[2017-09-20 17:04:44,536] multiqc [DEBUG ] No MultiQC config found: /nfs/users/bi/lcozzuto/.pyenv/versions/2.7.13/lib/python2.7/site-packages/multiqc_config.yaml [2017-09-20 17:04:44,536] multiqc [DEBUG ] No MultiQC config found: /users/bi/lcozzuto/.multiqc_config.yaml [2017-09-20 17:04:44,537] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2017-09-20 17:04:44,551] multiqc [DEBUG ] Loading config settings from: aaa.yaml [2017-09-20 17:04:44,551] multiqc [DEBUG ] New config 'custom_logo_url': https://biocore.crg.eu [2017-09-20 17:04:44,552] multiqc [DEBUG ] New config 'module_order': [{'fastqc': {'name': 'FastQC (raw)', 'path_filters': ['*_read*_fastqc.zip']}}, {'fastqc': {'info': 'This section of the report shows FastQC results after adapter trimming.', 'target': '', 'path_filters': ['*-trimmed-pair*_fastqc.zip'], 'name': 'FastQC (trimmed)'}}, 'skewer', 'qualimap', 'tools'] [2017-09-20 17:04:44,552] multiqc [DEBUG ] New config 'read_count_prefix': K [2017-09-20 17:04:44,552] multiqc [DEBUG ] New config 'subtitle': This part can be overridden by text about the project and the date etc. [2017-09-20 17:04:44,552] multiqc [DEBUG ] New config 'custom_logo_title': Bioinformatics Core Facility @ CRG [2017-09-20 17:04:44,552] multiqc [DEBUG ] New config 'intro_text': False [2017-09-20 17:04:44,553] multiqc [DEBUG ] New config 'title': Test RNAseq project [2017-09-20 17:04:44,553] multiqc [DEBUG ] New config 'table_columns_visible': {'QualiMap': {'5_3_bias': False}} [2017-09-20 17:04:44,553] multiqc [DEBUG ] New config 'report_header_info': [{'Contact E-mail': 'luca.cozzuto@crg.eu'}, {'Application Type': 'RNA-seq'}, {'Sequencing Platform': 'HiSeq 2500 High Output V4'}] [2017-09-20 17:04:44,553] multiqc [DEBUG ] New config 'read_count_multiplier': 0.001 [2017-09-20 17:04:44,554] multiqc [DEBUG ] New config 'custom_logo': /software/bi/biocore_tools/logo/biocore-logo.png [2017-09-20 17:04:44,554] multiqc [DEBUG ] New config 'read_count_desc': thousands [2017-09-20 17:04:44,554] multiqc [DEBUG ] Command used: /users/bi/lcozzuto/.pyenv/versions/2.7.13/bin/multiqc -f -c aaa.yaml . [2017-09-20 17:04:45,071] multiqc [DEBUG ] Latest MultiQC version is v1.2 [2017-09-20 17:04:45,071] multiqc [INFO ] This is MultiQC v1.3.dev0 (f36d735) [2017-09-20 17:04:45,071] multiqc [DEBUG ] Command : /users/bi/lcozzuto/.pyenv/versions/2.7.13/bin/multiqc -f -c aaa.yaml . [2017-09-20 17:04:45,072] multiqc [DEBUG ] Working dir : /nfs/software/bi/biocore_tools/nextflow_pipelines/RNAseq/RNAseq_0.3/BiocoreRNAseq/QC [2017-09-20 17:04:45,072] multiqc [INFO ] Template : default [2017-09-20 17:04:45,072] multiqc [INFO ] Report title: Test RNAseq project [2017-09-20 17:04:45,072] multiqc [INFO ] Searching '.' [2017-09-20 17:04:45,073] multiqc [DEBUG ] Analysing modules: rna_seqc, theta2, peddy, bismark, prokka, sortmerna, cutadapt, goleft_indexcov, qorts, kallisto, busco, samtools, clusterflow, picard, rseqc, quast, gatk, hicup, bowtie2, conpair, vcftools, featureCounts, star, adapterRemoval, flexbar, bcftools, disambiguate, rsem, salmon, fastq_screen, methylQA, htseq, preseq, snpeff, bamtools, bowtie1, trimmomatic, jellyfish, homer, bcl2fastq, slamdunk, leehom, biobloomtools, hisat2, afterqc, macs2, tophat, custom_content, samblaster, fastqc, fastqc, skewer, qualimap [2017-09-20 17:04:45,073] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpkHTt6P [2017-09-20 17:04:45,213] multiqc [DEBUG ] Ignoring directory as matched fn_ignore_dirs: ./test/multiqc_data [2017-09-20 17:04:45,235] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sim-trimmed-pair2_fastqc.html [2017-09-20 17:04:45,236] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: test_read2_fastqc.html [2017-09-20 17:04:45,236] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sim_read2_fastqc.html [2017-09-20 17:04:45,295] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: test_read1_fastqc.html [2017-09-20 17:04:45,296] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: test-trimmed-pair1_fastqc.html [2017-09-20 17:04:45,297] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sim-trimmed-pair1_fastqc.html [2017-09-20 17:04:45,370] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sim_read1_fastqc.html [2017-09-20 17:04:45,394] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: test-trimmed-pair2_fastqc.html [2017-09-20 17:04:45,397] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2017-09-20 17:04:46,009] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sim-trimmed-pair2_fastqc.html [2017-09-20 17:04:46,010] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: test_read2_fastqc.html [2017-09-20 17:04:46,010] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sim_read2_fastqc.html [2017-09-20 17:04:46,010] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: test_read1_fastqc.html [2017-09-20 17:04:46,011] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: test-trimmed-pair1_fastqc.html [2017-09-20 17:04:46,011] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sim-trimmed-pair1_fastqc.html [2017-09-20 17:04:46,011] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: multiqc_report.html [2017-09-20 17:04:46,030] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sim_read1_fastqc.html [2017-09-20 17:04:46,032] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: test-trimmed-pair2_fastqc.html [2017-09-20 17:04:46,034] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: qualimapReport.html [2017-09-20 17:04:47,300] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('.',) [2017-09-20 17:04:47,314] multiqc.modules.theta2.theta2 [DEBUG ] Could not find any reports in ('.',) [2017-09-20 17:04:47,328] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('.',) [2017-09-20 17:04:47,340] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('.',) [2017-09-20 17:04:47,354] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('.',) [2017-09-20 17:04:47,369] multiqc.modules.sortmerna.sortmerna [DEBUG ] Could not find any SortMeRNA data in ('.',) [2017-09-20 17:04:47,383] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('.',) [2017-09-20 17:04:47,396] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('.',) [2017-09-20 17:04:47,408] multiqc.modules.qorts.qorts [DEBUG ] Could not find any QoRTs data in ('.',) [2017-09-20 17:04:47,420] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('.',) [2017-09-20 17:04:47,432] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('.',) [2017-09-20 17:04:47,450] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('.',) [2017-09-20 17:04:47,464] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('.',) [2017-09-20 17:04:47,492] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('.',) [2017-09-20 17:04:47,519] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('.',) [2017-09-20 17:04:47,532] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('.',) [2017-09-20 17:04:47,546] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('.',) [2017-09-20 17:04:47,558] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('.',) [2017-09-20 17:04:47,571] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('.',) [2017-09-20 17:04:47,588] multiqc.modules.conpair.conpair [DEBUG ] Could not find any reports in ('.',) [2017-09-20 17:04:47,606] multiqc.modules.vcftools.vcftools [DEBUG ] Could not find any reports in ('.',) [2017-09-20 17:04:47,619] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('.',) [2017-09-20 17:04:47,632] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('.',) [2017-09-20 17:04:47,644] multiqc.modules.adapterRemoval.adapterRemoval [DEBUG ] Could not find any reports in ('.',) [2017-09-20 17:04:47,655] multiqc.modules.flexbar.flexbar [DEBUG ] Could not find any Flexbar data in ('.',) [2017-09-20 17:04:47,668] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('.',) [2017-09-20 17:04:47,680] multiqc.modules.disambiguate.disambiguate [DEBUG ] Could not find any data in ('.',) [2017-09-20 17:04:47,693] multiqc.modules.rsem.rsem [DEBUG ] Could not find any reports in ('.',) [2017-09-20 17:04:47,705] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('.',) [2017-09-20 17:04:47,716] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('.',) [2017-09-20 17:04:47,728] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('.',) [2017-09-20 17:04:47,739] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('.',) [2017-09-20 17:04:47,750] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('.',) [2017-09-20 17:04:47,760] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('.',) [2017-09-20 17:04:47,773] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('.',) [2017-09-20 17:04:47,783] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('.',) [2017-09-20 17:04:47,793] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('.',) [2017-09-20 17:04:47,804] multiqc.modules.jellyfish.jellyfish [DEBUG ] Could not find any data in ('.',) [2017-09-20 17:04:47,816] multiqc.modules.homer.homer [DEBUG ] Could not find any reports in ('.',) [2017-09-20 17:04:47,826] multiqc.modules.bcl2fastq.bcl2fastq [DEBUG ] Could not find any bcl2fastq data in ('.',) [2017-09-20 17:04:47,837] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2017-09-20 17:04:47,847] multiqc.modules.leehom.leehom [DEBUG ] Could not find any reports in ('.',) [2017-09-20 17:04:47,857] multiqc.modules.biobloomtools.biobloomtools [DEBUG ] Could not find any reports in ('.',) [2017-09-20 17:04:47,867] multiqc.modules.hisat2.hisat2 [DEBUG ] Could not find any reports in ('.',) [2017-09-20 17:04:47,880] multiqc.modules.afterqc.afterqc [DEBUG ] Could not find any reports in ('.',) [2017-09-20 17:04:47,893] multiqc.modules.macs2.macs2 [DEBUG ] Could not find any MACS2 data in ('.',) [2017-09-20 17:04:47,905] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('.',) [2017-09-20 17:04:47,927] multiqc.modules.custom_content.custom_content [INFO ] tools: Found 7 samples (table) [2017-09-20 17:04:47,939] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('.',) [2017-09-20 17:04:47,966] multiqc.modules.base_module [DEBUG ] fastqc/zip - Skipping 'test-trimmed-pair1_fastqc.zip' as didn't match module path filters [2017-09-20 17:04:47,967] multiqc.modules.base_module [DEBUG ] fastqc/zip - Skipping 'sim-trimmed-pair1_fastqc.zip' as didn't match module path filters [2017-09-20 17:04:47,967] multiqc.modules.base_module [DEBUG ] fastqc/zip - Skipping 'test-trimmed-pair2_fastqc.zip' as didn't match module path filters [2017-09-20 17:04:48,142] multiqc.modules.base_module [DEBUG ] fastqc/zip - Skipping 'sim-trimmed-pair2_fastqc.zip' as didn't match module path filters [2017-09-20 17:04:48,142] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'sim_read2_fastqc.zip' as already parsed 'sim_read2' [2017-09-20 17:04:48,142] multiqc.modules.base_module [DEBUG ] fastqc/zip - Skipping 'test-trimmed-pair1_fastqc.zip' as didn't match module path filters [2017-09-20 17:04:48,142] multiqc.modules.base_module [DEBUG ] fastqc/zip - Skipping 'sim-trimmed-pair1_fastqc.zip' as didn't match module path filters [2017-09-20 17:04:48,142] multiqc.modules.base_module [DEBUG ] fastqc/zip - Skipping 'test-trimmed-pair2_fastqc.zip' as didn't match module path filters [2017-09-20 17:04:48,143] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'test_read2_fastqc.zip' as already parsed 'test_read2' [2017-09-20 17:04:48,143] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'test_read1_fastqc.zip' as already parsed 'test_read1' [2017-09-20 17:04:48,143] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'sim_read1_fastqc.zip' as already parsed 'sim_read1' [2017-09-20 17:04:48,143] multiqc.modules.base_module [DEBUG ] fastqc/zip - Skipping 'sim-trimmed-pair2_fastqc.zip' as didn't match module path filters [2017-09-20 17:04:48,143] multiqc.modules.fastqc.fastqc [INFO ] Found 4 reports [2017-09-20 17:04:48,388] multiqc.modules.base_module [DEBUG ] fastqc/zip - Skipping 'sim_read2_fastqc.zip' as didn't match module path filters [2017-09-20 