galaxy-docker

 
tavaxy@c863b843f754:/var/www/tavaxy/engines/galaxy$ sh run.sh --reload
Starting subprocess with file monitor
python path is: /var/www/tavaxy/engines/galaxy/eggs/numpy-1.3.0-py2.6-linux-x86_64-ucs4.egg, /var/www/tavaxy/engines/galaxy/eggs/pysam-0.1.1_kanwei_90e03180969d-py2.6-linux-x86_64-ucs4.egg, /var/www/tavaxy/engines/galaxy/eggs/Whoosh-0.3.18-py2.6.egg, /var/www/tavaxy/engines/galaxy/eggs/pycrypto-2.5-py2.6-linux-x86_64-ucs4.egg, /var/www/tavaxy/engines/galaxy/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg, /var/www/tavaxy/engines/galaxy/eggs/bx_python-0.5.0_dev_f74aec067563-py2.6-linux-x86_64-ucs4.egg, /var/www/tavaxy/engines/galaxy/eggs/amqplib-0.6.1-py2.6.egg, /var/www/tavaxy/engines/galaxy/eggs/pexpect-2.4-py2.6.egg, /var/www/tavaxy/engines/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg, /var/www/tavaxy/engines/galaxy/eggs/Babel-0.9.4-py2.6.egg, /var/www/tavaxy/engines/galaxy/eggs/Beaker-1.4-py2.6.egg, /var/www/tavaxy/engines/galaxy/eggs/Mako-0.2.5-py2.6.egg, /var/www/tavaxy/engines/galaxy/eggs/WebHelpers-0.2-py2.6.egg, /var/www/tavaxy/engines/galaxy/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg, /var/www/tavaxy/engines/galaxy/eggs/docutils-0.4-py2.6.egg, /var/www/tavaxy/engines/galaxy/eggs/WebOb-0.8.5-py2.6.egg, /var/www/tavaxy/engines/galaxy/eggs/Routes-1.12.3-py2.6.egg, /var/www/tavaxy/engines/galaxy/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg, /var/www/tavaxy/engines/galaxy/eggs/PasteDeploy-1.3.3-py2.6.egg, /var/www/tavaxy/engines/galaxy/eggs/PasteScript-1.7.3-py2.6.egg, /var/www/tavaxy/engines/galaxy/eggs/Paste-1.6-py2.6.egg, /var/www/tavaxy/engines/galaxy/lib, /usr/lib/python2.6, /usr/lib/python2.6/plat-linux2, /usr/lib/python2.6/lib-tk, /usr/lib/python2.6/lib-old, /usr/lib/python2.6/lib-dynload, /usr/lib/python2.6/dist-packages, /usr/local/lib/python2.6/dist-packages
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:10,295 Loading datatypes from datatypes_conf.xml
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:10,303 Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:10,311 Loaded display application 'ensembl_bam' for datatype 'bam', inherit=False
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:10,312 Loaded display application 'genetrack_interval' for datatype 'bed', inherit=False
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:10,318 Loaded display application 'ucsc_bigbed' for datatype 'bigbed', inherit=False
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:10,324 Loaded display application 'ucsc_bigwig' for datatype 'bigwig', inherit=False
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:10,337 Loaded display application 'ensembl_gff' for datatype 'gff', inherit=True
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:10,339 Loaded display application 'genetrack_interval' for datatype 'interval', inherit=True
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:10,350 Loaded display application 'ensembl_interval' for datatype 'interval', inherit=True
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:10,355 Loaded display application 'gbrowse_interval_as_bed' for datatype 'interval', inherit=True
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:10,361 Loaded display application 'ucsc_maf_customtrack' for datatype 'mafcustomtrack', inherit=False
galaxy.datatypes.assembly DEBUG 2016-02-22 13:55:10,363 Velvet log info  JJ __init__
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:10,378 Loaded sniffer for datatype: galaxy.datatypes.binary:Bam
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:10,378 Loaded sniffer for datatype: galaxy.datatypes.binary:Sff
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:10,378 Loaded sniffer for datatype: galaxy.datatypes.xml:BlastXml
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:10,379 Loaded sniffer for datatype: galaxy.datatypes.sequence:Maf
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:10,379 Loaded sniffer for datatype: galaxy.datatypes.sequence:Lav
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:10,379 Loaded sniffer for datatype: galaxy.datatypes.sequence:csFasta
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:10,379 Loaded sniffer for datatype: galaxy.datatypes.qualityscore:QualityScoreSOLiD
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:10,380 Loaded sniffer for datatype: galaxy.datatypes.qualityscore:QualityScore454
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:10,380 Loaded sniffer for datatype: galaxy.datatypes.sequence:Fasta
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:10,380 Loaded sniffer for datatype: galaxy.datatypes.sequence:Fastq
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:10,380 Loaded sniffer for datatype: galaxy.datatypes.interval:Wiggle
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:10,381 Loaded sniffer for datatype: galaxy.datatypes.images:Html
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:10,381 Loaded sniffer for datatype: galaxy.datatypes.images:Pdf
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:10,381 Loaded sniffer for datatype: galaxy.datatypes.sequence:Axt
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:10,382 Loaded sniffer for datatype: galaxy.datatypes.interval:Bed
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:10,382 Loaded sniffer for datatype: galaxy.datatypes.interval:CustomTrack
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:10,382 Loaded sniffer for datatype: galaxy.datatypes.interval:Gff
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:10,382 Loaded sniffer for datatype: galaxy.datatypes.interval:Gff3
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:10,383 Loaded sniffer for datatype: galaxy.datatypes.tabular:Pileup
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:10,383 Loaded sniffer for datatype: galaxy.datatypes.interval:Interval
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:10,383 Loaded sniffer for datatype: galaxy.datatypes.tabular:Sam
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:10,384 Loaded sniffer for datatype: galaxy.datatypes.tabular:Vcf
galaxy.model.migrate.check DEBUG 2016-02-22 13:55:10,434 MySQL_python egg successfully loaded for mysql dialect
galaxy.model.migrate.check INFO 2016-02-22 13:55:10,528 At database version 0
galaxy.model.custom_types DEBUG 2016-02-22 13:55:10,536 MySQL_python egg successfully loaded for mysql dialect
galaxy.tools.data DEBUG 2016-02-22 13:55:10,540 Loaded tool data table 'all_fasta
galaxy.tools.data DEBUG 2016-02-22 13:55:10,541 Loaded tool data table 'bfast_indexes
galaxy.tools.data DEBUG 2016-02-22 13:55:10,541 Loaded tool data table 'blastdb
galaxy.tools.data DEBUG 2016-02-22 13:55:10,541 Loaded tool data table 'blastdb_p
galaxy.tools.data DEBUG 2016-02-22 13:55:10,542 Loaded tool data table 'bowtie_indexes
galaxy.tools.data DEBUG 2016-02-22 13:55:10,542 Loaded tool data table 'bowtie_indexes_color
galaxy.tools.data DEBUG 2016-02-22 13:55:10,543 Loaded tool data table 'bwa_indexes
galaxy.tools.data DEBUG 2016-02-22 13:55:10,543 Loaded tool data table 'indexed_maf_files
galaxy.tools.data DEBUG 2016-02-22 13:55:10,544 Loaded tool data table 'ngs_sim_fasta
galaxy.tools.data DEBUG 2016-02-22 13:55:10,544 Loaded tool data table 'lastz_seqs
galaxy.tools.data DEBUG 2016-02-22 13:55:10,544 Loaded tool data table 'perm_base_indexes
galaxy.tools.data DEBUG 2016-02-22 13:55:10,545 Loaded tool data table 'perm_color_indexes
galaxy.tools.data DEBUG 2016-02-22 13:55:10,545 Loaded tool data table 'srma_indexes
galaxy.tools.data DEBUG 2016-02-22 13:55:10,546 Loaded tool data table 'tophat_indexes
galaxy.tools INFO 2016-02-22 13:55:10,546 parsing the tool configuration
galaxy.tools DEBUG 2016-02-22 13:55:10,569 Loading section: Pipelines
galaxy.tools DEBUG 2016-02-22 13:55:10,569 Loading section: EMBOSS
galaxy.tools DEBUG 2016-02-22 13:55:10,666 Loaded tool: EMBOSS:cons 6.0.1
galaxy.tools DEBUG 2016-02-22 13:55:10,682 Loaded tool: EMBOSS:fprotdist 6.0.1
galaxy.tools DEBUG 2016-02-22 13:55:10,699 Loaded tool: EMBOSS:fneighbor 6.0.1
galaxy.tools DEBUG 2016-02-22 13:55:10,713 Loaded tool: EMBOSS:fdrawtree 6.0.1
galaxy.tools DEBUG 2016-02-22 13:55:10,727 Loaded tool: EMBOSS:fdrawgram 6.0.1
galaxy.tools DEBUG 2016-02-22 13:55:10,741 Loaded tool: EMBOSS:emma 6.0.1
galaxy.tools DEBUG 2016-02-22 13:55:10,770 Loaded tool: EMBOSS:patmatmotifs 6.0.1
galaxy.tools DEBUG 2016-02-22 13:55:10,787 Loaded tool: EMBOSS:pscan 6.0.1
