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('.', '/beegfs/mk5636/logs/html/HJMJ5DRXX/merged') [2020-01-28 01:50:52,561] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('.', '/beegfs/mk5636/logs/html/HJMJ5DRXX/merged') [2020-01-28 01:50:52,956] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('.', '/beegfs/mk5636/logs/html/HJMJ5DRXX/merged') [2020-01-28 01:50:52,970] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('.', '/beegfs/mk5636/logs/html/HJMJ5DRXX/merged') [2020-01-28 01:50:57,015] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('.', '/beegfs/mk5636/logs/html/HJMJ5DRXX/merged') [2020-01-28 01:50:57,034] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('.', '/beegfs/mk5636/logs/html/HJMJ5DRXX/merged') [2020-01-28 01:50:57,399] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('.', '/beegfs/mk5636/logs/html/HJMJ5DRXX/merged') [2020-01-28 01:50:58,590] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('.', '/beegfs/mk5636/logs/html/HJMJ5DRXX/merged') [2020-01-28 01:50:58,956] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('.', '/beegfs/mk5636/logs/html/HJMJ5DRXX/merged') [2020-01-28 01:50:59,004] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('.', '/beegfs/mk5636/logs/html/HJMJ5DRXX/merged') [2020-01-28 01:50:59,018] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('.', '/beegfs/mk5636/logs/html/HJMJ5DRXX/merged') [2020-01-28 01:50:59,041] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('.', '/beegfs/mk5636/logs/html/HJMJ5DRXX/merged') [2020-01-28 01:50:59,425] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('.', '/beegfs/mk5636/logs/html/HJMJ5DRXX/merged') [2020-01-28 01:51:01,895] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2020-01-28 01:51:01,918] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('.', '/beegfs/mk5636/logs/html/HJMJ5DRXX/merged') [2020-01-28 01:51:01,931] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('.', '/beegfs/mk5636/logs/html/HJMJ5DRXX/merged') [2020-01-28 01:51:02,318] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('.', '/beegfs/mk5636/logs/html/HJMJ5DRXX/merged') [2020-01-28 01:51:02,687] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('.', '/beegfs/mk5636/logs/html/HJMJ5DRXX/merged') [2020-01-28 01:51:03,051] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('.', '/beegfs/mk5636/logs/html/HJMJ5DRXX/merged') [2020-01-28 01:51:03,435] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('.', '/beegfs/mk5636/logs/html/HJMJ5DRXX/merged') [2020-01-28 01:51:03,818] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('.', '/beegfs/mk5636/logs/html/HJMJ5DRXX/merged') [2020-01-28 01:51:03,833] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('.', '/beegfs/mk5636/logs/html/HJMJ5DRXX/merged') [2020-01-28 01:51:12,549] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HJMJ5DRXX_n01_11_NxW_C4-2_fastqc.zip' as already parsed 'HJMJ5DRXX_n01_11_NxW_C4-2' [2020-01-28 01:51:12,550] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HJMJ5DRXX_n01_2_NxW_C1-2_fastqc.zip' as already parsed 'HJMJ5DRXX_n01_2_NxW_C1-2' [2020-01-28 01:51:12,551] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HJMJ5DRXX_n01_29_NxW_C10-2_fastqc.zip' as already parsed 'HJMJ5DRXX_n01_29_NxW_C10-2' [2020-01-28 01:51:12,551] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HJMJ5DRXX_n01_28_NxW_C10-1_fastqc.zip' as already parsed 'HJMJ5DRXX_n01_28_NxW_C10-1' [2020-01-28 01:51:12,552] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HJMJ5DRXX_n01_33_NxW_C11-3_fastqc.zip' as already parsed 'HJMJ5DRXX_n01_33_NxW_C11-3' [2020-01-28 01:51:12,553] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HJMJ5DRXX_n01_16_NxW_C6-1_fastqc.zip' as already parsed 'HJMJ5DRXX_n01_16_NxW_C6-1' [2020-01-28 01:51:12,553] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HJMJ5DRXX_n01_39_NxW_C13-3_fastqc.zip' as