17:04:48,538] multiqc.modules.base_module [DEBUG ] fastqc/zip - Skipping 'test_read2_fastqc.zip' as didn't match module path filters [2017-09-20 17:04:48,538] multiqc.modules.base_module [DEBUG ] fastqc/zip - Skipping 'test_read1_fastqc.zip' as didn't match module path filters [2017-09-20 17:04:48,538] multiqc.modules.base_module [DEBUG ] fastqc/zip - Skipping 'sim_read1_fastqc.zip' as didn't match module path filters [2017-09-20 17:04:48,548] multiqc.modules.base_module [DEBUG ] fastqc/zip - Skipping 'sim_read2_fastqc.zip' as didn't match module path filters [2017-09-20 17:04:48,548] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'test-trimmed-pair1_fastqc.zip' as already parsed 'test-trimmed-pair1' [2017-09-20 17:04:48,548] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'sim-trimmed-pair1_fastqc.zip' as already parsed 'sim-trimmed-pair1' [2017-09-20 17:04:48,548] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'test-trimmed-pair2_fastqc.zip' as already parsed 'test-trimmed-pair2' [2017-09-20 17:04:48,549] multiqc.modules.base_module [DEBUG ] fastqc/zip - Skipping 'test_read2_fastqc.zip' as didn't match module path filters [2017-09-20 17:04:48,549] multiqc.modules.base_module [DEBUG ] fastqc/zip - Skipping 'test_read1_fastqc.zip' as didn't match module path filters [2017-09-20 17:04:48,549] multiqc.modules.base_module [DEBUG ] fastqc/zip - Skipping 'sim_read1_fastqc.zip' as didn't match module path filters [2017-09-20 17:04:48,549] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'sim-trimmed-pair2_fastqc.zip' as already parsed 'sim-trimmed-pair2' [2017-09-20 17:04:48,549] multiqc.modules.fastqc.fastqc [INFO ] Found 4 reports [2017-09-20 17:04:48,750] multiqc.modules.skewer.skewer [DEBUG ] Duplicate sample name found in test-trimmed.log! Overwriting: test_read1 [2017-09-20 17:04:48,750] multiqc.modules.skewer.skewer [DEBUG ] Duplicate sample name found! Overwriting: test_read1 [2017-09-20 17:04:48,752] multiqc.modules.skewer.skewer [DEBUG ] Duplicate sample name found in sim-trimmed.log! Overwriting: sim_read1 [2017-09-20 17:04:48,752] multiqc.modules.skewer.skewer [DEBUG ] Duplicate sample name found! Overwriting: sim_read1 [2017-09-20 17:04:48,753] multiqc.modules.skewer.skewer [INFO ] Found 2 reports [2017-09-20 17:04:48,763] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2017-09-20 17:04:48,782] multiqc.modules.qualimap.qualimap [INFO ] Found 2 RNASeq reports [2017-09-20 17:04:48,801] multiqc [INFO ] Compressing plot data [2017-09-20 17:04:49,380] multiqc [INFO ] Report : multiqc_report.html [2017-09-20 17:04:49,380] multiqc [INFO ] Data : multiqc_data [2017-09-20 17:04:49,382] multiqc [DEBUG ] Moving data file from '/tmp/tmpkHTt6P/multiqc_data/multiqc_skewer_readlen_dist.txt' to '/nfs/software/bi/biocore_tools/nextflow_pipelines/RNAseq/RNAseq_0.3/BiocoreRNAseq/QC/multiqc_data' [2017-09-20 17:04:49,389] multiqc [DEBUG ] Moving data file from '/tmp/tmpkHTt6P/multiqc_data/multiqc_data.json' to '/nfs/software/bi/biocore_tools/nextflow_pipelines/RNAseq/RNAseq_0.3/BiocoreRNAseq/QC/multiqc_data' [2017-09-20 17:04:49,424] multiqc [DEBUG ] Moving data file from '/tmp/tmpkHTt6P/multiqc_data/multiqc_fastqc.txt' to '/nfs/software/bi/biocore_tools/nextflow_pipelines/RNAseq/RNAseq_0.3/BiocoreRNAseq/QC/multiqc_data' [2017-09-20 17:04:49,430] multiqc [DEBUG ] Moving data file from '/tmp/tmpkHTt6P/multiqc_data/multiqc_sources.txt' to '/nfs/software/bi/biocore_tools/nextflow_pipelines/RNAseq/RNAseq_0.3/BiocoreRNAseq/QC/multiqc_data' [2017-09-20 17:04:49,436] multiqc [DEBUG ] Moving data file from '/tmp/tmpkHTt6P/multiqc_data/multiqc_general_stats.txt' to '/nfs/software/bi/biocore_tools/nextflow_pipelines/RNAseq/RNAseq_0.3/BiocoreRNAseq/QC/multiqc_data' [2017-09-20 17:04:49,441] multiqc [DEBUG ] Moving data file from '/tmp/tmpkHTt6P/multiqc_data/multiqc_skewer.txt' to '/nfs/software/bi/biocore_tools/nextflow_pipelines/RNAseq/RNAseq_0.3/BiocoreRNAseq/QC/multiqc_data' [2017-09-20 17:04:49,651] multiqc [INFO ] MultiQC complete