galaxy.tools DEBUG 2016-02-22 13:55:10,804 Loaded tool: EMBOSS:newcpgreport57 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:10,820 Loaded tool: EMBOSS:primersearch81 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:10,842 Loaded tool: EMBOSS:coderet13 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:10,859 Loaded tool: EMBOSS:degapseq20 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:10,883 Loaded tool: EMBOSS:nthseq62 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:10,898 Loaded tool: EMBOSS:cpgplot15 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:10,912 Loaded tool: EMBOSS:pepnet70 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:10,927 Loaded tool: EMBOSS:pepstats71 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:10,946 Loaded tool: EMBOSS:checktrans9 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:10,966 Loaded tool: EMBOSS:digest23 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:10,983 Loaded tool: EMBOSS:newcpgseek58 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:11,001 Loaded tool: EMBOSS:palindrome65 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:11,018 Loaded tool: EMBOSS:merger54 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:11,032 Loaded tool: EMBOSS:chips10 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:11,052 Loaded tool: EMBOSS:revseq82 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:11,069 Loaded tool: EMBOSS:polydot77 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:11,092 Loaded tool: EMBOSS:getorf42 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:11,111 Loaded tool: EMBOSS:charge8 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:11,128 Loaded tool: EMBOSS:cusp17 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:11,142 Loaded tool: EMBOSS:pepinfo69 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:11,159 Loaded tool: EMBOSS:matcher52 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:11,176 Loaded tool: EMBOSS:dan19 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:11,193 Loaded tool: EMBOSS:vectorstrip106 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:11,213 Loaded tool: EMBOSS:etandem33 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:11,232 Loaded tool: EMBOSS:shuffleseq87 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:11,253 Loaded tool: EMBOSS:tranalign100 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:11,271 Loaded tool: EMBOSS:prettyseq80 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:11,285 Loaded tool: EMBOSS:octanol63 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:11,305 Loaded tool: EMBOSS:pasteseq66 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:11,325 Loaded tool: EMBOSS:splitter92 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:11,347 Loaded tool: EMBOSS:syco96 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:11,364 Loaded tool: EMBOSS:maskfeat50 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:11,384 Loaded tool: EMBOSS:megamerger53 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:11,524 Loaded tool: EMBOSS:notseq61 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:11,544 Loaded tool: EMBOSS:showfeat85 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:11,559 Loaded tool: EMBOSS:pepcoil68 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:11,587 Loaded tool: EMBOSS:codcmp12 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:11,632 Loaded tool: EMBOSS:isochore47 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:11,650 Loaded tool: EMBOSS:cirdna11 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:11,673 Loaded tool: EMBOSS:seqmatchall83 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:11,693 Loaded tool: EMBOSS:tcode97 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:11,712 Loaded tool: EMBOSS:marscan49 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:11,737 Loaded tool: EMBOSS:cutseq18 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:11,767 Loaded tool: EMBOSS:msbar55 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:11,789 Loaded tool: EMBOSS:cpgreport16 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:11,807 Loaded tool: EMBOSS:chaos7 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:11,836 Loaded tool: EMBOSS:sixpack90 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:11,854 Loaded tool: EMBOSS:btwisted5 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:11,881 Loaded tool: EMBOSS:fuzztran39 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:11,899 Loaded tool: EMBOSS:oddcomp64 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:11,921 Loaded tool: EMBOSS:noreturn60 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:11,942 Loaded tool: EMBOSS:wordcount109 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:11,963 Loaded tool: EMBOSS:textsearch98 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:11,988 Loaded tool: EMBOSS:biosed4 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:12,013 Loaded tool: EMBOSS:water107 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:12,036 Loaded tool: EMBOSS:extractfeat34 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:12,053 Loaded tool: EMBOSS:dreg27 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:12,076 Loaded tool: EMBOSS:tmap99 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:12,096 Loaded tool: EMBOSS:antigenic1 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:12,115 Loaded tool: EMBOSS:pepwheel72 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:12,135 Loaded tool: EMBOSS:supermatcher95 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:12,155 Loaded tool: EMBOSS:garnier40 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:12,189 Loaded tool: EMBOSS:backtranseq2 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:12,210 Loaded tool: EMBOSS:extractseq35 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:12,228 Loaded tool: EMBOSS:iep45 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:12,253 Loaded tool: EMBOSS:compseq14 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:12,275 Loaded tool: EMBOSS:helixturnhelix43 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:12,299 Loaded tool: EMBOSS:fuzznuc37 5.0.1
galaxy.tools DEBUG 2016-02-22 13:55:12,324 Loaded tool: EMBOSS:union105 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:12,346 Loaded tool: EMBOSS:wobble108 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:12,363 Loaded tool: EMBOSS:preg78 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:12,383 Loaded tool: EMBOSS:patmatdb67 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:12,410 Loaded tool: EMBOSS:equicktandem31 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:12,436 Loaded tool: EMBOSS:trimest102 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:12,453 Loaded tool: EMBOSS:banana3 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:12,510 Loaded tool: EMBOSS:needle56 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:12,530 Loaded tool: EMBOSS:fuzzpro38 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:12,548 Loaded tool: EMBOSS:hmoment44 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:12,570 Loaded tool: EMBOSS:infoseq46 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:12,593 Loaded tool: EMBOSS:sigcleave88 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:12,618 Loaded tool: EMBOSS:wordmatch110 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:12,638 Loaded tool: EMBOSS:skipseq91 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:12,669 Loaded tool: EMBOSS:cai6 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:12,690 Loaded tool: EMBOSS:plotorf76 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:12,718 Loaded tool: EMBOSS:sirna89 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:12,737 Loaded tool: EMBOSS:dottup26 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:12,765 Loaded tool: EMBOSS:transeq101 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:12,786 Loaded tool: EMBOSS:freak36 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:12,805 Loaded tool: EMBOSS:epestfind29 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:12,823 Loaded tool: EMBOSS:plotcon75 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:12,840 Loaded tool: EMBOSS:pepwindow73 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:12,859 Loaded tool: EMBOSS:dotpath25 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:12,882 Loaded tool: EMBOSS:prettyplot79 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:12,900 Loaded tool: EMBOSS:pepwindowall74 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:12,929 Loaded tool: EMBOSS:twofeat104 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:12,950 Loaded tool: EMBOSS:maskseq51 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:12,972 Loaded tool: EMBOSS:lindna48 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:12,994 Loaded tool: EMBOSS:descseq21 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:13,015 Loaded tool: EMBOSS:seqret84 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:13,037 Loaded tool: EMBOSS:newseq59 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:13,063 Loaded tool: EMBOSS:est2genome32 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:13,081 Loaded tool: EMBOSS:dotmatcher24 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:13,106 Loaded tool: EMBOSS:diffseq22 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:13,123 Loaded tool: EMBOSS:geecee41 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:13,145 Loaded tool: EMBOSS:einverted28 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:13,172 Loaded tool: EMBOSS:trimseq103 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:13,172 Loading section: Sam Tools
