[Jose Blanca]

Right, backbone_analysis has to know where is backbone.conf. You have two options:
- backbone_analysis looks for backbone.conf in ./ , so if you run it on the project directory, where backbone.conf is it find it.
- Use the -s parameter to tell the path to backbone.conf

[robertorun]

excute the command: python ./backbone_analysis.py -s ./temp001/ -a temp001

the error is following:

<type 'exceptions.KeyError'>
Python 2.6.5: /usr/local/bin/python
Tue May 25 20:11:43 2010

A problem occurred in a Python script. Here is the sequence of
function calls leading up to the error, in the order they occurred.

/home/ydj/soft_bio/ngs_backbone/build/scripts-2.6/backbone_analysis.py in <module>()
85 cgitb.handler()
86 raise
87
88 if __name__ == '__main__':
89 main()
main = <function main>

/home/ydj/soft_bio/ngs_backbone/build/scripts-2.6/backbone_analysis.py in main()
76 for action in actions:
77 start_time = datetime.datetime.today()
78 do_analysis(project_settings=settings_fpath, kind=action)
79 time_elapsed = datetime.datetime.today() - start_time
80 logger.info('Time elapsed %s' % str(time_elapsed))
global do_analysis = <function do_analysis>
project_settings undefined
settings_fpath = './temp001/'
kind undefined
action = 'temp001'

/usr/local/lib/python2.6/site-packages/franklin/backbone/backbone_runner.py in do_analysis(kind='temp001', project_settings='./temp001/', analysis_config={}, silent=False)
73
74
75 log_fpath = os.path.join(settings['General_settings']['project_path'],
76 BACKBONE_DIRECTORIES['log_file'])
77 _configure_logging(log_fpath, silent)
log_fpath undefined
global os = <module 'os' from '/usr/local/lib/python2.6/os.pyc'>
os.path = <module 'posixpath' from '/usr/local/lib/python2.6/posixpath.pyc'>
os.path.join = <function join>
settings = ConfigObj({})
global BACKBONE_DIRECTORIES = {'annotation_input': 'annotations/input', 'annotation_repr': 'annotations/repr', 'annotation_result': 'annotations/result', 'assemblies': ('assembly', ''), 'assembly_input': 'assembly/input', 'assembly_result': ('assembly', 'result'), 'blast_databases': 'annotations/blast/databases', 'blast_dir': 'annotations/blast', 'cleaned_reads': 'reads/cleaned', 'cleaned_reads_stats': 'reads/cleaned/stats', ...}

/usr/local/lib/python2.6/site-packages/configobj.py in __getitem__(self=ConfigObj({}), key='General_settings')
565 def __getitem__(self, key):
566 """Fetch the item and do string interpolation."""
567 val = dict.__getitem__(self, key)
568 if self.main.interpolation:
569 if isinstance(val, basestring):
val undefined
builtindict = <type 'dict'>
dict.__getitem__ = <method '__getitem__' of 'dict' objects>
self = ConfigObj({})
key = 'General_settings'
<type 'exceptions.KeyError'>: 'General_settings'
__class__ = <type 'exceptions.KeyError'>
__delattr__ = <method-wrapper '__delattr__' of exceptions.KeyError object>
__dict__ = {}
__doc__ = 'Mapping key not found.'
__format__ = <built-in method __format__ of exceptions.KeyError object>
__getattribute__ = <method-wrapper '__getattribute__' of exceptions.KeyError object>
__getitem__ = <method-wrapper '__getitem__' of exceptions.KeyError object>
__getslice__ = <method-wrapper '__getslice__' of exceptions.KeyError object>
__hash__ = <method-wrapper '__hash__' of exceptions.KeyError object>
__init__ = <method-wrapper '__init__' of exceptions.KeyError object>
__new__ = <built-in method __new__ of type object>
__reduce__ = <built-in method __reduce__ of exceptions.KeyError object>
__reduce_ex__ = <built-in method __reduce_ex__ of exceptions.KeyError object>
__repr__ = <method-wrapper '__repr__' of exceptions.KeyError object>
__setattr__ = <method-wrapper '__setattr__' of exceptions.KeyError object>
__setstate__ = <built-in method __setstate__ of exceptions.KeyError object>
__sizeof__ = <built-in method __sizeof__ of exceptions.KeyError object>
__str__ = <method-wrapper '__str__' of exceptions.KeyError object>
__subclasshook__ = <built-in method __subclasshook__ of type object>
__unicode__ = <built-in method __unicode__ of exceptions.KeyError object>
args = ('General_settings',)
message = 'General_settings'

