Hello,
I am just going by memory here, but are you setting Aria to use
unassigned peaks? It seems that it is removing all of your unassigned
peaks.
David
On 6/18/2012 12:44 AM, Sriinivas penumutchu wrote:
> Dear aria2.3 users
>
> I am getting following error while start aria2.3 run for homo-dimer protein !
>
>
>
> /home/hanmin/aria2.3/src/py/aria/Project.py:48: DeprecationWarning:
> the md5 module is deprecated; use hashlib instead
> import md5
>
> 96 % of the peaks of spectrum "c13noesy" have been removed. This might
> be due to a wrong choice of the peak size type ("volume" or
> "intensity") that will be used for calibration and the definition of
> distance bounds.
>
>
> actually I am using intensity as peak size type , i tried both separately ( volume or intensity ) , still it is complaining same !
>
>
> could you please suggest to do needful !
>
>
> Loading project "S100P_project3.xml"...
> MESSAGE [Project]: Temporary directory has been set to /home/hanmin/srinivas/
> aria_temp.tmpZ9nIC31339995374
> MESSAGE [Project]: Checking host list ...
> MESSAGE [Job manager]: Command "csh" ... ok.
> MESSAGE [Project]: -------------------- Reading data --------------------
> MESSAGE [Project]: Cache is enabled.
> /home/hanmin/aria2.3/src/py/aria/Project.py:48: DeprecationWarning:
> the md5 module is deprecated; use hashlib instead
> import md5
> MESSAGE [Project]: Loading cached data files...
> MESSAGE [Project]: Reading molecule definition /home/hanmin/srinivas/6/run5/
> data/sequence/sequence.xml.
> MESSAGE [Project]: Reading spectrum /home/hanmin/srinivas/6/run5/data/spectra/
> S100PN15.xml.
> MESSAGE [Project]: Reading chemical shift list /home/hanmin/srinivas/6/run5/
> data/spectra/shifts1.xml.
> MESSAGE [Project]: Reading spectrum /home/hanmin/srinivas/6/run5/data/spectra/
> S100Pc131.xml.
> MESSAGE [Project]: Reading chemical shift list /home/hanmin/srinivas/6/run5/
> data/spectra/shifts2.xml.
> MESSAGE [Project]: Reading spectrum /home/hanmin/srinivas/6/run5/data/spectra/
> c13filternoe1.xml.
> MESSAGE [Project]: Reading chemical shift list /home/hanmin/srinivas/6/run5/
> data/spectra/shifts3.xml.
> MESSAGE [Project]: Data files read.
> MESSAGE [Project]: ------------------- Filtering input data -------------------
> MESSAGE [Project]: Applying filters to spectrum/shiftlist "n15noesy":
> MESSAGE [Project]: Chemical shift list filtered: 696 / 2270 shifts (30.66 %)
> removed.
> MESSAGE [Project]: NOESY spectrum "n15noesy" filtered: 1990 / 2315 peaks (85.96
> %) removed. Details:
> MESSAGE [Project]: - no. of invalid proton 1 shifts: 0
> MESSAGE [Project]: - no. of invalid proton 2 shifts: 0
> MESSAGE [Project]: - no. of invalid peak sizes: 0
> MESSAGE [Project]: - no. of diagonal peaks: 88
> MESSAGE [Project]: - no. of unassigned peaks: 1908
> MESSAGE [Project]: Applying filters to spectrum/shiftlist "c13noesy":
> MESSAGE [Project]: Chemical shift list filtered: 696 / 2270 shifts (30.66 %)
> removed.
> MESSAGE [Project]: NOESY spectrum "c13noesy" filtered: 4107 / 4282 peaks (95.91
> %) removed. Details:
> MESSAGE [Project]: - no. of invalid proton 1 shifts: 8
> MESSAGE [Project]: - no. of invalid proton 2 shifts: 4
> MESSAGE [Project]: - no. of invalid peak sizes: 0
> MESSAGE [Project]: - no. of diagonal peaks: 477
> MESSAGE [Project]: - no. of unassigned peaks: 3986
> Traceback (most recent call last):
> File "/home/hanmin/aria2.3/aria2.py", line 903, in<module>
> verbose_level, use_condor=condor)
> File "/home/hanmin/aria2.3/aria2.py", line 811, in run_aria
> project.load_and_preprocess_data()
> File "/home/hanmin/aria2.3/src/py/aria/Project.py", line 1427, in
> load_and_preprocess_data
> self.preprocess_data()
> File "/home/hanmin/aria2.3/src/py/aria/Project.py", line 1444, in
> preprocess_data
> filter_results.append(self.apply_filters(experiment))
> File "/home/hanmin/aria2.3/src/py/aria/Project.py", line 1254, in
> apply_filters
> experiment.getName()))
> File "/home/hanmin/aria2.3/src/py/aria/ariabase.py", line 211, in error
> raise exception, msg
> ValueError: USER ERROR<aria.Project.ProjectSingleton> File
> "/home/hanmin/aria2.3/src/py/aria/Project.py", line 1444 in
> preprocess_data
> 96 % of the peaks of spectrum "c13noesy" have been removed. This might
> be due to a wrong choice of the peak size type ("volume" or
> "intensity") that will be used for calibration and the definition of
> distance bounds.
> [hanmin@HP133 ~/srinivas]$
>
>
> --
>
>
> *Best Regards
> *
>
> *Srinivasa Rao Penumutchu
> Ph.D. Research Scholar
> Protein NMR Lab , II floor-218
> Department of Chemistry
> National Tsing Hua University,
> Hsinchu, Taiwan.
> Ph: 886357151-35605,M:+886-912894534 , **
> Email- [log in to unmask] ,[log in to unmask]
> web:http://www.researchgate.net/profile/Srinivas_Penumutchu/
> *
>
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