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comparison test-data/pre_alignment_soft_log.txt @ 0:3bad335ccea9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
author iuc
date Tue, 24 Oct 2017 06:29:59 -0400
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children e0f4a651c6b9
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-1:000000000000 0:3bad335ccea9
1 [2017-09-28 17:24:01,554] multiqc [DEBUG ] No MultiQC config found: /Users/bebatut/miniconda3/envs/multiqc2/lib/python2.7/site-packages/multiqc-1.2-py2.7.egg/multiqc_config.yaml
2 [2017-09-28 17:24:01,554] multiqc [DEBUG ] No MultiQC config found: /Users/bebatut/.multiqc_config.yaml
3 [2017-09-28 17:24:01,554] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml
4 [2017-09-28 17:24:01,554] multiqc [DEBUG ] Command used: /Users/bebatut/miniconda3/envs/multiqc2/bin/multiqc multiqc_WDir
5 [2017-09-28 17:24:02,209] multiqc [DEBUG ] Latest MultiQC version is v1.2
6 [2017-09-28 17:24:02,210] multiqc [INFO ] This is MultiQC v1.2
7 [2017-09-28 17:24:02,210] multiqc [DEBUG ] Command : /Users/bebatut/miniconda3/envs/multiqc2/bin/multiqc multiqc_WDir
8 [2017-09-28 17:24:02,210] multiqc [DEBUG ] Working dir : /Users/bebatut/Documents/post_doc_freiburg/galaxy_projects/tools/tools-iuc/tools/multiqc
9 [2017-09-28 17:24:02,210] multiqc [INFO ] Template : default
10 [2017-09-28 17:24:02,210] multiqc [INFO ] Searching 'multiqc_WDir'
11 [2017-09-28 17:24:02,211] multiqc [DEBUG ] Analysing modules: afterqc, custom_content, conpair, peddy, methylQA, qualimap, preseq, quast, qorts, rna_seqc, 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
12 [2017-09-28 17:24:02,249] multiqc [DEBUG ] Using temporary directory for creating report: /var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmp7lPIig
13 [2017-09-28 17:24:05,021] multiqc.modules.afterqc.afterqc [DEBUG ] Could not find any reports in ('multiqc_WDir',)
14 [2017-09-28 17:24:05,098] multiqc.modules.custom_content.custom_content [DEBUG ] No custom content found
15 [2017-09-28 17:24:05,144] multiqc.modules.conpair.conpair [DEBUG ] Could not find any reports in ('multiqc_WDir',)
16 [2017-09-28 17:24:05,235] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('multiqc_WDir',)
17 [2017-09-28 17:24:05,259] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('multiqc_WDir',)
18 [2017-09-28 17:24:05,306] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50
19 [2017-09-28 17:24:05,306] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('multiqc_WDir',)
20 [2017-09-28 17:24:05,315] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('multiqc_WDir',)
21 [2017-09-28 17:24:05,329] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('multiqc_WDir',)
22 [2017-09-28 17:24:05,347] multiqc.modules.qorts.qorts [DEBUG ] Could not find any QoRTs data in ('multiqc_WDir',)
23 [2017-09-28 17:24:05,394] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('multiqc_WDir',)
24 [2017-09-28 17:24:05,424] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('multiqc_WDir',)
25 [2017-09-28 17:24:05,430] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('multiqc_WDir',)
26 [2017-09-28 17:24:05,469] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('multiqc_WDir',)
27 [2017-09-28 17:24:05,475] multiqc.modules.disambiguate.disambiguate [DEBUG ] Could not find any data in ('multiqc_WDir',)
28 [2017-09-28 17:24:05,499] multiqc.modules.homer.homer [DEBUG ] Could not find any reports in ('multiqc_WDir',)
29 [2017-09-28 17:24:05,513] multiqc.modules.macs2.macs2 [DEBUG ] Could not find any MACS2 data in ('multiqc_WDir',)
30 [2017-09-28 17:24:05,552] multiqc.modules.theta2.theta2 [DEBUG ] Could not find any reports in ('multiqc_WDir',)
31 [2017-09-28 17:24:05,571] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('multiqc_WDir',)
32 [2017-09-28 17:24:05,637] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('multiqc_WDir',)
33 [2017-09-28 17:24:05,693] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('multiqc_WDir',)
34 [2017-09-28 17:24:05,757] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('multiqc_WDir',)
35 [2017-09-28 17:24:05,787] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('multiqc_WDir',)
36 [2017-09-28 17:24:05,868] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('multiqc_WDir',)
37 [2017-09-28 17:24:05,874] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('multiqc_WDir',)
38 [2017-09-28 17:24:05,881] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('multiqc_WDir',)
39 [2017-09-28 17:24:05,915] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('multiqc_WDir',)
40 [2017-09-28 17:24:05,931] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('multiqc_WDir',)
41 [2017-09-28 17:24:05,942] multiqc.modules.jellyfish.jellyfish [DEBUG ] Could not find any data in ('multiqc_WDir',)
42 [2017-09-28 17:24:06,029] multiqc.modules.vcftools.vcftools [DEBUG ] Could not find any reports in ('multiqc_WDir',)
43 [2017-09-28 17:24:06,064] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('multiqc_WDir',)
44 [2017-09-28 17:24:06,083] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('multiqc_WDir',)
45 [2017-09-28 17:24:06,107] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('multiqc_WDir',)
46 [2017-09-28 17:24:06,145] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('multiqc_WDir',)
47 [2017-09-28 17:24:06,187] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found.
