[2017-10-11 15:35:01,593] multiqc [DEBUG ] No MultiQC config found: /nfs/users/bi/lcozzuto/.pyenv/versions/2.7.13/lib/python2.7/site-packages/multiqc_config.yaml [2017-10-11 15:35:01,594] multiqc [DEBUG ] No MultiQC config found: /users/bi/lcozzuto/.multiqc_config.yaml [2017-10-11 15:35:01,594] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2017-10-11 15:35:01,594] multiqc [DEBUG ] Command used: /users/bi/lcozzuto/.pyenv/versions/2.7.13/bin/multiqc . [2017-10-11 15:35:06,713] multiqc [DEBUG ] Could not connect to multiqc.info for version check: timed out [2017-10-11 15:35:06,714] multiqc [INFO ] This is MultiQC v1.3.dev0 (f36d735) [2017-10-11 15:35:06,714] multiqc [DEBUG ] Command : /users/bi/lcozzuto/.pyenv/versions/2.7.13/bin/multiqc . [2017-10-11 15:35:06,714] multiqc [DEBUG ] Working dir : /nfs/users/project/sacalalengua/test_saca2/trimmed/seqs_ori [2017-10-11 15:35:06,714] multiqc [INFO ] Template : default [2017-10-11 15:35:06,714] multiqc [INFO ] Searching '.' [2017-10-11 15:35:06,715] 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 [2017-10-11 15:35:06,715] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpPmk7mg [2017-10-11 15:35:07,548] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data1_150619_SLL-0115-0252_S1_L001_R2_001_50_fastqc.html [2017-10-11 15:35:07,605] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data2_150623_HM-782D3_S95_L001_R1_001_50.fastq [2017-10-11 15:35:07,607] multiqc [DEBUG ] Ignoring 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[2017-10-11 15:35:08,756] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data6ra_150717_HM-782D_S95_L001_R1_001.fastq.gz [2017-10-11 15:35:08,756] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data8_150727_HM-782D_S95_L001_R1_001_50.fastq [2017-10-11 15:35:08,757] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data8_150727_HM-783D_S190_L001_R1_001.fastq.gz [2017-10-11 15:35:08,757] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data5ra_150713_HM-783D_S191_L001_R2_001_50.fastq [2017-10-11 15:35:08,757] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data7_150724_HM-783D_S190_L001_R1_001_50_fastqc.html [2017-10-11 15:35:08,758] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data2_150623_HM-783D4_S192_L001_R2_001.fastq.gz [2017-10-11 15:35:08,786] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data4ra_150706_HM-782D_S95_L001_R2_001_50.fastq [2017-10-11 15:35:08,787] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data1_150619_SLL-0115-0252_S1_L001_R1_001_50.fastq [2017-10-11 15:35:08,788] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data1_150619_SLL-0115-0338_S3_L001_R2_001_50_fastqc.html [2017-10-11 15:35:08,789] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 21101-HM783D_S31_L001_R1_001.fastq.gz [2017-10-11 15:35:08,789] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data3_150702_HM-782D_S95_L001_R1_001_50.fastq [2017-10-11 15:35:08,789] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data2_150623_HM-783D3_S96_L001_R1_001.fastq.gz [2017-10-11 15:35:08,790] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data9_150907_HM-782D_S52_L001_R2_001_50_fastqc.html [2017-10-11 15:35:08,790] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data5ra_150713_HM-782D_S95_L001_R1_001_50_fastqc.html [2017-10-11 15:35:08,818] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 21101-HM783D_S31_L001_R2_001.fastq.gz [2017-10-11 15:35:08,843] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data6ra_150717_HM-782D_S95_L001_R1_001_50_fastqc.html [2017-10-11 15:35:08,870] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data2_150623_HM-782D3_S95_L001_R1_001.fastq.gz [2017-10-11 15:35:08,870] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data4ra_150706_HM-782D_S95_L001_R1_001.fastq.gz [2017-10-11 15:35:08,870] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data1_150619_SLL-0115-0252_S1_L001_R2_001.fastq [2017-10-11 15:35:08,871] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data2_150623_HM-782D3_S95_L001_R2_001_50.fastq [2017-10-11 15:35:08,871] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data1_150619_SLL-0115-0338_S3_L001_R1_001_50_fastqc.html [2017-10-11 15:35:08,898] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data6ra_150717_HM-782D_S95_L001_R1_001_50.fastq [2017-10-11 15:35:08,898] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data9_150907_HM-783D_S53_L001_R2_001_50_fastqc.html [2017-10-11 15:35:08,951] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data9_150907_HM-783D_S53_L001_R1_001_50.fastq [2017-10-11 15:35:08,952] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data6ra_150717_HM-783D_S191_L001_R2_001_50_fastqc.html [2017-10-11 15:35:08,952] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 21101-HM783D_S31_L001_R1_001_50.fastq [2017-10-11 15:35:08,979] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data2_150623_HM-783D3_S96_L001_R2_001_50_fastqc.html [2017-10-11 15:35:08,979] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data1_150619_SLL-0115-0357_S4_L001_R1_001_50.fastq [2017-10-11 15:35:08,980] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: data8_150727_HM-782D_S95_L001_R2_001_50.fastq [2017-10-11 15:35:15,200] multiqc.modules.afterqc.afterqc [DEBUG ] Could not find any reports in ('.',) [2017-10-11 15:35:15,428] multiqc.modules.custom_content.custom_content [DEBUG ] No custom content found [2017-10-11 15:35:15,459] multiqc.modules.conpair.conpair [DEBUG ] Could not find any reports in ('.',) [2017-10-11 