already parsed 'HJMJ5DRXX_n01_39_NxW_C13-3' [2020-01-28 01:51:12,553] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HJMJ5DRXX_n01_25_NxW_C9-1_fastqc.zip' as already parsed 'HJMJ5DRXX_n01_25_NxW_C9-1' [2020-01-28 01:51:12,554] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HJMJ5DRXX_n01_13_NxW_C5-1_fastqc.zip' as already parsed 'HJMJ5DRXX_n01_13_NxW_C5-1' [2020-01-28 01:51:12,555] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HJMJ5DRXX_n01_34_NxW_C12-1_fastqc.zip' as already parsed 'HJMJ5DRXX_n01_34_NxW_C12-1' [2020-01-28 01:51:12,555] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HJMJ5DRXX_n01_41_NxW_C14-2_fastqc.zip' as already parsed 'HJMJ5DRXX_n01_41_NxW_C14-2' [2020-01-28 01:51:12,556] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HJMJ5DRXX_n01_42_NxW_C14-3_fastqc.zip' as already parsed 'HJMJ5DRXX_n01_42_NxW_C14-3' [2020-01-28 01:51:12,556] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HJMJ5DRXX_n01_1_NxW_C1-1_fastqc.zip' as already parsed 'HJMJ5DRXX_n01_1_NxW_C1-1' [2020-01-28 01:51:12,557] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HJMJ5DRXX_n01_23_NxW_C8-2_fastqc.zip' as already parsed 'HJMJ5DRXX_n01_23_NxW_C8-2' [2020-01-28 01:51:12,557] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HJMJ5DRXX_n01_37_NxW_C13-1_fastqc.zip' as already parsed 'HJMJ5DRXX_n01_37_NxW_C13-1' [2020-01-28 01:51:12,558] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HJMJ5DRXX_n01_30_NxW_C10-3_fastqc.zip' as already parsed 'HJMJ5DRXX_n01_30_NxW_C10-3' [2020-01-28 01:51:12,558] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HJMJ5DRXX_n01_19_NxW_C7-1_fastqc.zip' as already parsed 'HJMJ5DRXX_n01_19_NxW_C7-1' [2020-01-28 01:51:12,559] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HJMJ5DRXX_n01_15_NxW_C5-3_fastqc.zip' as already parsed 'HJMJ5DRXX_n01_15_NxW_C5-3' [2020-01-28 01:51:12,559] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HJMJ5DRXX_n01_45_NxW_C15-3_fastqc.zip' as already parsed 'HJMJ5DRXX_n01_45_NxW_C15-3' [2020-01-28 01:51:12,560] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HJMJ5DRXX_n01_10_NxW_C4-1_fastqc.zip' as already parsed 'HJMJ5DRXX_n01_10_NxW_C4-1' [2020-01-28 01:51:12,560] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HJMJ5DRXX_n01_26_NxW_C9-2_fastqc.zip' as already parsed 'HJMJ5DRXX_n01_26_NxW_C9-2' [2020-01-28 01:51:12,561] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HJMJ5DRXX_n01_7_NxW_C3-1_fastqc.zip' as already parsed 'HJMJ5DRXX_n01_7_NxW_C3-1' [2020-01-28 01:51:12,561] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HJMJ5DRXX_n01_12_NxW_C4-3_fastqc.zip' as already parsed 'HJMJ5DRXX_n01_12_NxW_C4-3' [2020-01-28 01:51:12,562] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HJMJ5DRXX_n01_22_NxW_C8-1_fastqc.zip' as already parsed 'HJMJ5DRXX_n01_22_NxW_C8-1' [2020-01-28 01:51:12,562] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HJMJ5DRXX_n01_38_NxW_C13-2_fastqc.zip' as already parsed 'HJMJ5DRXX_n01_38_NxW_C13-2' [2020-01-28 01:51:12,563] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HJMJ5DRXX_n01_36_NxW_C12-3_fastqc.zip' as already parsed 'HJMJ5DRXX_n01_36_NxW_C12-3' [2020-01-28 01:51:12,563] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HJMJ5DRXX_n01_18_NxW_C6-3_fastqc.zip' as already parsed 'HJMJ5DRXX_n01_18_NxW_C6-3' [2020-01-28 01:51:12,564] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HJMJ5DRXX_n01_32_NxW_C11-2_fastqc.zip' as already parsed 'HJMJ5DRXX_n01_32_NxW_C11-2' [2020-01-28 01:51:12,564] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HJMJ5DRXX_n01_43_NxW_C15-1_fastqc.zip' as already parsed 'HJMJ5DRXX_n01_43_NxW_C15-1' [2020-01-28 01:51:12,565] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HJMJ5DRXX_n01_3_NxW_C2-3_fastqc.zip' as already parsed 'HJMJ5DRXX_n01_3_NxW_C2-3' [2020-01-28 01:51:12,565] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HJMJ5DRXX_n01_21_NxW_C7-3_fastqc.zip' as