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 [email protected] > Stanford Genome Technology Center > > MC: 8307 > office: 650-812-1994 > ******************************************************* > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/
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