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 
  File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 424, in 
    self.command_line = self.tool.build_command_line( param_dict )
  File "/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 1827, in 
    command_line = fill_template( self.command, context=param_dict )
  File "/home/galaxy/galaxy-dist/lib/galaxy/util/template.py", line 9, in 
    return str( Template( source=template_text, searchList=[context] ) )
 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 

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 

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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