[2018-09-27 18:56:52,873] 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 [2018-09-27 18:56:52,873] multiqc [DEBUG ] No MultiQC config found: /home/mk5636/.multiqc_config.yaml [2018-09-27 18:56:52,873] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2018-09-27 18:56:52,888] multiqc [DEBUG ] Loading config settings from: /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml [2018-09-27 18:56:52,888] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2018-09-27 18:56:52,889] multiqc [DEBUG ] Command used: /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/HMGFWBGX7/merged [2018-09-27 18:56:52,889] multiqc [DEBUG ] Could not connect to multiqc.info for version check [2018-09-27 18:56:52,889] multiqc [INFO ] This is MultiQC v1.0.dev0 [2018-09-27 18:56:52,889] multiqc [DEBUG ] Command : /share/apps/multiqc/20170330/intel/bin/multiqc -f -c /home/mk5636/SCRIPTS/hpcpipe/mqc_config.yaml /beegfs/mk5636/logs/html/HMGFWBGX7/merged [2018-09-27 18:56:52,889] multiqc [DEBUG ] Working dir : /beegfs/mk5636/logs/html/HMGFWBGX7/merged [2018-09-27 18:56:52,889] multiqc [INFO ] Template : default [2018-09-27 18:56:52,889] multiqc [DEBUG ] Running in --force mode, will overwrite any existing reports. [2018-09-27 18:56:52,889] multiqc [INFO ] Searching '/beegfs/mk5636/logs/html/HMGFWBGX7/merged' [2018-09-27 18:56:52,889] 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 [2018-09-27 18:56:52,889] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-8895696/tmp5kYACn [2018-09-27 18:56:52,909] multiqc [DEBUG ] Ignoring directory as matched fn_ignore_dirs: /beegfs/mk5636/logs/html/HMGFWBGX7/merged/multiqc_data [2018-09-27 18:56:53,209] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('/beegfs/mk5636/logs/html/HMGFWBGX7/merged',) [2018-09-27 18:56:53,314] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 19 samples (table) [2018-09-27 18:56:53,316] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2018-09-27 18:56:53,357] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMGFWBGX7/merged',) [2018-09-27 18:56:53,371] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMGFWBGX7/merged',) [2018-09-27 18:56:53,376] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2018-09-27 18:56:53,432] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMGFWBGX7/merged',) [2018-09-27 18:57:05,417] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('/beegfs/mk5636/logs/html/HMGFWBGX7/merged',) [2018-09-27 18:57:05,430] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMGFWBGX7/merged',) [2018-09-27 18:57:06,529] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMGFWBGX7/merged',) [2018-09-27 18:57:06,543] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMGFWBGX7/merged',) [2018-09-27 18:57:06,565] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('/beegfs/mk5636/logs/html/HMGFWBGX7/merged',) [2018-09-27 18:57:06,833] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HMGFWBGX7/merged',) [2018-09-27 18:57:07,104] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMGFWBGX7/merged',) [2018-09-27 18:57:07,373] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMGFWBGX7/merged',) [2018-09-27 18:57:07,638] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMGFWBGX7/merged',) [2018-09-27 18:57:07,652] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMGFWBGX7/merged',) [2018-09-27 18:57:10,502] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMGFWBGX7/merged',) [2018-09-27 18:57:10,517] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('/beegfs/mk5636/logs/html/HMGFWBGX7/merged',) [2018-09-27 18:57:10,785] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HMGFWBGX7/merged',) [2018-09-27 18:57:11,579] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMGFWBGX7/merged',) [2018-09-27 18:57:11,843] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMGFWBGX7/merged',) [2018-09-27 