Hello,
I’ve backtracked the Analysis 2.4.2 code to use the old-fashioned if statement syntax, so hopefully that will work with Python 2.5 now (there are a couple of other occurrences of the newer syntax in the 2.4.2 code but hopefully in files that Aria does not directly or indirectly import, otherwise I’ll have to change those as well).
Wayne
> On 23 Oct 2015, at 01:35, Xue Liu <[log in to unmask]> wrote:
>
> Dear Benjamin:
>
> Still can not get it to work. I used the python in ccpnmr directory to start aria2.py with -g option and get the following message:
>
> ARIA Version 2.3.1. Authors: Benjamin Bardiaux, Michael Habeck, Jens Linge,
> Therese Malliavin, Sean O'Donoghue, Wolfgang Rieping, and Michael Nilges.
>
> If you use this software, please quote the following reference(s):
>
> Rieping W., Habeck M., Bardiaux B., Bernard A., Malliavin T.E.,
> Nilges M.(2007) ARIA2: automated NOE assignment and data integration in NMR
> structure calculation. Bioinformatics 23:381-382
>
> Segmentation fault
>
> Should I update the system's python to 2.7?
>
> Regards,
>
> Xuehui
>
>
> --------------------------------------------
> On Thu, 10/22/15, Benjamin Bardiaux <[log in to unmask]> wrote:
>
> Subject: Re: Aria2.3 not working with ccpnmr2.4.2
> To: [log in to unmask]
> Date: Thursday, October 22, 2015, 4:35 PM
>
> Dear Xuehui,
>
> Try running aria2.3 with
> python >= 2.5 (best is to use the same python
> as ccpnmr)
>
> Regards,
>
> Benjamin
>
> On
> 10/22/15 9:55 AM, Xue Liu wrote:
>>
> Hello,
>> I could not get aria2.3 work
> with ccpnmr anymore which was fine months ago.
>> Since I haven't been using the aria
> for a while, the only thing I remembered is that I upgraded
> the ccpnmr someday. I did whatever I could and still could
> not get aria2.3 to work. I've noticed that while
> ccpnmr2.4.1 use python2.6, 2.4.2 is using python2.7 now.
> Could this be the cause of the problem? Or should I download
> the whole 2.4.2 package rather than upgrade from 2.4.1?
> Thank you very much for any advice!
>>
>> Here is the error:
>>
> Loading project "run.xml"...
>>
> MESSAGE [Project]: Temporary directory has been set to
> /home/xhliu/Data/
>>
>
> Projects/mry_N2_20151022/aria_temp.tmpgVhg0Y1445500714
>> MESSAGE [Project]: List of available
> machines is empty. Running calculations on
>>
> localhost "localhost.localdomain",
> assuming 1 CPU. Using /
>>
> usr/bin/cns as structure
> engine.
>> MESSAGE [Project]: Checking
> host list ...
>> MESSAGE [Job manager]:
> Command "csh -f" ... ok.
>>
> MESSAGE [Project]: Cache is disabled.
>>
> Model read finished. Duration 2.40438103676
>> Model validity check skipped
>> MESSAGE [Project]: ------------ Reading
> data from CCPN data model ------------
>>
> MESSAGE [Project]: Opening CCPN data model
> "/home/xhliu/Data/Projects/
>>
>
> mry_N2_20151022"...
>>
> MESSAGE [Project]: CCPN data model opened.
>> MESSAGE [Project]: Retrieving molecular
> system "MS1", chain code(s) "A"...
>> MESSAGE [Project]: Retrieving peak list
> "(project=defaultProject, experiment=2,
>>
> data_source=1, serial=1)", shift list
> "1" ...
>> Traceback (most
> recent call last):
>> File
> "/home/xhliu/programs/aria2.3/aria2.py", line 903,
> in ?
>> verbose_level,
> use_condor=condor)
>> File
> "/home/xhliu/programs/aria2.3/aria2.py", line 811,
> in run_aria
>>
> project.load_and_preprocess_data()
>>
> File
> "/home/xhliu/programs/aria2.3/src/py/aria/Project.py",
> line 1426, in load_and_preprocess_data
>> self.read_data()
>> File
> "/home/xhliu/programs/aria2.3/src/py/aria/Project.py",
> line 1186, in read_data
>>
> self.read_ccpn_data()
>> File
> "/home/xhliu/programs/aria2.3/src/py/aria/Project.py",
> line 709, in read_ccpn_data
>>
> from aria.exportToCcpn import getAriaRun
>> File
> "/home/xhliu/programs/aria2.3/src/py/aria/exportToCcpn.py",
> line 1, in ?
>> from
> ccpnmr.analysis.core.ConstraintBasic import
> makeNmrConstraintStore, makeStructureGeneration,
> getFixedResonance
>> File
> "/home/xhliu/programs/ccpnmr/ccpnmr2.4/python/ccpnmr/analysis/core/ConstraintBasic.py",
> line 1637
>> minFreq =
> expDimRef.minAliasedFreq if expDimRef.minAliasedFreq is not
> None else valRange[0]
>>
> ^
>> SyntaxError: invalid syntax
>>
>>
>>
> Best,
>>
>>
> Xuehui
>>
>
>
> --
> ---------------------------------------------
> Dr Benjamin Bardiaux [log in to unmask]
> Unité de Bioinformatique Structurale
> CNRS UMR3528 - Institut Pasteur
> 25,28 rue du Docteur Roux 75015 Paris,
> France
> ---------------------------------------------
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