already parsed 'HJMJ5DRXX_n01_21_NxW_C7-3' [2020-01-28 01:51:12,566] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HJMJ5DRXX_n01_14_NxW_C5-2_fastqc.zip' as already parsed 'HJMJ5DRXX_n01_14_NxW_C5-2' [2020-01-28 01:51:12,566] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HJMJ5DRXX_n01_46_NxW_C16-1_fastqc.zip' as already parsed 'HJMJ5DRXX_n01_46_NxW_C16-1' [2020-01-28 01:51:12,567] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HJMJ5DRXX_n01_17_NxW_C6-2_fastqc.zip' as already parsed 'HJMJ5DRXX_n01_17_NxW_C6-2' [2020-01-28 01:51:12,567] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HJMJ5DRXX_n01_47_NxW_C16-2_fastqc.zip' as already parsed 'HJMJ5DRXX_n01_47_NxW_C16-2' [2020-01-28 01:51:12,568] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HJMJ5DRXX_n01_35_NxW_C12-2_fastqc.zip' as already parsed 'HJMJ5DRXX_n01_35_NxW_C12-2' [2020-01-28 01:51:12,569] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HJMJ5DRXX_n01_27_NxW_C9-3_fastqc.zip' as already parsed 'HJMJ5DRXX_n01_27_NxW_C9-3' [2020-01-28 01:51:12,569] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HJMJ5DRXX_n01_8_NxW_C3-2_fastqc.zip' as already parsed 'HJMJ5DRXX_n01_8_NxW_C3-2' [2020-01-28 01:51:12,570] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HJMJ5DRXX_n01_44_NxW_C15-2_fastqc.zip' as already parsed 'HJMJ5DRXX_n01_44_NxW_C15-2' [2020-01-28 01:51:12,570] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HJMJ5DRXX_n01_31_NxW_C11-1_fastqc.zip' as already parsed 'HJMJ5DRXX_n01_31_NxW_C11-1' [2020-01-28 01:51:12,571] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HJMJ5DRXX_n01_9_NxW_C3-3_fastqc.zip' as already parsed 'HJMJ5DRXX_n01_9_NxW_C3-3' [2020-01-28 01:51:12,571] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HJMJ5DRXX_n01_4_NxW_C2-1_fastqc.zip' as already parsed 'HJMJ5DRXX_n01_4_NxW_C2-1' [2020-01-28 01:51:12,572] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HJMJ5DRXX_n01_6_NxW_C2-3_fastqc.zip' as already parsed 'HJMJ5DRXX_n01_6_NxW_C2-3' [2020-01-28 01:51:12,572] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HJMJ5DRXX_n01_40_NxW_C14-1_fastqc.zip' as already parsed 'HJMJ5DRXX_n01_40_NxW_C14-1' [2020-01-28 01:51:12,573] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HJMJ5DRXX_n01_5_NxW_C2-2_fastqc.zip' as already parsed 'HJMJ5DRXX_n01_5_NxW_C2-2' [2020-01-28 01:51:12,573] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HJMJ5DRXX_n01_20_NxW_C7-2_fastqc.zip' as already parsed 'HJMJ5DRXX_n01_20_NxW_C7-2' [2020-01-28 01:51:12,574] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HJMJ5DRXX_n01_24_NxW_C8-3_fastqc.zip' as already parsed 'HJMJ5DRXX_n01_24_NxW_C8-3' [2020-01-28 01:51:12,574] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HJMJ5DRXX_n01_undetermined_fastqc.zip' as already parsed 'HJMJ5DRXX_n01_undetermined' [2020-01-28 01:51:12,575] multiqc.modules.fastqc.fastqc [INFO ] Found 48 reports [2020-01-28 01:51:15,656] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('.', '/beegfs/mk5636/logs/html/HJMJ5DRXX/merged') [2020-01-28 01:51:15,711] multiqc [INFO ] Report : multiqc_report.html [2020-01-28 01:51:15,713] multiqc [INFO ] Data : multiqc_data [2020-01-28 01:51:15,713] multiqc [DEBUG ] Moving data file from '/state/partition1/job-7106275/tmpz5BRX3/multiqc_data/multiqc_general_stats.txt' to '/beegfs/mk5636/logs/html/HJMJ5DRXX/merged/multiqc_data' [2020-01-28 01:51:15,716] multiqc [DEBUG ] Moving data file from '/state/partition1/job-7106275/tmpz5BRX3/multiqc_data/multiqc_fastqc.txt' to '/beegfs/mk5636/logs/html/HJMJ5DRXX/merged/multiqc_data' [2020-01-28 01:51:15,718] multiqc [DEBUG ] Moving data file from '/state/partition1/job-7106275/tmpz5BRX3/multiqc_data/multiqc_sources.txt' to '/beegfs/mk5636/logs/html/HJMJ5DRXX/merged/multiqc_data' [2020-01-28 01:51:15,836] multiqc [INFO ] MultiQC complete