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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