15:35:15,517] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('.',) [2017-10-11 15:35:15,578] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('.',) [2017-10-11 15:35:15,658] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 [2017-10-11 15:35:15,659] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('.',) [2017-10-11 15:35:15,768] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('.',) [2017-10-11 15:35:15,837] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('.',) [2017-10-11 15:35:15,956] multiqc.modules.qorts.qorts [DEBUG ] Could not find any QoRTs data in ('.',) [2017-10-11 15:35:16,040] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('.',) [2017-10-11 15:35:16,150] multiqc.modules.rsem.rsem [DEBUG ] Could not find any reports in ('.',) [2017-10-11 15:35:16,554] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('.',) [2017-10-11 15:35:16,654] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('.',) [2017-10-11 15:35:16,704] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('.',) [2017-10-11 15:35:16,777] multiqc.modules.disambiguate.disambiguate [DEBUG ] Could not find any data in ('.',) [2017-10-11 15:35:16,965] multiqc.modules.homer.homer [DEBUG ] Could not find any reports in ('.',) [2017-10-11 15:35:17,072] multiqc.modules.macs2.macs2 [DEBUG ] Could not find any MACS2 data in ('.',) [2017-10-11 15:35:17,153] multiqc.modules.theta2.theta2 [DEBUG ] Could not find any reports in ('.',) [2017-10-11 15:35:17,247] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('.',) [2017-10-11 15:35:17,321] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('.',) [2017-10-11 15:35:17,429] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('.',) [2017-10-11 15:35:17,531] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('.',) [2017-10-11 15:35:17,568] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('.',) [2017-10-11 15:35:18,020] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('.',) [2017-10-11 15:35:18,106] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('.',) [2017-10-11 15:35:18,145] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('.',) [2017-10-11 15:35:18,422] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('.',) [2017-10-11 15:35:18,498] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('.',) [2017-10-11 15:35:18,576] multiqc.modules.jellyfish.jellyfish [DEBUG ] Could not find any data in ('.',) [2017-10-11 15:35:18,772] multiqc.modules.vcftools.vcftools [DEBUG ] Could not find any reports in ('.',) [2017-10-11 15:35:18,878] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('.',) [2017-10-11 15:35:18,936] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('.',) [2017-10-11 15:35:19,027] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('.',) [2017-10-11 15:35:19,129] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('.',) [2017-10-11 15:35:19,207] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. [2017-10-11 15:35:19,277] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('.',) [2017-10-11 15:35:19,341] multiqc.modules.hisat2.hisat2 [DEBUG ] Could not find any reports in ('.',) [2017-10-11 15:35:19,380] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('.',) [2017-10-11 15:35:19,465] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('.',) [2017-10-11 15:35:19,563] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('.',) [2017-10-11 15:35:19,662] multiqc.modules.leehom.leehom [DEBUG ] Could not find any reports in ('.',) [2017-10-11 15:35:19,718] multiqc.modules.adapterRemoval.adapterRemoval [DEBUG ] Could not find any reports in ('.',) [2017-10-11 15:35:19,801] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('.',) [2017-10-11 15:35:19,868] multiqc.modules.flexbar.flexbar [DEBUG ] Could not find any Flexbar data in ('.',) [2017-10-11 15:35:19,912] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('.',) [2017-10-11 15:35:20,016] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('.',) [2017-10-11 15:35:20,093] multiqc.modules.sortmerna.sortmerna [DEBUG ] Could not find any SortMeRNA data in ('.',) [2017-10-11 15:35:20,214] multiqc.modules.biobloomtools.biobloomtools [DEBUG ] Could not find any reports in ('.',) [2017-10-11 15:35:20,262] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('.',) [2017-10-11 15:35:23,740] multiqc.modules.fastqc.fastqc [INFO ] Found 47 reports [2017-10-11 15:35:28,681] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('.',) [2017-10-11 15:35:28,771] multiqc.modules.bcl2fastq.bcl2fastq [DEBUG ] Could not find any bcl2fastq data in ('.',) [2017-10-11 15:35:28,962] multiqc [INFO ] Compressing plot data [2017-10-11 15:35:32,615] multiqc [INFO ] Report : multiqc_report.html [2017-10-11 15:35:32,615] multiqc [INFO ] Data : multiqc_data [2017-10-11 15:35:32,617] multiqc [DEBUG ] Moving data file from '/tmp/tmpPmk7mg/multiqc_data/multiqc_data.json' to '/nfs/users/project/sacalalengua/test_saca2/trimmed/seqs_ori/multiqc_data' [2017-10-11 15:35:32,636] multiqc [DEBUG ] Moving data file from '/tmp/tmpPmk7mg/multiqc_data/multiqc_sources.txt' to '/nfs/users/project/sacalalengua/test_saca2/trimmed/seqs_ori/multiqc_data' [2017-10-11 15:35:32,642] multiqc [DEBUG ] Moving data file from '/tmp/tmpPmk7mg/multiqc_data/multiqc_general_stats.txt' to '/nfs/users/project/sacalalengua/test_saca2/trimmed/seqs_ori/multiqc_data' [2017-10-11 15:35:32,649] multiqc [DEBUG ] Moving data file from '/tmp/tmpPmk7mg/multiqc_data/multiqc_fastqc.txt' to '/nfs/users/project/sacalalengua/test_saca2/trimmed/seqs_ori/multiqc_data' [2017-10-11 15:35:33,971] multiqc [INFO ] MultiQC complete