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
*******************************************************
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