galaxy.tools DEBUG 2016-02-22 13:55:13,308 Loaded tool: pileup_parser 1.0.2
galaxy.tools DEBUG 2016-02-22 13:55:13,441 Loaded tool: pileup_interval 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:13,478 Loaded tool: sam_pileup 1.1.0
galaxy.tools DEBUG 2016-02-22 13:55:13,495 Loaded tool: sam_to_bam 1.1.0
galaxy.tools DEBUG 2016-02-22 13:55:13,511 Loaded tool: bam_to_sam 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:13,531 Loaded tool: sam2interval 1.0.1
galaxy.tools DEBUG 2016-02-22 13:55:13,546 Loaded tool: sam_merge 1.1.0
galaxy.tools DEBUG 2016-02-22 13:55:13,557 Loaded tool: samtools_extractunmapped 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:13,557 Loading section: VCF Tools
galaxy.tools DEBUG 2016-02-22 13:55:13,567 Loaded tool: VCF_Annotate 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:13,581 Loaded tool: Vcf_compare 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:13,592 Loaded tool: VCF:Concat 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:13,602 Loaded tool: VCF:Consensus 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:13,613 Loaded tool: VCF:Convert 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:13,628 Loaded tool: VCF:FixPloidy 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:13,642 Loaded tool: VCF:IndelStats 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:13,653 Loaded tool: VCF:Isec 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:13,665 Loaded tool: VCF:Merge 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:13,676 Loaded tool: VCF:PhasedJoin 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:13,688 Loaded tool: VCF:ShuffleCols 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:13,698 Loaded tool: VCF:Sort 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:13,709 Loaded tool: VCF:Stats 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:13,720 Loaded tool: VCF:Subset 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:13,735 Loaded tool: VCF:ToTab 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:13,745 Loaded tool: VCF:Tstv 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:13,746 Loading section: fastx_toolkit
galaxy.tools DEBUG 2016-02-22 13:55:13,769 Loaded tool: cshl_fastx_reverse_complement 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:13,791 Loaded tool: cshl_fastx_artifacts_filter 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:13,814 Loaded tool: cshl_fastx_trimmer 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:13,833 Loaded tool: cshl_fastx_barcode_splitter 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:13,871 Loaded tool: cshl_fastq_quality_boxplot 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:13,892 Loaded tool: cshl_fastx_collapser 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:13,906 Loaded tool: cshl_fasta_nucleotides_changer 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:13,923 Loaded tool: cshl_fasta_formatter 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:13,953 Loaded tool: cshl_fastx_nucleotides_distribution 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:13,975 Loaded tool: cshl_fastx_renamer 0.0.11
galaxy.tools DEBUG 2016-02-22 13:55:13,997 Loaded tool: cshl_fastq_quality_converter 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:14,017 Loaded tool: cshl_fastq_to_fasta 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:14,048 Loaded tool: cshl_fastq_quality_filter 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:14,077 Loaded tool: cshl_fastq_quality_trimmer 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:14,109 Loaded tool: cshl_fasta_clipping_histogram 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:14,175 Loaded tool: cshl_fastx_quality_statistics 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:14,175 Loading section: SIMPLEX Pipeline
galaxy.tools DEBUG 2016-02-22 13:55:14,176 Loaded tool: repeat 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:14,194 Loaded tool: foldcoverage 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:14,203 Loaded tool: picardcmm 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:14,237 Loaded tool: rgPicFixMate 1.56.0
docutils WARNING 2016-02-22 13:55:14,306 <string>:52: (SEVERE/4) Unexpected section title or transition.

------
galaxy.tools ERROR 2016-02-22 13:55:14,306 error in help for tool Add or Replace Groups
Traceback (most recent call last):
  File "/var/www/tavaxy/engines/galaxy/lib/galaxy/tools/__init__.py", line 533, in parse_help
    self.help = util.rst_to_html(self.help.text)
  File "/var/www/tavaxy/engines/galaxy/lib/galaxy/util/__init__.py", line 254, in rst_to_html
    return docutils.core.publish_string( s, writer=HTMLFragWriter(), settings_overrides=dict( warning_stream=FakeStream() ) )
  File "/var/www/tavaxy/engines/galaxy/eggs/docutils-0.4-py2.6.egg/docutils/core.py", line 397, in publish_string
    enable_exit_status=enable_exit_status)
  File "/var/www/tavaxy/engines/galaxy/eggs/docutils-0.4-py2.6.egg/docutils/core.py", line 612, in publish_programmatically
    output = pub.publish(enable_exit_status=enable_exit_status)
  File "/var/www/tavaxy/engines/galaxy/eggs/docutils-0.4-py2.6.egg/docutils/core.py", line 204, in publish
    self.settings)
  File "/var/www/tavaxy/engines/galaxy/eggs/docutils-0.4-py2.6.egg/docutils/readers/__init__.py", line 71, in read
    self.parse()
  File "/var/www/tavaxy/engines/galaxy/eggs/docutils-0.4-py2.6.egg/docutils/readers/__init__.py", line 77, in parse
    self.parser.parse(self.input, document)
  File "/var/www/tavaxy/engines/galaxy/eggs/docutils-0.4-py2.6.egg/docutils/parsers/rst/__init__.py", line 155, in parse
    self.statemachine.run(inputlines, document, inliner=self.inliner)
  File "/var/www/tavaxy/engines/galaxy/eggs/docutils-0.4-py2.6.egg/docutils/parsers/rst/states.py", line 171, in run
    input_source=document['source'])
  File "/var/www/tavaxy/engines/galaxy/eggs/docutils-0.4-py2.6.egg/docutils/statemachine.py", line 234, in run
    context, state, transitions)
  File "/var/www/tavaxy/engines/galaxy/eggs/docutils-0.4-py2.6.egg/docutils/statemachine.py", line 422, in check_line
    return method(match, context, next_state)
  File "/var/www/tavaxy/engines/galaxy/eggs/docutils-0.4-py2.6.egg/docutils/parsers/rst/states.py", line 1083, in indent
    blockquote, messages = self.block_quote(indented, line_offset)
  File "/var/www/tavaxy/engines/galaxy/eggs/docutils-0.4-py2.6.egg/docutils/parsers/rst/states.py", line 1094, in block_quote
    self.nested_parse(blockquote_lines, line_offset, blockquote)
  File "/var/www/tavaxy/engines/galaxy/eggs/docutils-0.4-py2.6.egg/docutils/parsers/rst/states.py", line 267, in nested_parse
    node=node, match_titles=match_titles)
  File "/var/www/tavaxy/engines/galaxy/eggs/docutils-0.4-py2.6.egg/docutils/parsers/rst/states.py", line 196, in run
    results = StateMachineWS.run(self, input_lines, input_offset)
  File "/var/www/tavaxy/engines/galaxy/eggs/docutils-0.4-py2.6.egg/docutils/statemachine.py", line 234, in run
    context, state, transitions)
  File "/var/www/tavaxy/engines/galaxy/eggs/docutils-0.4-py2.6.egg/docutils/statemachine.py", line 422, in check_line
    return method(match, context, next_state)
  File "/var/www/tavaxy/engines/galaxy/eggs/docutils-0.4-py2.6.egg/docutils/parsers/rst/states.py", line 2269, in line
    line=self.state_machine.abs_line_number())
  File "/var/www/tavaxy/engines/galaxy/eggs/docutils-0.4-py2.6.egg/docutils/utils.py", line 217, in severe
    return self.system_message(4, *args, **kwargs)
  File "/var/www/tavaxy/engines/galaxy/eggs/docutils-0.4-py2.6.egg/docutils/utils.py", line 175, in system_message
    raise SystemMessage(msg, level)
SystemMessage: <string>:52: (SEVERE/4) Unexpected section title or transition.