The above is a description of an error in a Python program. Here is
the original traceback:

Traceback (most recent call last):
File "./backbone_analysis.py", line 89, in <module>
main()
File "./backbone_analysis.py", line 78, in main
do_analysis(project_settings=settings_fpath, kind=action)
File "/usr/local/lib/python2.6/site-packages/franklin/backbone/backbone_runner.py", line 75, in do_analysis
log_fpath = os.path.join(settings['General_settings']['project_path'],
File "/usr/local/lib/python2.6/site-packages/configobj.py", line 567, in __getitem__
val = dict.__getitem__(self, key)
KeyError: 'General_settings'

There are two quetions:

1. As the web the command is "ngs_backbone_create_project.py -p project_name
", but i can't find ngs_backbone_create_project.py file , the only similar file is backbone_create_project.py at the path of "./ngs_backbone/build/scripts-2.6/", so i must let the current path is "scripts-2.6";

2.At the command "ngs_backbone_analysis.py -a analysis_name", the parameter "-a" is mean project name or else what?

[Jose Blanca]

1. As the web the command is "ngs_backbone_create_project.py -p project_name
", but i can't find ngs_backbone_create_project.py file , the only similar file is backbone_create_project.py at the path of "./ngs_backbone/build/scripts-2.6/", so i must let the current path is "scripts-2.6";

We have fixed that in the current git documentation.

2.At the command "ngs_backbone_analysis.py -a analysis_name", the parameter "-a" is mean project name or else what?

For action or analysis.

~$ backbone_analysis.py -h
Usage: backbone_analysis.py [options]

Options:
-h, --help show this help message and exit
-a ACTION, --action=ACTION
Possible analyses to run(You can run more than one
analysis. list with commas): annotate_orthologs,
annotate_gos, prepare_mira_assembly,
write_annotations, annotate_snvs, read_stats,
mapping_stats, mira_assembly, annotate_introns,
mapping, filter_snvs, clean_reads,
annotate_microsatellites, annotate_orfs,
set_assembly_as_reference, realign_bam, merge_bams,
annotate_descriptions
-s SETTINGS, --settings=SETTINGS
Settings file path

Regarding the error. Are your using the latest git version or the 0.1 release?

[robertorun]

the 0.1 release

[Jose Blanca]

Could you try the github one?

http://github.com/JoseBlanca/psubprocess/archives/master

[robertorun]

OK,thanks! I will try

[robertorun]

Could you try the github one?

http://github.com/JoseBlanca/psubpro...rchives/master

is the psubprocess all the package of NGS_backbone???

[KevinLam]

Hi Robert
have you considered using the approach listed here?

http://www.bio.utexas.edu/research/matz_lab/matzlab/Methods.html

1stly it sounds like you may not have enough coverage to do a "complete transcriptome"

2ndly although you didn't mention the organism but de novo assembly uses huge ram

The method by Matz lab seems to work fine for them. although you might need tweaking

[robertorun]

Thanks！ I have read your paper and also will try to run this scripts!

Hi Robert
have you considered using the approach listed here?

http://www.bio.utexas.edu/research/matz_lab/matzlab/Methods.html

1stly it sounds like you may not have enough coverage to do a "complete transcriptome"

2ndly although you didn't mention the organism but de novo assembly uses huge ram

The method by Matz lab seems to work fine for them. although you might need tweaking

[Bruins]

Fedora 7?

@Robertorun
Hi,
Bit offtopic but...
I am a hardcore Fedora user. May I suggest you update to at least Fedora 12?

Support (updates and security fixes) is maintained for any given version until two new versions have been released, plus one month. This means that Fedora 11 will retire one month from now, because Fedora 13 was released two days ago. Yes, that quickly: a new release every half year.

You are still using Fedora 7, the first release that is no longer called 'Fedora Core' - they dropped 'Core' after merging the Core and Extras repos. This release has been retired since June 13, 2008. This means that you are working with outdated software packages and drivers, potentially causing many problems. (ugh, I make 2008 sound eons ago...)

If you do decide to change to a newer version of Fedora, I would recommend a fresh install instead of an upgrade (if that is even possible) to avoid trouble. It would probably be best to install Fedora 13, because then you'll have another year before having to upgrade it. If you are a KDE user (like me), don't be spooked by KDE 4. It takes some getting used to but you'll never want to go back to the not-nearly-as-slick KDE 3. I used to fall back to the Unofficial Fedora FAQ when in trouble but this website seems to no longer be supported.

Hope this helps...

Wil