[2019-08-28 10:39:03,625] 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 [2019-08-28 10:39:03,626] multiqc [DEBUG ] No MultiQC config found: /home/mk5636/.multiqc_config.yaml [2019-08-28 10:39:03,626] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2019-08-28 10:39:03,638] multiqc [DEBUG ] Loading config settings from: /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml [2019-08-28 10:39:03,639] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2019-08-28 10:39:03,639] multiqc [DEBUG ] Command used: /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/H2HY7BGXC/merged [2019-08-28 10:39:03,639] multiqc [DEBUG ] Could not connect to multiqc.info for version check [2019-08-28 10:39:03,639] multiqc [INFO ] This is MultiQC v1.0.dev0 [2019-08-28 10:39:03,639] multiqc [DEBUG ] Command : /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/H2HY7BGXC/merged [2019-08-28 10:39:03,639] multiqc [DEBUG ] Working dir : /beegfs/mk5636/logs/html/H2HY7BGXC/merged [2019-08-28 10:39:03,639] multiqc [INFO ] Template : default [2019-08-28 10:39:03,639] multiqc [DEBUG ] Running in --force mode, will overwrite any existing reports. [2019-08-28 10:39:03,639] multiqc [INFO ] Searching '/beegfs/mk5636/logs/html/H2HY7BGXC/merged' [2019-08-28 10:39:03,639] 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 [2019-08-28 10:39:03,640] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-2807947/tmpUVeTIv [2019-08-28 10:39:03,724] multiqc [DEBUG ] Ignoring directory as matched fn_ignore_dirs: /beegfs/mk5636/logs/html/H2HY7BGXC/merged/multiqc_data [2019-08-28 10:39:03,773] multiqc [DEBUG ] Ignoring file as too large: undetermined_barcodes.txt [2019-08-28 10:39:04,158] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('/beegfs/mk5636/logs/html/H2HY7BGXC/merged',) [2019-08-28 10:39:04,217] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 29 samples (table) [2019-08-28 10:39:04,229] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2019-08-28 10:39:04,231] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2019-08-28 10:39:04,289] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H2HY7BGXC/merged',) [2019-08-28 10:39:04,311] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H2HY7BGXC/merged',) [2019-08-28 10:39:04,322] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2019-08-28 10:39:04,398] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H2HY7BGXC/merged',) [2019-08-28 10:39:07,613] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('/beegfs/mk5636/logs/html/H2HY7BGXC/merged',) [2019-08-28 10:39:07,635] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H2HY7BGXC/merged',) [2019-08-28 10:39:09,333] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H2HY7BGXC/merged',) [2019-08-28 10:39:09,355] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H2HY7BGXC/merged',) [2019-08-28 10:39:09,388] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('/beegfs/mk5636/logs/html/H2HY7BGXC/merged',) [2019-08-28 10:39:09,866] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/H2HY7BGXC/merged',) [2019-08-28 10:39:10,233] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H2HY7BGXC/merged',) [2019-08-28 10:39:10,594] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H2HY7BGXC/merged',) [2019-08-28 10:39:11,003] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H2HY7BGXC/merged',) [2019-08-28 10:39:11,024] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H2HY7BGXC/merged',) [2019-08-28 10:39:15,324] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H2HY7BGXC/merged',) [2019-08-28 10:39:15,348] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('/beegfs/mk5636/logs/html/H2HY7BGXC/merged',) [2019-08-28 10:39:15,767] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/H2HY7BGXC/merged',) [2019-08-28 10:39:16,977] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H2HY7BGXC/merged',) [2019-08-28 10:39:17,338] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H2HY7BGXC/merged',) [2019-08-28 10:39:17,410] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H2HY7BGXC/merged',) [2019-08-28 10:39:17,431] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('/beegfs/mk5636/logs/html/H2HY7BGXC/merged',) [2019-08-28 10:39:17,465] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('/beegfs/mk5636/logs/html/H2HY7BGXC/merged',) [2019-08-28 10:39:17,821] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H2HY7BGXC/merged',) [2019-08-28 10:39:20,278] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2019-08-28 10:39:20,313] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H2HY7BGXC/merged',) [2019-08-28 10:39:20,334] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H2HY7BGXC/merged',) [2019-08-28 10:39:20,726] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H2HY7BGXC/merged',) [2019-08-28 