Hi Curt,

This should be fixed in -central (https://bitbucket.org/galaxy/galaxy-central) 
in changeset 6778:35be930b21be and will be available in the next dist release. 
If you don't want to wait until the next dist release, you can also pull 
directly from central or apply the changes manually.


Thanks for using Galaxy,

Dan


On Mar 1, 2012, at 5:12 PM, Curt Palm wrote:

> I am trying to run GATK's DepthOFCoverage  using intervals and get the 
> following error:
> 
> failure preparing job
> Traceback (most recent call last):
>   File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 59, 
> in run_job
>     job_wrapper.prepare()
>   File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 424, in 
> prepare
>     self.command_line = self.tool.build_command_line( param_dict )
>   File "/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 1827, in 
> build_command_line
>     command_line = fill_template( self.command, context=param_dict )
>   File "/home/galaxy/galaxy-dist/lib/galaxy/util/template.py", line 9, in 
> fill_template
>     return str( Template( source=template_text, searchList=[context] ) )
>   File 
> "/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg/Cheetah/Template.py",
>  line 1004, in __str__
>     return getattr(self, mainMethName)()
>   File "cheetah_DynamicallyCompiledCheetahTemplate_1330381526_3_23629.py", 
> line 402, in respond
> NotFound: cannot find 'omit_interval_statistics' while searching for 
> 'gatk_param_type.omit_interval_statistics'
> 
> the parameters used are: 
> 
> Tool: Depth of Coverage
> Name: Depth of Coverage on data 35 and data 27 (per locus coverage)
> Created:      Feb 27, 2012
> Filesize:     0 bytes
> Dbkey:        human_g1k_v37
> Format:       rtable
> Tool Version: None
> Tool Standard Output: stdout
> Tool Standard Error:  stderr
> 
> Input Parameter       Value
> Conditional (reference_source)        0
> BAM file      35: Table Recalibration on data 33, data 31, and data 27 (BAM)
> Using reference genome        human_g1k_v37
> RefSeq Rod    No dataset
> Partition type for depth of coverage  sample
> Output format rtable
> Conditional (gatk_param_type) 1
> How strict should we be in validating the pedigree information        STRICT
> Genomic intervals     27: 5um_amplicons_hg19.picard.list
> Interval set rule     UNION
> Conditional (downsampling_type)       0
> Type of BAQ calculation to apply in the engine        OFF
> BAQ gap open penalty (Phred Scaled)   40.0
> Use the original base quality scores from the OQ tag  False
> Value to be used for all base quality scores, when some are missing   -1
> How strict should we be with validation       STRICT
> Interval merging rule ALL
> Disable experimental low-memory sharding functionality.       False
> Makes the GATK behave non deterministically, that is, the random numbers 
> generated will be different in every run     False
> Conditional (analysis_param_type)     0
> 
> 
> I can run this analysis outside of Galaxy with the command: 
> 
> java -jar /opt/GenomeAnalysisTK/GenomeAnalysisTK.jar -T DepthOfCoverage -et 
> NO_ET -R /home/galaxy/genome/human_g1k_v37/picard/human_g1k_v37.fasta 
> --partitionType sample --out out.txt --outputFormat rtable -I bamfile.bam 
> --intervals intervals_picardList.list
> 
> 
> I'd like to add the DepthOfCoverage to the end of a work flow and get per 
> base coverage for a set of amplicon  coordinates, so using an interval file 
> is needed. 
> 
> any suggestions on what is wrong?
> 
> 
> 
> *******************************************************
> Curtis J. Palm             cp...@stanford.edu
> Stanford Genome Technology Center
> 
> MC:  8307
> office: 650-812-1994        
> *******************************************************
> 
> ___________________________________________________________
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