------
galaxy.tools DEBUG 2016-02-22 13:55:14,311 Loaded tool: picard_ARRG 1.56.0
galaxy.tools DEBUG 2016-02-22 13:55:14,320 Loaded tool: gatk_realigner_target_creator 0.0.4
galaxy.tools DEBUG 2016-02-22 13:55:14,329 Loaded tool: gatk:indelrealigner 0.0.6
galaxy.tools DEBUG 2016-02-22 13:55:14,337 Loaded tool: recalibrate_base_quality 0.0.6
galaxy.tools DEBUG 2016-02-22 13:55:14,346 Loaded tool: gatk_print_reads 0.0.1
galaxy.tools DEBUG 2016-02-22 13:55:14,360 Loaded tool: filterreads 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:14,392 Loaded tool: rgPicardMarkDups 1.56.0
galaxy.tools DEBUG 2016-02-22 13:55:14,418 Loaded tool: gatk2_reduce_reads 0.0.7
galaxy.tools DEBUG 2016-02-22 13:55:14,436 Loaded tool: exonfilter 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:14,447 Loaded tool: PicardASMetrics 1.56.0
galaxy.tools DEBUG 2016-02-22 13:55:14,460 Loaded tool: calcstats 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:14,493 Loaded tool: PicardInsertSize 1.56.0
galaxy.tools DEBUG 2016-02-22 13:55:14,507 Loaded tool: bedcoverage 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:14,521 Loaded tool: covstats 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:14,530 Loaded tool: gatk_unified_genotyper 0.0.6
galaxy.tools DEBUG 2016-02-22 13:55:14,544 Loaded tool: vcftoanno 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:14,561 Loaded tool: anoo 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:14,575 Loaded tool: splitindels 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:14,584 Loaded tool: gatk_haplotyper 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:14,592 Loaded tool: gatk_variant_eval 0.0.8
galaxy.tools DEBUG 2016-02-22 13:55:14,601 Loaded tool: gatk_variant_filtration 0.0.5
galaxy.tools DEBUG 2016-02-22 13:55:14,610 Loaded tool: gatk_variant_recalibrator 0.0.4
galaxy.tools DEBUG 2016-02-22 13:55:14,619 Loaded tool: gatk_variant_apply_recalibration 0.0.4
galaxy.tools DEBUG 2016-02-22 13:55:14,627 Loaded tool: gatk_divide 0.0.5
galaxy.tools DEBUG 2016-02-22 13:55:14,637 Loaded tool: gatk_variant_annotator 0.0.5
galaxy.tools DEBUG 2016-02-22 13:55:14,650 Loaded tool: igvtools 1.5.15
galaxy.tools DEBUG 2016-02-22 13:55:14,665 Loaded tool: amtmerge 5.0.0
galaxy.tools DEBUG 2016-02-22 13:55:14,677 Loaded tool: genotyper 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:14,677 Loading section: NGS Mapping Tools
galaxy.tools DEBUG 2016-02-22 13:55:14,687 Loaded tool: maq 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:14,730 Loaded tool: bfast_wrapper 0.1.2
galaxy.tools DEBUG 2016-02-22 13:55:14,772 Loaded tool: bwa_wrapper 1.1.0
galaxy.tools DEBUG 2016-02-22 13:55:14,781 Loaded tool: bam_to_bwa 1.0.0
galaxy.tools ERROR 2016-02-22 13:55:14,787 error in help for tool Map CS with Shrimp
Traceback (most recent call last):
  File "/var/www/tavaxy/engines/galaxy/lib/galaxy/tools/__init__.py", line 533, in parse_help
    self.help = util.rst_to_html(self.help.text)
  File "/var/www/tavaxy/engines/galaxy/lib/galaxy/util/__init__.py", line 254, in rst_to_html
    return docutils.core.publish_string( s, writer=HTMLFragWriter(), settings_overrides=dict( warning_stream=FakeStream() ) )
  File "/var/www/tavaxy/engines/galaxy/eggs/docutils-0.4-py2.6.egg/docutils/core.py", line 397, in publish_string
    enable_exit_status=enable_exit_status)
  File "/var/www/tavaxy/engines/galaxy/eggs/docutils-0.4-py2.6.egg/docutils/core.py", line 612, in publish_programmatically
    output = pub.publish(enable_exit_status=enable_exit_status)
  File "/var/www/tavaxy/engines/galaxy/eggs/docutils-0.4-py2.6.egg/docutils/core.py", line 204, in publish
    self.settings)
  File "/var/www/tavaxy/engines/galaxy/eggs/docutils-0.4-py2.6.egg/docutils/readers/__init__.py", line 70, in read
    self.input = self.source.read()
  File "/var/www/tavaxy/engines/galaxy/eggs/docutils-0.4-py2.6.egg/docutils/io.py", line 318, in read
    return self.decode(self.source)
  File "/var/www/tavaxy/engines/galaxy/eggs/docutils-0.4-py2.6.egg/docutils/io.py", line 100, in decode
    decoded = unicode(data, enc, self.error_handler)
TypeError: coercing to Unicode: need string or buffer, NoneType found
galaxy.tools DEBUG 2016-02-22 13:55:14,789 Loaded tool: shrimp_cs 1.1.0
galaxy.tools DEBUG 2016-02-22 13:55:14,797 Loaded tool: shrimp_ls_wrapper 1.1.0
galaxy.tools DEBUG 2016-02-22 13:55:14,878 Loaded tool: bowtie_wrapper 1.1.0
galaxy.tools DEBUG 2016-02-22 13:55:14,973 Loaded tool: bowtie_color_wrapper 1.1.0
galaxy.tools DEBUG 2016-02-22 13:55:14,973 Loading section: Target Prediction
galaxy.tools DEBUG 2016-02-22 13:55:14,983 Loaded tool: microPred 0.0.1
galaxy.tools DEBUG 2016-02-22 13:55:14,994 Loaded tool: RNAmicro 0.0.1
galaxy.tools DEBUG 2016-02-22 13:55:15,005 Loaded tool: Blast_miRNA 0.0.1
galaxy.tools DEBUG 2016-02-22 13:55:15,015 Loaded tool: shortner 0.0.1
galaxy.tools DEBUG 2016-02-22 13:55:15,025 Loaded tool: Complementary_Sequence 0.0.1
galaxy.tools DEBUG 2016-02-22 13:55:15,037 Loaded tool: Fasta_from_Seq_or_ID 0.0.1
galaxy.tools DEBUG 2016-02-22 13:55:15,051 Loaded tool: Join_fasta_to_id 0.0.1
galaxy.tools DEBUG 2016-02-22 13:55:15,061 Loaded tool: remove_repeats 0.0.1
galaxy.tools DEBUG 2016-02-22 13:55:15,161 Loaded tool: Seed_matching 0.0.1
galaxy.tools DEBUG 2016-02-22 13:55:15,172 Loaded tool: Targetminer_results 0.0.1
galaxy.tools DEBUG 2016-02-22 13:55:15,183 Loaded tool: Unioin_checker 0.0.1
galaxy.tools DEBUG 2016-02-22 13:55:15,193 Loaded tool: Expirement_checker 0.0.1
galaxy.tools DEBUG 2016-02-22 13:55:15,204 Loaded tool: Pre_TargetMiner 0.0.1
galaxy.tools DEBUG 2016-02-22 13:55:15,214 Loaded tool: TargetMiner 0.0.1
galaxy.tools DEBUG 2016-02-22 13:55:15,225 Loaded tool: TargetRank 0.0.1
galaxy.tools DEBUG 2016-02-22 13:55:15,235 Loaded tool: targetscan 0.0.1
galaxy.tools DEBUG 2016-02-22 13:55:15,246 Loaded tool: targetscanscores 0.0.1
galaxy.tools DEBUG 2016-02-22 13:55:15,257 Loaded tool: miranda 0.0.1
galaxy.tools DEBUG 2016-02-22 13:55:15,270 Loaded tool: Rough_Selection 0.0.1
galaxy.tools DEBUG 2016-02-22 13:55:15,281 Loaded tool: Motiv_Checker 0.0.1
galaxy.tools DEBUG 2016-02-22 13:55:15,291 Loaded tool: miRabela 0.0.1
galaxy.tools DEBUG 2016-02-22 13:55:15,301 Loaded tool: triplet_svm_classifier 0.0.1
galaxy.tools DEBUG 2016-02-22 13:55:15,312 Loaded tool: svmpredict 0.0.1
galaxy.tools DEBUG 2016-02-22 13:55:15,312 Loading section: Bibiserv Tools
galaxy.tools DEBUG 2016-02-22 13:55:15,323 Loaded tool: guugle 0.0.1
galaxy.tools DEBUG 2016-02-22 13:55:15,333 Loaded tool: GUUGle_results 0.0.1
galaxy.tools DEBUG 2016-02-22 13:55:15,344 Loaded tool: rnahybrid 0.0.1
galaxy.tools DEBUG 2016-02-22 13:55:15,355 Loaded tool: RNAhybrid_results 0.0.1
galaxy.tools DEBUG 2016-02-22 13:55:15,365 Loaded tool: RNAfold 0.0.1
galaxy.tools DEBUG 2016-02-22 13:55:15,366 Loading section: AB Solid Tools
galaxy.tools DEBUG 2016-02-22 13:55:15,377 Loaded tool: algorithm1_2_stdin 0.0.1
galaxy.tools DEBUG 2016-02-22 13:55:15,387 Loaded tool: algorithm2_4_stdin 0.0.1
galaxy.tools DEBUG 2016-02-22 13:55:15,398 Loaded tool: algorithm2_6_stdin 0.0.1
galaxy.tools DEBUG 2016-02-22 13:55:15,411 Loaded tool: coverage_histogram 0.0.1
galaxy.tools DEBUG 2016-02-22 13:55:15,421 Loaded tool: algorithm3_stdin 0.0.1
galaxy.tools DEBUG 2016-02-22 13:55:15,431 Loaded tool: sorted_bam_repeats 0.0.1
galaxy.tools DEBUG 2016-02-22 13:55:15,441 Loaded tool: algorithm4_2_stdin 0.0.1
galaxy.tools DEBUG 2016-02-22 13:55:15,452 Loaded tool: gops_subtract 0.0.1
galaxy.tools DEBUG 2016-02-22 13:55:15,462 Loaded tool: calcAvg 0.0.1
galaxy.tools DEBUG 2016-02-22 13:55:15,473 Loaded tool: createIntervals 0.0.1
galaxy.tools DEBUG 2016-02-22 13:55:15,483 Loaded tool: xsq_converter 0.0.1
galaxy.tools DEBUG 2016-02-22 13:55:15,495 Loaded tool: joinclusters 0.0.1
galaxy.tools DEBUG 2016-02-22 13:55:15,505 Loaded tool: merge_contigs 1.0.0
galaxy.tools ERROR 2016-02-22 13:55:15,520 error in help for tool Velvet
Traceback (most recent call last):
  File "/var/www/tavaxy/engines/galaxy/lib/galaxy/tools/__init__.py", line 533, in parse_help
    self.help = util.rst_to_html(self.help.text)
  File "/var/www/tavaxy/engines/galaxy/lib/galaxy/util/__init__.py", line 254, in rst_to_html
    return docutils.core.publish_string( s, writer=HTMLFragWriter(), settings_overrides=dict( warning_stream=FakeStream() ) )
  File "/var/www/tavaxy/engines/galaxy/eggs/docutils-0.4-py2.6.egg/docutils/core.py", line 397, in publish_string
    enable_exit_status=enable_exit_status)
  File "/var/www/tavaxy/engines/galaxy/eggs/docutils-0.4-py2.6.egg/docutils/core.py", line 612, in publish_programmatically
