view test-data/pre_alignment_soft_log.txt @ 11:f0ec41881020 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
author iuc
date Mon, 06 Aug 2018 10:42:11 -0400
parents e0f4a651c6b9
children
line wrap: on
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[2018-04-05 12:06:46,534] multiqc                                            [DEBUG  ]  No MultiQC config found: /Users/bebatut/miniconda3/envs/multiqc/lib/python3.5/site-packages/multiqc_config.yaml
[2018-04-05 12:06:46,534] multiqc                                            [DEBUG  ]  No MultiQC config found: /Users/bebatut/.multiqc_config.yaml
[2018-04-05 12:06:46,534] multiqc                                            [DEBUG  ]  No MultiQC config found: multiqc_config.yaml
[2018-04-05 12:06:46,534] multiqc                                            [DEBUG  ]  Command used: /Users/bebatut/miniconda3/envs/multiqc/bin/multiqc multiqc_WDir
[2018-04-05 12:06:47,547] multiqc                                            [DEBUG  ]  Latest MultiQC version is v1.5
[2018-04-05 12:06:47,547] multiqc                                            [INFO   ]  This is MultiQC v1.5
[2018-04-05 12:06:47,548] multiqc                                            [DEBUG  ]  Command     : /Users/bebatut/miniconda3/envs/multiqc/bin/multiqc multiqc_WDir
[2018-04-05 12:06:47,548] multiqc                                            [DEBUG  ]  Working dir : /Users/bebatut/Documents/galaxy/tools/tools-iuc/tools/multiqc
[2018-04-05 12:06:47,548] multiqc                                            [INFO   ]  Template    : default
[2018-04-05 12:06:47,548] multiqc                                            [INFO   ]  Searching 'multiqc_WDir'
[2018-04-05 12:06:47,549] multiqc                                            [DEBUG  ]  Analysing modules: custom_content, conpair, peddy, methylQA, qualimap, preseq, quast, qorts, rna_seqc, rsem, rseqc, busco, goleft_indexcov, disambiguate, supernova, deeptools, sargasso, verifybamid, homer, macs2, theta2, snpeff, gatk, htseq, bcftools, featureCounts, dedup, picard, prokka, samblaster, samtools, bamtools, jellyfish, vcftools, bbmap, bismark, hicexplorer, hicup, salmon, kallisto, slamdunk, star, hisat2, tophat, bowtie2, bowtie1, leehom, adapterRemoval, clipandmerge, cutadapt, flexbar, trimmomatic, skewer, sortmerna, biobloomtools, fastq_screen, afterqc, fastqc, clusterflow, bcl2fastq, interop
[2018-04-05 12:06:47,554] multiqc                                            [DEBUG  ]  Using temporary directory for creating report: /var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmpd75q9s93
[2018-04-05 12:06:48,019] multiqc                                            [DEBUG  ]  No samples found: custom_content
[2018-04-05 12:06:48,025] multiqc                                            [DEBUG  ]  No samples found: conpair
[2018-04-05 12:06:48,030] multiqc                                            [DEBUG  ]  No samples found: peddy
[2018-04-05 12:06:48,035] multiqc                                            [DEBUG  ]  No samples found: methylQA
[2018-04-05 12:06:48,040] multiqc                                            [DEBUG  ]  No samples found: qualimap
[2018-04-05 12:06:48,045] multiqc                                            [DEBUG  ]  No samples found: preseq
[2018-04-05 12:06:48,050] multiqc                                            [DEBUG  ]  No samples found: quast
[2018-04-05 12:06:48,054] multiqc                                            [DEBUG  ]  No samples found: qorts
[2018-04-05 12:06:48,059] multiqc                                            [DEBUG  ]  No samples found: rna_seqc
[2018-04-05 12:06:48,063] multiqc                                            [DEBUG  ]  No samples found: rsem
[2018-04-05 12:06:48,070] multiqc                                            [DEBUG  ]  No samples found: rseqc
[2018-04-05 12:06:48,074] multiqc                                            [DEBUG  ]  No samples found: busco
[2018-04-05 12:06:48,079] multiqc                                            [DEBUG  ]  No samples found: goleft_indexcov
