[2017-10-04 16:27:21,028] multiqc [DEBUG ] No MultiQC config found: /nfs/users/bi/lcozzuto/.pyenv/versions/2.7.13/lib/python2.7/site-packages/multiqc_config.yaml [2017-10-04 16:27:21,028] multiqc [DEBUG ] No MultiQC config found: /users/bi/lcozzuto/.multiqc_config.yaml [2017-10-04 16:27:21,029] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2017-10-04 16:27:21,029] multiqc [DEBUG ] Command used: /users/bi/lcozzuto/.pyenv/versions/2.7.13/bin/multiqc . [2017-10-04 16:27:21,152] multiqc [DEBUG ] Latest MultiQC version is v1.2 [2017-10-04 16:27:21,152] multiqc [INFO ] This is MultiQC v1.3.dev0 (f36d735) [2017-10-04 16:27:21,152] multiqc [DEBUG ] Command : /users/bi/lcozzuto/.pyenv/versions/2.7.13/bin/multiqc . [2017-10-04 16:27:21,152] multiqc [DEBUG ] Working dir : /nfs/users/project/sacalalengua/test_saca2/all [2017-10-04 16:27:21,152] multiqc [INFO ] Template : default [2017-10-04 16:27:21,152] multiqc [INFO ] Searching '.' [2017-10-04 16:27:21,153] multiqc [DEBUG ] Analysing modules: afterqc, custom_content, conpair, peddy, methylQA, qualimap, preseq, quast, qorts, rna_seqc, rsem, rseqc, busco, goleft_indexcov, disambiguate, homer, macs2, theta2, snpeff, gatk, htseq, bcftools, featureCounts, picard, prokka, samblaster, samtools, bamtools, jellyfish, vcftools, bismark, hicup, salmon, kallisto, slamdunk, star, hisat2, tophat, bowtie2, bowtie1, leehom, adapterRemoval, cutadapt, flexbar, trimmomatic, skewer, sortmerna, biobloomtools, fastq_screen, fastqc, clusterflow, bcl2fastq [2017-10-04 16:27:21,153] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpK4prav [2017-10-04 16:27:21,302] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data4ra_150706_HM-782D_S95_L001_R2_001_fastqc.html [2017-10-04 16:27:21,303] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data2_150623_HM-782D4_S191_L001_R2_001_fastqc.html [2017-10-04 16:27:21,303] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data7_150724_HM-782D_S95_L001_R1_001_fastqc.html [2017-10-04 16:27:21,304] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data2_150623_HM-782D4_S191_L001_R1_001_fastqc.html [2017-10-04 16:27:21,304] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data7_150724_HM-783D_S190_L001_R2_001_fastqc.html [2017-10-04 16:27:21,305] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data2_150623_HM-783D4_S192_L001_R2_001_fastqc.html [2017-10-04 16:27:21,306] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data5ra_150713_HM-782D_S95_L001_R1_001_fastqc.html [2017-10-04 16:27:21,307] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data3_150702_HM-783D_S96_L001_R1_001_fastqc.html [2017-10-04 16:27:21,307] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data9_150907_HM-782D_S52_L001_R2_001_fastqc.html [2017-10-04 16:27:21,307] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data6ra_150717_HM-783D_S191_L001_R2_001_fastqc.html [2017-10-04 16:27:21,307] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 21101-HM783D_S31_L001_R1_001_fastqc.html [2017-10-04 16:27:21,308] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data6ra_150717_HM-782D_S95_L001_R1_001_fastqc.html [2017-10-04 16:27:21,309] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data4ra_150706_HM-782D_S95_L001_R1_001_fastqc.html [2017-10-04 16:27:21,310] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data7_150724_HM-782D_S95_L001_R2_001_fastqc.html [2017-10-04 16:27:21,310] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data9_150907_HM-782D_S52_L001_R1_001_fastqc.html [2017-10-04 16:27:21,311] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data8_150727_HM-782D_S95_L001_R2_001_fastqc.html [2017-10-04 16:27:21,312] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data5ra_150713_HM-783D_S191_L001_R2_001_fastqc.html [2017-10-04 16:27:21,314] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data5ra_150713_HM-782D_S95_L001_R2_001_fastqc.html [2017-10-04 16:27:21,314] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data2_150623_HM-783D4_S192_L001_R1_001_fastqc.html [2017-10-04 16:27:21,316] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data8_150727_HM-783D_S190_L001_R2_001_fastqc.html [2017-10-04 