    output = pub.publish(enable_exit_status=enable_exit_status)
  File "/var/www/tavaxy/engines/galaxy/eggs/docutils-0.4-py2.6.egg/docutils/core.py", line 204, in publish
    self.settings)
  File "/var/www/tavaxy/engines/galaxy/eggs/docutils-0.4-py2.6.egg/docutils/readers/__init__.py", line 70, in read
    self.input = self.source.read()
  File "/var/www/tavaxy/engines/galaxy/eggs/docutils-0.4-py2.6.egg/docutils/io.py", line 318, in read
    return self.decode(self.source)
  File "/var/www/tavaxy/engines/galaxy/eggs/docutils-0.4-py2.6.egg/docutils/io.py", line 100, in decode
    decoded = unicode(data, enc, self.error_handler)
TypeError: coercing to Unicode: need string or buffer, NoneType found
galaxy.tools DEBUG 2016-02-22 13:55:15,521 Loaded tool: velvet 1.2.10
galaxy.tools DEBUG 2016-02-22 13:55:15,532 Loaded tool: contigstats 0.0.1
galaxy.tools DEBUG 2016-02-22 13:55:15,542 Loaded tool: repeat_masker 0.0.1
galaxy.tools DEBUG 2016-02-22 13:55:15,552 Loaded tool: gene_annotation 0.0.1
galaxy.tools DEBUG 2016-02-22 13:55:15,563 Loaded tool: unmapped_reads 0.0.1
galaxy.tools DEBUG 2016-02-22 13:55:15,576 Loaded tool: extractfastq 0.0.1
galaxy.tools DEBUG 2016-02-22 13:55:15,576 Loading section: Galaxy Tools
galaxy.tools DEBUG 2016-02-22 13:55:15,594 Loaded tool: fasta_compute_length 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:15,615 Loaded tool: fasta_concatenate0 0.0.0
galaxy.tools DEBUG 2016-02-22 13:55:15,639 Loaded tool: fasta_filter_by_length 1.1
galaxy.tools DEBUG 2016-02-22 13:55:15,657 Loaded tool: fasta2tab 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:15,675 Loaded tool: tab2fasta 1.1.0
galaxy.tools DEBUG 2016-02-22 13:55:15,753 Loaded tool: Filter1 1.0.1
galaxy.tools DEBUG 2016-02-22 13:55:15,776 Loaded tool: addValue 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:15,801 Loaded tool: Convert_characters1 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:15,854 Loaded tool: Cut1 1.0.1
galaxy.tools DEBUG 2016-02-22 13:55:15,874 Loaded tool: createInterval 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:15,909 Loaded tool: ChangeCase 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:15,953 Loaded tool: join1 2.0.2
galaxy.tools DEBUG 2016-02-22 13:55:16,024 Loaded tool: gops_join_1 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:16,156 Loaded tool: Grep1 1.0.1
galaxy.tools DEBUG 2016-02-22 13:55:16,193 Loaded tool: trimmer 0.0.1
galaxy.tools DEBUG 2016-02-22 13:55:16,233 Loaded tool: Add_a_column1 1.1.0
galaxy.tools DEBUG 2016-02-22 13:55:16,259 Loaded tool: comp1 1.0.2
galaxy.tools DEBUG 2016-02-22 13:55:16,331 Loaded tool: Summary_Statistics1 1.1.0
galaxy.tools DEBUG 2016-02-22 13:55:16,376 Loaded tool: fastq_groomer 1.0.3
galaxy.tools DEBUG 2016-02-22 13:55:16,395 Loaded tool: fastq_paired_end_splitter 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:16,413 Loaded tool: fastq_paired_end_joiner 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:16,503 Loaded tool: fastq_stats 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:16,515 Loaded tool: fastq_to_fasta_python 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:16,528 Loaded tool: fastq_to_tabular 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:16,541 Loaded tool: tabular_to_fastq 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:16,565 Loaded tool: fastq_trimmer 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:16,589 Loaded tool: fastq_quality_trimmer 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:16,603 Loaded tool: fastq_masker_by_quality 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:16,639 Loaded tool: solid2fastq 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:16,683 Loaded tool: quality_score_distribution 1.0.2
galaxy.tools DEBUG 2016-02-22 13:55:16,712 Loaded tool: trim_reads 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:16,778 Loaded tool: solid_qual_stats 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:16,817 Loaded tool: solid_qual_boxplot 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:16,840 Loaded tool: sam_indel_filter 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:16,862 Loaded tool: indel_sam2interval 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:16,889 Loaded tool: indel_analysis 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:16,925 Loaded tool: Fetch_Taxonomic_Ranks 1.1.0
galaxy.tools DEBUG 2016-02-22 13:55:16,948 Loaded tool: t2t_report 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:17,015 Loaded tool: Draw_phylogram 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:17,149 Loaded tool: find_diag_hits 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:17,183 Loaded tool: lca1 1.0.1
galaxy.tools DEBUG 2016-02-22 13:55:17,249 Loaded tool: poisson2test 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:17,250 Loading section: Taverna Tools
galaxy.tools DEBUG 2016-02-22 13:55:17,260 Loaded tool: GetNucleotideFASTA 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:17,273 Loaded tool: GetNucleotideGBSeq_XML 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:17,282 Loaded tool: GetNucleotideINSDSeq_XML 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:17,292 Loaded tool: GetNucleotideTinySeq_XML 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:17,301 Loaded tool: GetProteinFASTA 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:17,309 Loaded tool: GetProteinGBSeq_XML 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:17,316 Loaded tool: GetProteinINSDSeq_XML 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:17,324 Loaded tool: GetProteinTinySeq_XML 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:17,332 Loaded tool: TranscribeDNA 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:17,340 Loaded tool: ReverseComplementDNA 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:17,348 Loaded tool: GetPubMedXMLByPMID 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:17,356 Loaded tool: SearchPubMedXML 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:17,365 Loaded tool: HomoloGeneXML 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:17,373 Loaded tool: EMBLEBIClustalW2 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:17,381 Loaded tool: NCBIBlast 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:17,381 Loading section: Tavaxy Tools
galaxy.tools DEBUG 2016-02-22 13:55:17,436 Loaded tool: megablast_dai_wrapper 1.1.0
galaxy.tools DEBUG 2016-02-22 13:55:17,444 Loaded tool: align_postprocess 1.0.0
galaxy.tools ERROR 2016-02-22 13:55:17,450 error in help for tool Annotate with annovar
Traceback (most recent call last):
  File "/var/www/tavaxy/engines/galaxy/lib/galaxy/tools/__init__.py", line 533, in parse_help
    self.help = util.rst_to_html(self.help.text)
  File "/var/www/tavaxy/engines/galaxy/lib/galaxy/util/__init__.py", line 254, in rst_to_html
    return docutils.core.publish_string( s, writer=HTMLFragWriter(), settings_overrides=dict( warning_stream=FakeStream() ) )
  File "/var/www/tavaxy/engines/galaxy/eggs/docutils-0.4-py2.6.egg/docutils/core.py", line 397, in publish_string
    enable_exit_status=enable_exit_status)
  File "/var/www/tavaxy/engines/galaxy/eggs/docutils-0.4-py2.6.egg/docutils/core.py", line 612, in publish_programmatically
    output = pub.publish(enable_exit_status=enable_exit_status)
  File "/var/www/tavaxy/engines/galaxy/eggs/docutils-0.4-py2.6.egg/docutils/core.py", line 204, in publish
    self.settings)
  File "/var/www/tavaxy/engines/galaxy/eggs/docutils-0.4-py2.6.egg/docutils/readers/__init__.py", line 70, in read
    self.input = self.source.read()
  File "/var/www/tavaxy/engines/galaxy/eggs/docutils-0.4-py2.6.egg/docutils/io.py", line 318, in read
    return self.decode(self.source)
  File "/var/www/tavaxy/engines/galaxy/eggs/docutils-0.4-py2.6.egg/docutils/io.py", line 100, in decode
    decoded = unicode(data, enc, self.error_handler)
TypeError: coercing to Unicode: need string or buffer, NoneType found
galaxy.tools DEBUG 2016-02-22 13:55:17,451 Loaded tool: annovar_annotation 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:17,464 Loaded tool: local_clustalw 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:17,475 Loaded tool: local_clustalw_phylo 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:17,484 Loaded tool: local_muscle 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:17,540 Loaded tool: ncbi_blastn_wrapper 0.0.5
galaxy.tools DEBUG 2016-02-22 13:55:17,595 Loaded tool: ncbi_tblastn_wrapper 0.0.5
galaxy.tools DEBUG 2016-02-22 13:55:17,655 Loaded tool: ncbi_tblastx_wrapper 0.0.5
galaxy.tools DEBUG 2016-02-22 13:55:17,716 Loaded tool: ncbi_blastp_wrapper 0.0.5