[2018-04-05 12:06:48,083] multiqc                                            [DEBUG  ]  No samples found: disambiguate
[2018-04-05 12:06:48,088] multiqc                                            [DEBUG  ]  No samples found: supernova
[2018-04-05 12:06:48,097] multiqc                                            [DEBUG  ]  No samples found: deeptools
[2018-04-05 12:06:48,103] multiqc                                            [DEBUG  ]  No samples found: sargasso
[2018-04-05 12:06:48,108] multiqc                                            [DEBUG  ]  No samples found: verifybamid
[2018-04-05 12:06:48,113] multiqc                                            [DEBUG  ]  No samples found: homer
[2018-04-05 12:06:48,118] multiqc                                            [DEBUG  ]  No samples found: macs2
[2018-04-05 12:06:48,124] multiqc                                            [DEBUG  ]  No samples found: theta2
[2018-04-05 12:06:48,130] multiqc                                            [DEBUG  ]  No samples found: snpeff
[2018-04-05 12:06:48,136] multiqc                                            [DEBUG  ]  No samples found: gatk
[2018-04-05 12:06:48,141] multiqc                                            [DEBUG  ]  No samples found: htseq
[2018-04-05 12:06:48,145] multiqc                                            [DEBUG  ]  No samples found: bcftools
[2018-04-05 12:06:48,151] multiqc                                            [DEBUG  ]  No samples found: featureCounts
[2018-04-05 12:06:48,157] multiqc                                            [DEBUG  ]  No samples found: dedup
[2018-04-05 12:06:48,166] multiqc                                            [DEBUG  ]  No samples found: picard
[2018-04-05 12:06:48,170] multiqc                                            [DEBUG  ]  No samples found: prokka
[2018-04-05 12:06:48,174] multiqc                                            [DEBUG  ]  No samples found: samblaster
[2018-04-05 12:06:48,180] multiqc                                            [DEBUG  ]  No samples found: samtools
[2018-04-05 12:06:48,184] multiqc                                            [DEBUG  ]  No samples found: bamtools
[2018-04-05 12:06:48,189] multiqc                                            [DEBUG  ]  No samples found: jellyfish
[2018-04-05 12:06:48,194] multiqc                                            [DEBUG  ]  No samples found: vcftools
[2018-04-05 12:06:48,202] multiqc                                            [DEBUG  ]  No samples found: bbmap
[2018-04-05 12:06:48,206] multiqc                                            [DEBUG  ]  No samples found: bismark
[2018-04-05 12:06:48,211] multiqc                                            [DEBUG  ]  No samples found: hicexplorer
[2018-04-05 12:06:48,215] multiqc                                            [DEBUG  ]  No samples found: hicup
[2018-04-05 12:06:48,219] multiqc                                            [DEBUG  ]  No samples found: salmon
[2018-04-05 12:06:48,225] multiqc                                            [DEBUG  ]  No samples found: kallisto
[2018-04-05 12:06:48,231] multiqc                                            [DEBUG  ]  No samples found: slamdunk
[2018-04-05 12:06:48,236] multiqc                                            [DEBUG  ]  No samples found: star
[2018-04-05 12:06:48,242] multiqc                                            [DEBUG  ]  No samples found: hisat2
[2018-04-05 12:06:48,246] multiqc                                            [DEBUG  ]  No samples found: tophat
[2018-04-05 12:06:48,250] multiqc                                            [DEBUG  ]  No samples found: bowtie2
[2018-04-05 12:06:48,255] multiqc                                            [DEBUG  ]  No samples found: bowtie1
[2018-04-05 12:06:48,259] multiqc                                            [DEBUG  ]  No samples found: leehom
[2018-04-05 12:06:48,263] multiqc                                            [DEBUG  ]  No samples found: adapterRemoval