10:39:21,113] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H2HY7BGXC/merged',) [2019-08-28 10:39:21,503] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H2HY7BGXC/merged',) [2019-08-28 10:39:21,898] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('/beegfs/mk5636/logs/html/H2HY7BGXC/merged',) [2019-08-28 10:39:22,287] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/H2HY7BGXC/merged',) [2019-08-28 10:39:22,308] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H2HY7BGXC/merged',) [2019-08-28 10:39:26,243] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'H2HY7BGXC_n01_Lu_RNAseq_Aug2019_Sample_15_fastqc.zip' - Bad zip file [2019-08-28 10:39:26,244] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-08-28 10:39:26,711] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'H2HY7BGXC_n02_Lu_RNAseq_Aug2019_Sample_24_fastqc.zip' - Bad zip file [2019-08-28 10:39:26,711] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-08-28 10:39:27,168] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'H2HY7BGXC_n01_Lu_RNAseq_Aug2019_Sample_25_fastqc.zip' - Bad zip file [2019-08-28 10:39:27,168] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-08-28 10:39:27,640] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'H2HY7BGXC_n01_Lu_RNAseq_Aug2019_Sample_3_fastqc.zip' - Bad zip file [2019-08-28 10:39:27,640] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-08-28 10:39:29,470] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'H2HY7BGXC_n01_Lu_RNAseq_Aug2019_Sample_17_fastqc.zip' - Bad zip file [2019-08-28 10:39:29,470] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-08-28 10:39:35,784] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'H2HY7BGXC_n02_Lu_RNAseq_Aug2019_Sample_3_fastqc.zip' - Bad zip file [2019-08-28 10:39:35,785] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-08-28 10:39:36,263] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'H2HY7BGXC_n01_Lu_RNAseq_Aug2019_Sample_16_fastqc.zip' - Bad zip file [2019-08-28 10:39:36,264] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-08-28 10:39:36,973] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'H2HY7BGXC_n02_Lu_RNAseq_Aug2019_Sample_16_fastqc.zip' - Bad zip file [2019-08-28 10:39:36,973] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-08-28 10:39:37,858] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'H2HY7BGXC_n02_Lu_RNAseq_Aug2019_Sample_25_fastqc.zip' - Bad zip file [2019-08-28 10:39:37,858] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-08-28 10:39:38,343] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'H2HY7BGXC_n01_Lu_RNAseq_Aug2019_Sample_4_fastqc.zip' - Bad zip file [2019-08-28 10:39:38,343] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-08-28 10:39:40,593] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'H2HY7BGXC_n02_Lu_RNAseq_Aug2019_Sample_4_fastqc.zip' - Bad zip file [2019-08-28 10:39:40,593] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-08-28 10:39:43,258] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'H2HY7BGXC_n02_Lu_RNAseq_Aug2019_Sample_17_fastqc.zip' - Bad zip file [2019-08-28 10:39:43,258] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-08-28 10:39:43,688] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'H2HY7BGXC_n01_Lu_RNAseq_Aug2019_Sample_24_fastqc.zip' - Bad zip file [2019-08-28 10:39:43,688] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-08-28 10:39:43,689] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'H2HY7BGXC_n02_Lu_RNAseq_Aug2019_Sample_15_fastqc.zip' - Bad zip file [2019-08-28 10:39:43,689] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2019-08-28 10:39:45,041] multiqc.modules.fastqc.fastqc [INFO ] Found 100 reports [2019-08-28 10:39:47,492] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/H2HY7BGXC/merged',) [2019-08-28 10:39:47,637] multiqc [WARNING] Deleting : multiqc_report.html (-f was specified) [2019-08-28 10:39:47,639] multiqc [INFO ] Report : multiqc_report.html [2019-08-28 10:39:47,639] multiqc [WARNING] Deleting : multiqc_data (-f was specified) [2019-08-28 10:39:47,744] multiqc [INFO ] Data : multiqc_data [2019-08-28 10:39:47,745] multiqc [DEBUG ] Moving data file from '/state/partition1/job-2807947/tmpUVeTIv/multiqc_data/multiqc_sources.txt' to '/beegfs/mk5636/logs/html/H2HY7BGXC/merged/multiqc_data' [2019-08-28 10:39:47,748] multiqc [DEBUG ] Moving data file from '/state/partition1/job-2807947/tmpUVeTIv/multiqc_data/multiqc_general_stats.txt' to '/beegfs/mk5636/logs/html/H2HY7BGXC/merged/multiqc_data' [2019-08-28 10:39:47,751] multiqc [DEBUG ] Moving data file from '/state/partition1/job-2807947/tmpUVeTIv/multiqc_data/multiqc_fastqc.txt' to '/beegfs/mk5636/logs/html/H2HY7BGXC/merged/multiqc_data' [2019-08-28 10:39:47,906] multiqc [INFO ] MultiQC complete