18:57:11,894] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMGFWBGX7/merged',) [2018-09-27 18:57:11,907] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('/beegfs/mk5636/logs/html/HMGFWBGX7/merged',) [2018-09-27 18:57:11,929] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('/beegfs/mk5636/logs/html/HMGFWBGX7/merged',) [2018-09-27 18:57:12,194] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMGFWBGX7/merged',) [2018-09-27 18:57:13,798] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2018-09-27 18:57:13,822] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMGFWBGX7/merged',) [2018-09-27 18:57:13,835] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMGFWBGX7/merged',) [2018-09-27 18:57:14,100] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMGFWBGX7/merged',) [2018-09-27 18:57:14,368] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMGFWBGX7/merged',) [2018-09-27 18:57:14,645] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMGFWBGX7/merged',) [2018-09-27 18:57:14,910] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('/beegfs/mk5636/logs/html/HMGFWBGX7/merged',) [2018-09-27 18:57:15,171] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('/beegfs/mk5636/logs/html/HMGFWBGX7/merged',) [2018-09-27 18:57:15,185] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMGFWBGX7/merged',) [2018-09-27 18:57:17,541] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HMGFWBGX7_n02_ZmTARGET.0808-3357-CHXDEX-02_fastqc.zip' as already parsed 'HMGFWBGX7_n02_ZmTARGET.0808-3357-CHXDEX-02' [2018-09-27 18:57:21,995] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HMGFWBGX7_n01_ZmTARGET.0830-6435-CHXDEX-01_fastqc.zip' as already parsed 'HMGFWBGX7_n01_ZmTARGET.0830-6435-CHXDEX-01' [2018-09-27 18:57:22,376] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: HMGFWBGX7_n01_ZmTARGET.0830-6435-CHX-02 [2018-09-27 18:57:24,535] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: HMGFWBGX7_n01_ZmTARGET.0808-3357-CHXDEX-01 [2018-09-27 18:57:25,002] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: HMGFWBGX7_n02_ZmTARGET.0808-3357-CHXDEX-01 [2018-09-27 18:57:26,508] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HMGFWBGX7_n02_ZmTARGET.0830-183-CHXDEX-01_fastqc.zip' as already parsed 'HMGFWBGX7_n02_ZmTARGET.0830-183-CHXDEX-01' [2018-09-27 18:57:26,593] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: HMGFWBGX7_n01_ZmTARGET.0808-3357-CHXDEX-02 [2018-09-27 18:57:27,927] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HMGFWBGX7_n02_ZmTARGET.0808-183-CHXDEX-02_fastqc.zip' as already parsed 'HMGFWBGX7_n02_ZmTARGET.0808-183-CHXDEX-02' [2018-09-27 18:57:28,455] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: HMGFWBGX7_n02_ZmTARGET.0830-6435-CHXDEX-01 [2018-09-27 18:57:30,711] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: HMGFWBGX7_n01_ZmTARGET.0830-183-CHXDEX-03 [2018-09-27 18:57:31,250] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: HMGFWBGX7_n01_ZmTARGET.0830-6435-CHXDEX-03 [2018-09-27 18:57:32,180] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: HMGFWBGX7_n02_ZmTARGET.0830-6435-CHX-02 [2018-09-27 18:57:32,710] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: HMGFWBGX7_n01_ZmTARGET.0830-6435-CHX-01 [2018-09-27 18:57:33,137] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HMGFWBGX7_n01_ZmTARGET.0830-183-CHXDEX-02_fastqc.zip' as already parsed 'HMGFWBGX7_n01_ZmTARGET.0830-183-CHXDEX-02' [2018-09-27 18:57:33,138] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HMGFWBGX7_n01_ZmTARGET.0808-3357-CHX-01_fastqc.zip' as already parsed 'HMGFWBGX7_n01_ZmTARGET.0808-3357-CHX-01' [2018-09-27 18:57:33,168] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: HMGFWBGX7_n01_ZmTARGET.0830-6435-CHX-03 [2018-09-27 18:57:33,615] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: HMGFWBGX7_n02_ZmTARGET.0808-3357-CHX-02 [2018-09-27 18:57:34,121] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: HMGFWBGX7_n02_ZmTARGET.0830-6435-CHXDEX-03 [2018-09-27 18:57:34,572] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: HMGFWBGX7_n02_ZmTARGET.0808-3357-CHXDEX-03 [2018-09-27 18:57:35,086] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: HMGFWBGX7_n02_ZmTARGET.0830-6435-CHX-01 [2018-09-27 18:57:36,050] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: HMGFWBGX7_n02_ZmTARGET.0808-3357-CHX-01 [2018-09-27 18:57:36,497] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: HMGFWBGX7_n01_ZmTARGET.0808-183-CHXDEX-02 [2018-09-27 18:57:36,958] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: HMGFWBGX7_n01_ZmTARGET.0808-3357-CHX-02 [2018-09-27 18:57:37,505] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: HMGFWBGX7_n02_ZmTARGET.0830-6435-CHXDEX-02 [2018-09-27 18:57:37,967] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: HMGFWBGX7_n02_ZmTARGET.0830-6435-CHX-03 [2018-09-27 18:57:39,482] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: HMGFWBGX7_n01_ZmTARGET.0808-3357-CHX-03 [2018-09-27 18:57:41,170] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: HMGFWBGX7_n02_ZmTARGET.0808-3357-CHX-03 [2018-09-27 18:57:41,603] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: HMGFWBGX7_n02_ZmTARGET.0830-183-CHXDEX-03 [2018-09-27 18:57:42,027] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HMGFWBGX7_n02_ZmTARGET.0808-183-CHXDEX-01_fastqc.zip' as already parsed 'HMGFWBGX7_n02_ZmTARGET.0808-183-CHXDEX-01' [2018-09-27 18:57:42,059] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: HMGFWBGX7_n01_ZmTARGET.0830-6435-CHXDEX-02 [2018-09-27 18:57:42,577] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: HMGFWBGX7_n01_ZmTARGET.0808-183-CHXDEX-01 [2018-09-27 18:57:43,050] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: HMGFWBGX7_n01_ZmTARGET.0830-183-CHXDEX-01 [2018-09-27 18:57:43,473] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HMGFWBGX7_n02_ZmTARGET.0830-183-CHXDEX-02_fastqc.zip' as already parsed 'HMGFWBGX7_n02_ZmTARGET.0830-183-CHXDEX-02' [2018-09-27 18:57:43,474] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HMGFWBGX7_n02_ZmTARGET.0808-183-CHXDEX-03_fastqc.zip' as already parsed 'HMGFWBGX7_n02_ZmTARGET.0808-183-CHXDEX-03' [2018-09-27 18:57:43,475] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HMGFWBGX7_n01_ZmTARGET.0808-183-CHXDEX-03_fastqc.zip' as already parsed 'HMGFWBGX7_n01_ZmTARGET.0808-183-CHXDEX-03' [2018-09-27 18:57:43,475] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'HMGFWBGX7_n01_ZmTARGET.0808-3357-CHXDEX-03_fastqc.zip' as already parsed 'HMGFWBGX7_n01_ZmTARGET.0808-3357-CHXDEX-03' [2018-09-27 18:57:43,475] multiqc.modules.fastqc.fastqc [INFO ] Found 38 reports [2018-09-27 18:57:47,579] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('/beegfs/mk5636/logs/html/HMGFWBGX7/merged',) [2018-09-27 18:57:47,636] multiqc [WARNING] Deleting : multiqc_report.html (-f was specified) [2018-09-27 18:57:47,637] multiqc [INFO ] Report : multiqc_report.html [2018-09-27 18:57:47,638] multiqc [WARNING] Deleting : multiqc_data (-f was specified) [2018-09-27 18:57:47,646] multiqc [INFO ] Data : multiqc_data [2018-09-27 18:57:47,646] multiqc [DEBUG ] Moving data file from '/state/partition1/job-8895696/tmp5kYACn/multiqc_data/multiqc_fastqc.txt' to '/beegfs/mk5636/logs/html/HMGFWBGX7/merged/multiqc_data' [2018-09-27 18:57:47,693] multiqc [DEBUG ] Moving data file from '/state/partition1/job-8895696/tmp5kYACn/multiqc_data/multiqc_general_stats.txt' to '/beegfs/mk5636/logs/html/HMGFWBGX7/merged/multiqc_data' [2018-09-27 18:57:47,713] multiqc [DEBUG ] Moving data file from '/state/partition1/job-8895696/tmp5kYACn/multiqc_data/multiqc_sources.txt' to '/beegfs/mk5636/logs/html/HMGFWBGX7/merged/multiqc_data' [2018-09-27 18:57:48,062] multiqc [INFO ] MultiQC complete