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'
| 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 |