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hallamlab / MetaPathways

A modular pipeline for constructing Pathway/Genome Databases from environmental sequence information
http://hallam.microbiology.ubc.ca/MetaPathways
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Percent completed bar has some funky behaviour. #15

Closed hallamlab closed 11 years ago

hallamlab commented 11 years ago

This might be just an aesthetic thing but the completion bar has some funky behaviour, it might be better just to go back to fractions with a percentage in brackets.

6. Blasting  ORFs against reference database - metacyc-v4-2011-07-03 ....
     Server bugaboo.westgrid.ca is working 
     Successfully copied daemon script
     'MetaPathways'
                 found
     'MetaPathways/databases'
                 found
     'MetaPathways/executables'
                 found
     MetaPathways/executables/blastp
                 found
     MetaPathways/executables/formatdb
                 found
     MetaPathways/databases/metacyc-v4-2011-07-03
                 found
                 already formatted
     Sample  folder TP62008_30ft_454
                 NOT found
                 created!
     MetaPathways/TP62008_30ft_454/.qstatdir
                 NOT found
                 created!
     MetaPathways/TP62008_30ft_454/TP62008_30ft_454.qced.faa
                 NOT found
                 copied
     Number of sequence files created :2432

[ ------------------                                                                                 ]

Issuing Command : {'run_type': 'overlay', 'dbnames': ['kegg'], 'sample_name': 'output//TP62008_30ft_454', 'max_parallel_jobs': '400', 'server': 'bugaboo.westgrid.ca', 'database_files': ['kegg-pep-2011-06-18'], 'batch_size': '200', 'user': 'nielsh'}

                                               kegg-pep-2011-06-18 ....
     Server bugaboo.westgrid.ca is working 
     Successfully copied daemon script
     'MetaPathways'
                 found
     'MetaPathways/databases'
                 found
     'MetaPathways/executables'
                 found
     MetaPathways/executables/blastp
                 found
     MetaPathways/executables/formatdb
                 found
     MetaPathways/databases/kegg-pep-2011-06-18
                 found
                 already formatted
     Sample  folder TP62008_30ft_454
                 found
     MetaPathways/TP62008_30ft_454/.qstatdir
                 found
     MetaPathways/TP62008_30ft_454/TP62008_30ft_454.qced.faa
                 found
     Number of sequence files created :4864

[ -------------------                                                                                ]

Issuing Command : {'run_type': 'overlay', 'dbnames': ['cog'], 'sample_name': 'output//TP62008_30ft_454', 'max_parallel_jobs': '400', 'server': 'bugaboo.westgrid.ca', 'database_files': ['cog-2007-10-30'], 'batch_size': '200', 'user': 'nielsh'}

                                               cog-2007-10-30 ....
     Server bugaboo.westgrid.ca is working 
     Successfully copied daemon script
     'MetaPathways'
                 found
     'MetaPathways/databases'
                 found
     'MetaPathways/executables'
                 found
     MetaPathways/executables/blastp
                 found
     MetaPathways/executables/formatdb
                 found
     MetaPathways/databases/cog-2007-10-30
                 found
                 already formatted
     Sample  folder TP62008_30ft_454
                 found
     MetaPathways/TP62008_30ft_454/.qstatdir
                 found
     MetaPathways/TP62008_30ft_454/TP62008_30ft_454.qced.faa
                 found
     Number of sequence files created :7296

[ ---------------                                                                                    ]

Issuing Command : {'run_type': 'overlay', 'dbnames': ['refseq'], 'sample_name': 'output//TP62008_30ft_454', 'max_parallel_jobs': '400', 'server': 'bugaboo.westgrid.ca', 'database_files': ['refseq_protein-2009-04-27'], 'batch_size': '200', 'user': 'nielsh'}

                                               refseq_protein-2009-04-27 ....
     Server bugaboo.westgrid.ca is working 
     Successfully copied daemon script
     'MetaPathways'
                 found
     'MetaPathways/databases'
                 found
     'MetaPathways/executables'
                 found
     MetaPathways/executables/blastp
                 found
     MetaPathways/executables/formatdb
                 found
     MetaPathways/databases/refseq_protein-2009-04-27
                 found
                 already formatted
     Sample  folder TP62008_30ft_454
                 found
     MetaPathways/TP62008_30ft_454/.qstatdir
                 found
     MetaPathways/TP62008_30ft_454/TP62008_30ft_454.qced.faa
                 found
     Number of sequence files created :9728

[ -----------                                                                                        ]