galaxy.tools DEBUG 2016-02-22 13:55:17,771 Loaded tool: ncbi_blastx_wrapper 0.0.5
galaxy.tools DEBUG 2016-02-22 13:55:17,780 Loaded tool: getsequenceslocal 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:17,789 Loaded tool: getsequences 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:17,798 Loaded tool: countcg 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:17,806 Loaded tool: clustalw 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:17,817 Loaded tool: tcoffee 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:17,825 Loaded tool: confind 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:17,825 Loading section: Utilities
galaxy.tools DEBUG 2016-02-22 13:55:17,834 Loaded tool: passvalue 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:17,847 Loaded tool: script 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:17,855 Loaded tool: stringconstant 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:17,866 Loaded tool: increment 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:17,874 Loaded tool: alwaysfail 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:17,883 Loaded tool: concatstrings 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:17,895 Loaded tool: flattenlist 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:17,906 Loaded tool: splitintolist 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:17,923 Loaded tool: concatDatasets 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:17,945 Loaded tool: concat3Datasets 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:17,945 Loading section: Cloud Utilities
galaxy.tools DEBUG 2016-02-22 13:55:17,954 Loaded tool: s3put 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:17,962 Loaded tool: s3get 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:17,962 Loading section: Sandbox
galaxy.tools DEBUG 2016-02-22 13:55:17,963 Loading section: test tools
galaxy.tools DEBUG 2016-02-22 13:55:17,972 Loaded tool: param_test 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:17,981 Loaded tool: test_simple 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:17,989 Loaded tool: test_conditional 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:18,006 Loaded tool: test_repeat 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:18,006 Loading section: Runners
galaxy.tools DEBUG 2016-02-22 13:55:18,016 Loaded tool: beanshellRunner 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:18,026 Loaded tool: tavernaRunner 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:18,036 Loaded tool: taverna2Runner 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:18,037 Loading section: controls
galaxy.tools DEBUG 2016-02-22 13:55:18,045 Loaded tool: switch 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:18,053 Loaded tool: join 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:18,064 Loaded tool: merge 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:18,076 Loaded tool: iteration 1.0.0
galaxy.tools DEBUG 2016-02-22 13:55:18,088 Loaded tool: subworkflow 1.0.0
galaxy.tools ERROR 2016-02-22 13:55:18,088 error reading tool from path: patterns/subworkflow_iterable.xml
Traceback (most recent call last):
  File "/var/www/tavaxy/engines/galaxy/lib/galaxy/tools/__init__.py", line 77, in load_tool
    tool = self.load_tool( os.path.join( self.tool_root_dir, path ) )
  File "/var/www/tavaxy/engines/galaxy/lib/galaxy/tools/__init__.py", line 131, in load_tool
    tree = util.parse_xml( config_file )
  File "/var/www/tavaxy/engines/galaxy/lib/galaxy/util/__init__.py", line 102, in parse_xml
    tree = ElementTree.parse(fname)
  File "/usr/local/lib/python2.6/dist-packages/elementtree/ElementTree.py", line 859, in parse
    tree.parse(source, parser)
  File "/usr/local/lib/python2.6/dist-packages/elementtree/ElementTree.py", line 576, in parse
    source = open(source, "rb")
IOError: [Errno 2] No such file or directory: './tools/patterns/subworkflow_iterable.xml'
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:19,176 Loaded converter: CONVERTER_Bam_Bai_0
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:19,189 Loaded converter: CONVERTER_bam_to_summary_tree_0
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:19,199 Loaded converter: CONVERTER_bed_to_gff_0
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:19,208 Loaded converter: CONVERTER_interval_to_coverage_0
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:19,217 Loaded converter: CONVERTER_bed_to_interval_index_0
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:19,227 Loaded converter: CONVERTER_bed_to_summary_tree_0
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:19,237 Loaded converter: CONVERTER_BedGraph_0
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:19,246 Loaded converter: CONVERTER_bed_to_genetrack_0
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:19,255 Loaded converter: CONVERTER_fasta_to_tabular
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:19,265 Loaded converter: CONVERTER_fasta_to_bowtie_base_index
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:19,274 Loaded converter: CONVERTER_fasta_to_bowtie_color_index
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:19,284 Loaded converter: CONVERTER_gff_to_bed_0
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:19,293 Loaded converter: CONVERTER_gff_to_interval_index_0
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:19,303 Loaded converter: CONVERTER_gff_to_summary_tree_0
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:19,312 Loaded converter: CONVERTER_interval_to_bed_0
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:19,322 Loaded converter: CONVERTER_interval_to_bedstrict_0
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:19,334 Loaded converter: CONVERTER_interval_to_bed6_0
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:19,343 Loaded converter: CONVERTER_interval_to_bed12_0
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:19,353 Loaded converter: CONVERTER_maf_to_fasta_0
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:19,362 Loaded converter: CONVERTER_maf_to_interval_0
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:19,371 Loaded converter: CONVERTER_vcf_to_interval_index_0
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:19,381 Loaded converter: CONVERTER_vcf_to_summary_tree_0
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:19,390 Loaded converter: CONVERTER_Wiggle_0
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:19,392 Loaded converter: CONVERTER_wiggle_to_interval_0
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:19,401 Loaded converter: lped2fpedconvert
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:19,410 Loaded converter: lped2pbedconvert
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:19,420 Loaded converter: pbed2lpedconvert
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:19,430 Loaded converter: pbed2ldindepconvert
galaxy.tools.imp_exp DEBUG 2016-02-22 13:55:19,434 Loaded history export tool: __EXPORT_HISTORY__
galaxy.tools.imp_exp DEBUG 2016-02-22 13:55:19,435 Loaded history import tool: __IMPORT_HISTORY__
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:19,438 Loaded external metadata tool: __SET_METADATA__
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:19,447 Loaded indexer: INDEXER_Coverage_0
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:19,456 Loaded indexer: INDEXER_Coverage_0
galaxy.datatypes.registry DEBUG 2016-02-22 13:55:19,466 Loaded indexer: INDEXER_Interval_0
galaxy.jobs.runners.local INFO 2016-02-22 13:55:19,468 starting workers
galaxy.jobs.runners.local DEBUG 2016-02-22 13:55:19,471 5 workers ready
galaxy.jobs INFO 2016-02-22 13:55:19,472 job manager started
Traceback (most recent call last):
  File "/var/www/tavaxy/engines/galaxy/lib/galaxy/web/buildapp.py", line 82, in app_factory
    app = UniverseApplication( global_conf = global_conf, **kwargs )
  File "/var/www/tavaxy/engines/galaxy/lib/galaxy/app.py", line 79, in __init__
    self.job_manager = jobs.JobManager( self )
  File "/var/www/tavaxy/engines/galaxy/lib/galaxy/jobs/__init__.py", line 43, in __init__
    self.job_queue = JobQueue( app, self.dispatcher )
  File "/var/www/tavaxy/engines/galaxy/lib/galaxy/jobs/__init__.py", line 96, in __init__
    self.__check_jobs_at_startup()
  File "/var/www/tavaxy/engines/galaxy/lib/galaxy/jobs/__init__.py", line 105, in __check_jobs_at_startup
    for job in self.sa_session.query( model.Job ).filter( model.Job.state == model.Job.states.NEW ):
  File "/var/www/tavaxy/engines/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1361, in __iter__
