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 cpalm@stanford.edu Stanford Genome Technology Center
MC: 8307 office: 650-812-1994 *******************************************************
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