[2018-04-05 12:06:48,268] multiqc                                            [DEBUG  ]  No samples found: clipandmerge
[2018-04-05 12:06:48,276] multiqc.modules.cutadapt.cutadapt                  [INFO   ]  Found 1 reports
[2018-04-05 12:06:48,307] multiqc.modules.flexbar.flexbar                    [INFO   ]  Found 1 logs
[2018-04-05 12:06:48,318] multiqc.modules.trimmomatic.trimmomatic            [INFO   ]  Found 1 logs
[2018-04-05 12:06:48,325] multiqc                                            [DEBUG  ]  No samples found: skewer
[2018-04-05 12:06:48,334] multiqc.modules.sortmerna.sortmerna                [INFO   ]  Found 1 logs
[2018-04-05 12:06:48,339] multiqc                                            [DEBUG  ]  No samples found: biobloomtools
[2018-04-05 12:06:48,346] multiqc                                            [DEBUG  ]  No samples found: fastq_screen
[2018-04-05 12:06:48,352] multiqc                                            [DEBUG  ]  No samples found: afterqc
[2018-04-05 12:06:48,434] multiqc.modules.fastqc.fastqc                      [INFO   ]  Found 2 reports
[2018-04-05 12:06:48,495] multiqc                                            [DEBUG  ]  No samples found: clusterflow
[2018-04-05 12:06:48,500] multiqc                                            [DEBUG  ]  No samples found: bcl2fastq
[2018-04-05 12:06:48,505] multiqc                                            [DEBUG  ]  No samples found: interop
[2018-04-05 12:06:48,514] multiqc                                            [INFO   ]  Compressing plot data
[2018-04-05 12:06:48,596] multiqc                                            [INFO   ]  Report      : multiqc_report.html
[2018-04-05 12:06:48,597] multiqc                                            [INFO   ]  Data        : multiqc_data
[2018-04-05 12:06:48,597] multiqc                                            [DEBUG  ]  Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmpd75q9s93/multiqc_data/multiqc_cutadapt.txt' to '/Users/bebatut/Documents/galaxy/tools/tools-iuc/tools/multiqc/multiqc_data'
[2018-04-05 12:06:48,597] multiqc                                            [DEBUG  ]  Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmpd75q9s93/multiqc_data/multiqc_data.json' to '/Users/bebatut/Documents/galaxy/tools/tools-iuc/tools/multiqc/multiqc_data'
[2018-04-05 12:06:48,598] multiqc                                            [DEBUG  ]  Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmpd75q9s93/multiqc_data/multiqc_fastqc.txt' to '/Users/bebatut/Documents/galaxy/tools/tools-iuc/tools/multiqc/multiqc_data'
[2018-04-05 12:06:48,598] multiqc                                            [DEBUG  ]  Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmpd75q9s93/multiqc_data/multiqc_flexbar.txt' to '/Users/bebatut/Documents/galaxy/tools/tools-iuc/tools/multiqc/multiqc_data'
[2018-04-05 12:06:48,598] multiqc                                            [DEBUG  ]  Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmpd75q9s93/multiqc_data/multiqc_general_stats.txt' to '/Users/bebatut/Documents/galaxy/tools/tools-iuc/tools/multiqc/multiqc_data'
[2018-04-05 12:06:48,598] multiqc                                            [DEBUG  ]  Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmpd75q9s93/multiqc_data/multiqc_sortmerna.txt' to '/Users/bebatut/Documents/galaxy/tools/tools-iuc/tools/multiqc/multiqc_data'
[2018-04-05 12:06:48,598] multiqc                                            [DEBUG  ]  Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmpd75q9s93/multiqc_data/multiqc_sources.txt' to '/Users/bebatut/Documents/galaxy/tools/tools-iuc/tools/multiqc/multiqc_data'
[2018-04-05 12:06:48,599] multiqc                                            [DEBUG  ]  Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmpd75q9s93/multiqc_data/multiqc_trimmomatic.txt' to '/Users/bebatut/Documents/galaxy/tools/tools-iuc/tools/multiqc/multiqc_data'
[2018-04-05 12:06:48,809] multiqc                                            [INFO   ]  MultiQC complete