16:27:21,316] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 21101-HM782D_S30_L001_R1_001_fastqc.html [2017-10-04 16:27:21,318] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data9_150907_HM-783D_S53_L001_R1_001_fastqc.html [2017-10-04 16:27:21,322] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data2_150623_HM-783D3_S96_L001_R2_001_fastqc.html [2017-10-04 16:27:21,323] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 21101-HM782D_S30_L001_R2_001_fastqc.html [2017-10-04 16:27:21,323] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data3_150702_HM-783D_S96_L001_R2_001_fastqc.html [2017-10-04 16:27:21,323] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 21101-HM783D_S31_L001_R2_001_fastqc.html [2017-10-04 16:27:21,324] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data6ra_150717_HM-783D_S191_L001_R1_001_fastqc.html [2017-10-04 16:27:21,324] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data3_150702_HM-782D_S95_L001_R2_001_fastqc.html [2017-10-04 16:27:21,325] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data8_150727_HM-782D_S95_L001_R1_001_fastqc.html [2017-10-04 16:27:21,326] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data8_150727_HM-783D_S190_L001_R1_001_fastqc.html [2017-10-04 16:27:21,328] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data3_150702_HM-782D_S95_L001_R1_001_fastqc.html [2017-10-04 16:27:21,328] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data2_150623_HM-783D3_S96_L001_R1_001_fastqc.html [2017-10-04 16:27:21,329] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data7_150724_HM-783D_S190_L001_R1_001_fastqc.html [2017-10-04 16:27:21,329] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data4ra_150706_HM-783D_S191_L001_R2_001_fastqc.html [2017-10-04 16:27:21,329] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data4ra_150706_HM-783D_S191_L001_R1_001_fastqc.html [2017-10-04 16:27:21,329] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data2_150623_HM-782D3_S95_L001_R2_001_fastqc.html [2017-10-04 16:27:21,330] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data6ra_150717_HM-782D_S95_L001_R2_001_fastqc.html [2017-10-04 16:27:21,330] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data5ra_150713_HM-783D_S191_L001_R1_001_fastqc.html [2017-10-04 16:27:21,330] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data9_150907_HM-783D_S53_L001_R2_001_fastqc.html [2017-10-04 16:27:21,331] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data2_150623_HM-782D3_S95_L001_R1_001_fastqc.html [2017-10-04 16:27:21,817] multiqc.modules.afterqc.afterqc [DEBUG ] Could not find any reports in ('.',) [2017-10-04 16:27:21,826] multiqc.modules.custom_content.custom_content [DEBUG ] No custom content found [2017-10-04 16:27:21,833] multiqc.modules.conpair.conpair [DEBUG ] Could not find any reports in ('.',) [2017-10-04 16:27:21,849] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('.',) [2017-10-04 16:27:21,855] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('.',) [2017-10-04 16:27:21,863] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2017-10-04 16:27:21,863] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('.',) [2017-10-04 16:27:21,880] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('.',) [2017-10-04 16:27:21,886] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('.',) [2017-10-04 16:27:21,902] multiqc.modules.qorts.qorts [DEBUG ] Could not find any QoRTs data in ('.',) [2017-10-04 16:27:21,908] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('.',) [2017-10-04 16:27:21,914] multiqc.modules.rsem.rsem [DEBUG ] Could not find any reports in ('.',) [2017-10-04 16:27:21,937] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('.',) [2017-10-04 16:27:21,943] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('.',) [2017-10-04 16:27:21,949] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('.',) [2017-10-04 16:27:21,968] multiqc.modules.disambiguate.disambiguate [DEBUG ] Could not find any data in ('.',) [2017-10-04 16:27:21,975] multiqc.modules.homer.homer [DEBUG ] Could not find any reports in ('.',) [2017-10-04 16:27:21,989] multiqc.modules.macs2.macs2 [DEBUG ] Could not find any MACS2 data in ('.',) [2017-10-04 16:27:21,995] multiqc.modules.theta2.theta2 [DEBUG ] Could not find any reports in ('.',) [2017-10-04 16:27:22,001] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('.',) [2017-10-04 16:27:22,018] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('.',) [2017-10-04 16:27:22,024] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('.',) [2017-10-04 16:27:22,031] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('.',) [2017-10-04 16:27:22,048] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('.',) [2017-10-04 16:27:22,064] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('.',) [2017-10-04 16:27:22,070] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('.',) [2017-10-04 16:27:22,077] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('.',) [2017-10-04 16:27:22,094] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('.',) [2017-10-04 16:27:22,101] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('.',) [2017-10-04 16:27:22,113] multiqc.modules.jellyfish.jellyfish [DEBUG ] Could not find any data in ('.',) [2017-10-04 16:27:22,128] multiqc.modules.vcftools.vcftools [DEBUG ] Could not find any reports in ('.',) [2017-10-04 16:27:22,134] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('.',) [2017-10-04 16:27:22,149] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('.',) [2017-10-04 16:27:22,155] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('.',) [2017-10-04 16:27:22,164] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('.',) [2017-10-04 16:27:22,170] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2017-10-04 16:27:22,186] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('.',) [2017-10-04 16:27:22,192] multiqc.modules.hisat2.hisat2 [DEBUG ] Could not find any reports in ('.',) [2017-10-04 16:27:22,199] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('.',) [2017-10-04 16:27:22,209] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('.',) [2017-10-04 16:27:22,227] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('.',) [2017-10-04 16:27:22,233] multiqc.modules.leehom.leehom [DEBUG ] Could not find any reports in ('.',) [2017-10-04 16:27:22,239] multiqc.modules.adapterRemoval.adapterRemoval [DEBUG ] Could not find any reports in ('.',) [2017-10-04 16:27:22,248] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('.',) [2017-10-04 16:27:22,265] multiqc.modules.flexbar.flexbar [DEBUG ] Could not find any Flexbar data in ('.',) [2017-10-04 16:27:22,271] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('.',) [2017-10-04 16:27:22,277] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('.',) [2017-10-04 16:27:22,288] multiqc.modules.sortmerna.sortmerna [DEBUG ] Could not find any SortMeRNA data in ('.',) [2017-10-04 16:27:22,304] multiqc.modules.biobloomtools.biobloomtools [DEBUG ] Could not find any reports in ('.',) [2017-10-04 16:27:22,310] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('.',) [2017-10-04 16:27:25,627] multiqc.modules.fastqc.fastqc [INFO ] Found 40 reports [2017-10-04 16:27:30,936] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('.',) [2017-10-04 16:27:30,949] multiqc.modules.bcl2fastq.bcl2fastq [DEBUG ] Could not find any bcl2fastq data in ('.',) [2017-10-04 16:27:31,016] multiqc [INFO ] Compressing plot data [2017-10-04 16:27:33,987] multiqc [INFO ] Report : multiqc_report.html [2017-10-04 16:27:33,987] multiqc [INFO ] Data : multiqc_data [2017-10-04 16:27:33,989] multiqc [DEBUG ] Moving data file from '/tmp/tmpK4prav/multiqc_data/multiqc_data.json' to '/nfs/users/project/sacalalengua/test_saca2/all/multiqc_data' [2017-10-04 16:27:34,010] multiqc [DEBUG ] Moving data file from '/tmp/tmpK4prav/multiqc_data/multiqc_fastqc.txt' to '/nfs/users/project/sacalalengua/test_saca2/all/multiqc_data' [2017-10-04 16:27:34,038] multiqc [DEBUG ] Moving data file from '/tmp/tmpK4prav/multiqc_data/multiqc_sources.txt' to '/nfs/users/project/sacalalengua/test_saca2/all/multiqc_data' [2017-10-04 16:27:34,045] multiqc [DEBUG ] Moving data file from '/tmp/tmpK4prav/multiqc_data/multiqc_general_stats.txt' to '/nfs/users/project/sacalalengua/test_saca2/all/multiqc_data' [2017-10-04 16:27:34,358] multiqc [INFO ] MultiQC complete