    return self._execute_and_instances(context)
  File "/var/www/tavaxy/engines/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1364, in _execute_and_instances
    result = self.session.execute(querycontext.statement, params=self._params, mapper=self._mapper_zero_or_none())
  File "/var/www/tavaxy/engines/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 755, in execute
    clause, params or {})
  File "/var/www/tavaxy/engines/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 824, in execute
    return Connection.executors[c](self, object, multiparams, params)
  File "/var/www/tavaxy/engines/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 874, in _execute_clauseelement
    return self.__execute_context(context)
  File "/var/www/tavaxy/engines/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 896, in __execute_context
    self._cursor_execute(context.cursor, context.statement, context.parameters[0], context=context)
  File "/var/www/tavaxy/engines/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 950, in _cursor_execute
    self._handle_dbapi_exception(e, statement, parameters, cursor, context)
  File "/var/www/tavaxy/engines/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 931, in _handle_dbapi_exception
    raise exc.DBAPIError.instance(statement, parameters, e, connection_invalidated=is_disconnect)
ProgrammingError: (ProgrammingError) (1146, "Table 'galaxy0.job_to_output_library_dataset' doesn't exist") u'SELECT job.id AS job_id, job.create_time AS job_create_time, job.update_time AS job_update_time, job.history_id AS job_history_id, job.library_folder_id AS job_library_folder_id, job.tool_id AS job_tool_id, job.tool_version AS job_tool_version, job.state AS job_state, job.info AS job_info, job.command_line AS job_command_line, job.param_filename AS job_param_filename, job.runner_name AS job_runner_name_1, job.stdout AS job_stdout, job.stderr AS job_stderr, job.traceback AS job_traceback, job.session_id AS job_session_id, job.user_id AS job_user_id, job.job_runner_name AS job_job_runner_name, job.job_runner_external_id AS job_job_runner_external_id, job.imported AS job_imported, job.step_id AS job_step_id, job.workflow_id AS job_workflow_id, job_parameter_1.id AS job_parameter_1_id, job_parameter_1.job_id AS job_parameter_1_job_id, job_parameter_1.name AS job_parameter_1_name, job_parameter_1.value AS job_parameter_1_value, library_dataset_dataset_association_1.id AS library_dataset_dataset_association_1_id, library_dataset_dataset_association_1.library_dataset_id AS library_dataset_dataset_association_1_library_dataset_id, library_dataset_dataset_association_1.dataset_id AS library_dataset_dataset_association_1_dataset_id, library_dataset_dataset_association_1.create_time AS library_dataset_dataset_association_1_create_time, library_dataset_dataset_association_1.update_time AS library_dataset_dataset_association_1_update_time, library_dataset_dataset_association_1.state AS library_dataset_dataset_association_1_state, library_dataset_dataset_association_1.copied_from_history_dataset_association_id AS library_dataset_dataset_association_1_copied_from_history_dataset_association_id, library_dataset_dataset_association_1.copied_from_library_dataset_dataset_association_id AS library_dataset_dataset_association_1_copied_from_library_dataset_dataset_association_id, library_dataset_dataset_association_1.name AS library_dataset_dataset_association_1_name, library_dataset_dataset_association_1.info AS library_dataset_dataset_association_1_info, library_dataset_dataset_association_1.blurb AS library_dataset_dataset_association_1_blurb, library_dataset_dataset_association_1.peek AS library_dataset_dataset_association_1_peek, library_dataset_dataset_association_1.extension AS library_dataset_dataset_association_1_extension, library_dataset_dataset_association_1.metadata AS library_dataset_dataset_association_1_metadata, library_dataset_dataset_association_1.parent_id AS library_dataset_dataset_association_1_parent_id, library_dataset_dataset_association_1.designation AS library_dataset_dataset_association_1_designation, library_dataset_dataset_association_1.deleted AS library_dataset_dataset_association_1_deleted, library_dataset_dataset_association_1.visible AS library_dataset_dataset_association_1_visible, library_dataset_dataset_association_1.user_id AS library_dataset_dataset_association_1_user_id, library_dataset_dataset_association_1.message AS library_dataset_dataset_association_1_message, job_to_output_library_dataset_1.id AS job_to_output_library_dataset_1_id, job_to_output_library_dataset_1.job_id AS job_to_output_library_dataset_1_job_id, job_to_output_library_dataset_1.ldda_id AS job_to_output_library_dataset_1_ldda_id, job_to_output_library_dataset_1.name AS job_to_output_library_dataset_1_name, post_job_action_association_1.id AS post_job_action_association_1_id, post_job_action_association_1.job_id AS post_job_action_association_1_job_id, post_job_action_association_1.post_job_action_id AS post_job_action_association_1_post_job_action_id, dataset_1.id AS dataset_1_id, dataset_1.create_time AS dataset_1_create_time, dataset_1.update_time AS dataset_1_update_time, dataset_1.state AS dataset_1_state, dataset_1.deleted AS dataset_1_deleted, dataset_1.purged AS dataset_1_purged, dataset_1.purgable AS dataset_1_purgable, dataset_1.external_filename AS dataset_1_external_filename, dataset_1._extra_files_path AS dataset_1__extra_files_path, dataset_1.file_size AS dataset_1_file_size, history_dataset_association_1.id AS history_dataset_association_1_id, history_dataset_association_1.history_id AS history_dataset_association_1_history_id, history_dataset_association_1.dataset_id AS history_dataset_association_1_dataset_id, history_dataset_association_1.create_time AS history_dataset_association_1_create_time, history_dataset_association_1.update_time AS history_dataset_association_1_update_time, history_dataset_association_1.state AS history_dataset_association_1_state, history_dataset_association_1.copied_from_history_dataset_association_id AS history_dataset_association_1_copied_from_history_dataset_association_id, history_dataset_association_1.copied_from_library_dataset_dataset_association_id AS history_dataset_association_1_copied_from_library_dataset_dataset_association_id, history_dataset_association_1.hid AS history_dataset_association_1_hid, history_dataset_association_1.name AS history_dataset_association_1_name, history_dataset_association_1.info AS history_dataset_association_1_info, history_dataset_association_1.blurb AS history_dataset_association_1_blurb, history_dataset_association_1.peek AS history_dataset_association_1_peek, history_dataset_association_1.extension AS history_dataset_association_1_extension, history_dataset_association_1.metadata AS history_dataset_association_1_metadata, history_dataset_association_1.parent_id AS history_dataset_association_1_parent_id, history_dataset_association_1.designation AS history_dataset_association_1_designation, history_dataset_association_1.deleted AS history_dataset_association_1_deleted, history_dataset_association_1.workflow_id AS history_dataset_association_1_workflow_id, history_dataset_association_1.visible AS history_dataset_association_1_visible, library_dataset_dataset_association_2.id AS library_dataset_dataset_association_2_id, library_dataset_dataset_association_2.library_dataset_id AS library_dataset_dataset_association_2_library_dataset_id, library_dataset_dataset_association_2.dataset_id AS library_dataset_dataset_association_2_dataset_id, library_dataset_dataset_association_2.create_time AS library_dataset_dataset_association_2_create_time, library_dataset_dataset_association_2.update_time AS library_dataset_dataset_association_2_update_time, library_dataset_dataset_association_2.state AS library_dataset_dataset_association_2_state, library_dataset_dataset_association_2.copied_from_history_dataset_association_id AS library_dataset_dataset_association_2_copied_from_history_dataset_association_id, library_dataset_dataset_association_2.copied_from_library_dataset_dataset_association_id AS library_dataset_dataset_association_2_copied_from_library_dataset_dataset_association_id, library_dataset_dataset_association_2.name AS library_dataset_dataset_association_2_name, library_dataset_dataset_association_2.info AS library_dataset_dataset_association_2_info, library_dataset_dataset_association_2.blurb AS library_dataset_dataset_association_2_blurb, library_dataset_dataset_association_2.peek AS library_dataset_dataset_association_2_peek, library_dataset_dataset_association_2.extension