48 [2017-09-28 17:24:06,207] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('multiqc_WDir',)
49 [2017-09-28 17:24:06,225] multiqc.modules.hisat2.hisat2 [DEBUG ] Could not find any reports in ('multiqc_WDir',)
50 [2017-09-28 17:24:06,238] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('multiqc_WDir',)
51 [2017-09-28 17:24:06,245] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('multiqc_WDir',)
52 [2017-09-28 17:24:06,250] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('multiqc_WDir',)
53 [2017-09-28 17:24:06,263] multiqc.modules.leehom.leehom [DEBUG ] Could not find any reports in ('multiqc_WDir',)
54 [2017-09-28 17:24:06,273] multiqc.modules.adapterRemoval.adapterRemoval [DEBUG ] Could not find any reports in ('multiqc_WDir',)
55 [2017-09-28 17:24:06,299] multiqc.modules.cutadapt.cutadapt [INFO ] Found 1 reports
56 [2017-09-28 17:24:06,351] multiqc.modules.flexbar.flexbar [INFO ] Found 1 logs
57 [2017-09-28 17:24:06,378] multiqc.modules.trimmomatic.trimmomatic [INFO ] Found 1 logs
58 [2017-09-28 17:24:06,403] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('multiqc_WDir',)
59 [2017-09-28 17:24:06,421] multiqc.modules.sortmerna.sortmerna [INFO ] Found 1 logs
60 [2017-09-28 17:24:06,441] multiqc.modules.biobloomtools.biobloomtools [DEBUG ] Could not find any reports in ('multiqc_WDir',)
61 [2017-09-28 17:24:06,448] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('multiqc_WDir',)
62 [2017-09-28 17:24:06,605] multiqc.modules.fastqc.fastqc [INFO ] Found 2 reports
63 [2017-09-28 17:24:06,908] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('multiqc_WDir',)
64 [2017-09-28 17:24:06,914] multiqc.modules.bcl2fastq.bcl2fastq [DEBUG ] Could not find any bcl2fastq data in ('multiqc_WDir',)
65 [2017-09-28 17:24:06,923] multiqc [INFO ] Compressing plot data
66 [2017-09-28 17:24:07,121] multiqc [INFO ] Report : multiqc_report.html
67 [2017-09-28 17:24:07,121] multiqc [INFO ] Data : multiqc_data
68 [2017-09-28 17:24:07,121] multiqc [DEBUG ] Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmp7lPIig/multiqc_data/multiqc_cutadapt.txt' to '/Users/bebatut/Documents/post_doc_freiburg/galaxy_projects/tools/tools-iuc/tools/multiqc/multiqc_data'
69 [2017-09-28 17:24:07,121] multiqc [DEBUG ] Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmp7lPIig/multiqc_data/multiqc_fastqc.txt' to '/Users/bebatut/Documents/post_doc_freiburg/galaxy_projects/tools/tools-iuc/tools/multiqc/multiqc_data'
70 [2017-09-28 17:24:07,122] multiqc [DEBUG ] Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmp7lPIig/multiqc_data/multiqc_flexbar.txt' to '/Users/bebatut/Documents/post_doc_freiburg/galaxy_projects/tools/tools-iuc/tools/multiqc/multiqc_data'
71 [2017-09-28 17:24:07,122] multiqc [DEBUG ] Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmp7lPIig/multiqc_data/multiqc_general_stats.txt' to '/Users/bebatut/Documents/post_doc_freiburg/galaxy_projects/tools/tools-iuc/tools/multiqc/multiqc_data'
72 [2017-09-28 17:24:07,122] multiqc [DEBUG ] Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmp7lPIig/multiqc_data/multiqc_sortmerna.txt' to '/Users/bebatut/Documents/post_doc_freiburg/galaxy_projects/tools/tools-iuc/tools/multiqc/multiqc_data'
73 [2017-09-28 17:24:07,122] multiqc [DEBUG ] Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmp7lPIig/multiqc_data/multiqc_sources.txt' to '/Users/bebatut/Documents/post_doc_freiburg/galaxy_projects/tools/tools-iuc/tools/multiqc/multiqc_data'
74 [2017-09-28 17:24:07,122] multiqc [DEBUG ] Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmp7lPIig/multiqc_data/multiqc_trimmomatic.txt' to '/Users/bebatut/Documents/post_doc_freiburg/galaxy_projects/tools/tools-iuc/tools/multiqc/multiqc_data'
75 [2017-09-28 17:24:07,952] multiqc [INFO ] MultiQC complete