AS library_dataset_dataset_association_2_extension, library_dataset_dataset_association_2.metadata AS library_dataset_dataset_association_2_metadata, library_dataset_dataset_association_2.parent_id AS library_dataset_dataset_association_2_parent_id, library_dataset_dataset_association_2.designation AS library_dataset_dataset_association_2_designation, library_dataset_dataset_association_2.deleted AS library_dataset_dataset_association_2_deleted, library_dataset_dataset_association_2.visible AS library_dataset_dataset_association_2_visible, library_dataset_dataset_association_2.user_id AS library_dataset_dataset_association_2_user_id, library_dataset_dataset_association_2.message AS library_dataset_dataset_association_2_message, job_external_output_metadata_1.id AS job_external_output_metadata_1_id, job_external_output_metadata_1.job_id AS job_external_output_metadata_1_job_id, job_external_output_metadata_1.history_dataset_association_id AS job_external_output_metadata_1_history_dataset_association_id, job_external_output_metadata_1.library_dataset_dataset_association_id AS job_external_output_metadata_1_library_dataset_dataset_association_id, job_external_output_metadata_1.filename_in AS job_external_output_metadata_1_filename_in, job_external_output_metadata_1.filename_out AS job_external_output_metadata_1_filename_out, job_external_output_metadata_1.filename_results_code AS job_external_output_metadata_1_filename_results_code, job_external_output_metadata_1.filename_kwds AS job_external_output_metadata_1_filename_kwds, job_external_output_metadata_1.filename_override_metadata AS job_external_output_metadata_1_filename_override_metadata, job_external_output_metadata_1.job_runner_external_pid AS job_external_output_metadata_1_job_runner_external_pid, dataset_2.id AS dataset_2_id, dataset_2.create_time AS dataset_2_create_time, dataset_2.update_time AS dataset_2_update_time, dataset_2.state AS dataset_2_state, dataset_2.deleted AS dataset_2_deleted, dataset_2.purged AS dataset_2_purged, dataset_2.purgable AS dataset_2_purgable, dataset_2.external_filename AS dataset_2_external_filename, dataset_2._extra_files_path AS dataset_2__extra_files_path, dataset_2.file_size AS dataset_2_file_size, history_dataset_association_2.id AS history_dataset_association_2_id, history_dataset_association_2.history_id AS history_dataset_association_2_history_id, history_dataset_association_2.dataset_id AS history_dataset_association_2_dataset_id, history_dataset_association_2.create_time AS history_dataset_association_2_create_time, history_dataset_association_2.update_time AS history_dataset_association_2_update_time, history_dataset_association_2.state AS history_dataset_association_2_state, history_dataset_association_2.copied_from_history_dataset_association_id AS history_dataset_association_2_copied_from_history_dataset_association_id, history_dataset_association_2.copied_from_library_dataset_dataset_association_id AS history_dataset_association_2_copied_from_library_dataset_dataset_association_id, history_dataset_association_2.hid AS history_dataset_association_2_hid, history_dataset_association_2.name AS history_dataset_association_2_name, history_dataset_association_2.info AS history_dataset_association_2_info, history_dataset_association_2.blurb AS history_dataset_association_2_blurb, history_dataset_association_2.peek AS history_dataset_association_2_peek, history_dataset_association_2.extension AS history_dataset_association_2_extension, history_dataset_association_2.metadata AS history_dataset_association_2_metadata, history_dataset_association_2.parent_id AS history_dataset_association_2_parent_id, history_dataset_association_2.designation AS history_dataset_association_2_designation, history_dataset_association_2.deleted AS history_dataset_association_2_deleted, history_dataset_association_2.workflow_id AS history_dataset_association_2_workflow_id, history_dataset_association_2.visible AS history_dataset_association_2_visible, job_to_output_dataset_1.id AS job_to_output_dataset_1_id, job_to_output_dataset_1.job_id AS job_to_output_dataset_1_job_id, job_to_output_dataset_1.dataset_id AS job_to_output_dataset_1_dataset_id, job_to_output_dataset_1.name AS job_to_output_dataset_1_name, dataset_3.id AS dataset_3_id, dataset_3.create_time AS dataset_3_create_time, dataset_3.update_time AS dataset_3_update_time, dataset_3.state AS dataset_3_state, dataset_3.deleted AS dataset_3_deleted, dataset_3.purged AS dataset_3_purged, dataset_3.purgable AS dataset_3_purgable, dataset_3.external_filename AS dataset_3_external_filename, dataset_3._extra_files_path AS dataset_3__extra_files_path, dataset_3.file_size AS dataset_3_file_size, history_dataset_association_3.id AS history_dataset_association_3_id, history_dataset_association_3.history_id AS history_dataset_association_3_history_id, history_dataset_association_3.dataset_id AS history_dataset_association_3_dataset_id, history_dataset_association_3.create_time AS history_dataset_association_3_create_time, history_dataset_association_3.update_time AS history_dataset_association_3_update_time, history_dataset_association_3.state AS history_dataset_association_3_state, history_dataset_association_3.copied_from_history_dataset_association_id AS history_dataset_association_3_copied_from_history_dataset_association_id, history_dataset_association_3.copied_from_library_dataset_dataset_association_id AS history_dataset_association_3_copied_from_library_dataset_dataset_association_id, history_dataset_association_3.hid AS history_dataset_association_3_hid, history_dataset_association_3.name AS history_dataset_association_3_name, history_dataset_association_3.info AS history_dataset_association_3_info, history_dataset_association_3.blurb AS history_dataset_association_3_blurb, history_dataset_association_3.peek AS history_dataset_association_3_peek, history_dataset_association_3.extension AS history_dataset_association_3_extension, history_dataset_association_3.metadata AS history_dataset_association_3_metadata, history_dataset_association_3.parent_id AS history_dataset_association_3_parent_id, history_dataset_association_3.designation AS history_dataset_association_3_designation, history_dataset_association_3.deleted AS history_dataset_association_3_deleted, history_dataset_association_3.workflow_id AS history_dataset_association_3_workflow_id, history_dataset_association_3.visible AS history_dataset_association_3_visible, job_to_input_dataset_1.id AS job_to_input_dataset_1_id, job_to_input_dataset_1.job_id AS job_to_input_dataset_1_job_id, job_to_input_dataset_1.dataset_id AS job_to_input_dataset_1_dataset_id, job_to_input_dataset_1.name AS job_to_input_dataset_1_name \nFROM job LEFT OUTER JOIN job_parameter AS job_parameter_1 ON job.id = job_parameter_1.job_id LEFT OUTER JOIN job_to_output_library_dataset AS job_to_output_library_dataset_1 ON job.id = job_to_output_library_dataset_1.job_id LEFT OUTER JOIN library_dataset_dataset_association AS library_dataset_dataset_association_1 ON library_dataset_dataset_association_1.id = job_to_output_library_dataset_1.ldda_id LEFT OUTER JOIN post_job_action_association AS post_job_action_association_1 ON job.id = post_job_action_association_1.job_id LEFT OUTER JOIN job_external_output_metadata AS job_external_output_metadata_1 ON job.id = job_external_output_metadata_1.job_id LEFT OUTER JOIN history_dataset_association AS history_dataset_association_1 ON history_dataset_association_1.id = job_external_output_metadata_1.history_dataset_association_id LEFT OUTER JOIN dataset AS dataset_1 ON dataset_1.id = history_dataset_association_1.dataset_id LEFT OUTER JOIN library_dataset_dataset_association AS library_dataset_dataset_association_2 ON library_dataset_dataset_association_2.id = job_external_output_metadata_1.library_dataset_dataset_association_id LEFT OUTER JOIN job_to_output_dataset AS job_to_output_dataset_1 ON job.id = job_to_output_dataset_1.job_id LEFT OUTER JOIN history_dataset_association AS history_dataset_association_2 ON history_dataset_association_2.id = job_to_output_dataset_1.dataset_id LEFT OUTER JOIN dataset AS dataset_2 ON dataset_2.id = history_dataset_association_2.dataset_id LEFT OUTER JOIN job_to_input_dataset AS job_to_input_dataset_1 ON job.id = job_to_input_dataset_1.job_id LEFT OUTER JOIN history_dataset_association AS history_dataset_association_3 ON history_dataset_association_3.id = job_to_input_dataset_1.dataset_id LEFT OUTER JOIN dataset AS dataset_3 ON dataset_3.id = history_dataset_association_3.dataset_id \nWHERE job.state = %s' ['new']