GATK: Unified Genotyper Error

Question: GATK: Unified Genotyper Error

3.9 years ago by

Canada

Greetings,

I get the following error when running the GATK's Unified Genotyper using default settings:

Traceback (most recent call last):
  File "/galaxy-repl/main/server/lib/galaxy/jobs/runners/__init__.py", line 157, in prepare_job
    job_wrapper.prepare()
  File "/galaxy-repl/main/server/lib/galaxy/jobs/__init__.py", line 828, in prepare
    self.command_line, self.extra_filenames = tool_evaluator.build()
  File "/galaxy-repl/main/server/lib/galaxy/tools/evaluation.py", line 371, in build
    self.__build_command_line( )
  File "/galaxy-repl/main/server/lib/galaxy/tools/evaluation.py", line 387, in __build_command_line
    command_line = fill_template( command, context=param_dict )
  File "/galaxy-repl/main/server/lib/galaxy/util/template.py", line 9, in fill_template
    return str( Template( source=template_text, searchList=[context] ) )
  File "/galaxy-repl/main/server/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 1004, in __str__
    return getattr(self, mainMethName)()
  File "cheetah_DynamicallyCompiledCheetahTemplate_1421284329_57_48736.py", line 175, in respond
  File "/galaxy-repl/main/server/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 1570, in _handleCheetahInclude
    nestedTemplateClass = compiler.compile(source=source,file=file)
  File "/galaxy-repl/main/server/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 592, in compile
    raise TypeError(errmsg % ('source', 'string or None'))
TypeError: arg 'source' must be string or None

My input BAM was made as follows:

1) Fastq files uploaded

2) converted to FastqIllumina using Fastq Groomer.

3) BWA alignment

4) SamToBam

All with default settings.

The error seems to be associated with Parsing the xml file for Unified Genotyper.

I was using the "usegalaxy" instance available on the WWW.

Any thoughts are greatly appreciated, Thanks!

galaxy gatk typeerror • 1.1k views

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modified 3.9 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.9 years ago by marcoalbuquerque.sfu • 50

3.9 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hi,

If you click on the green "bug" icon for the error, the specific GATK error will be at the bottom. I suspect it will have something to do with format. You do not need to actually submit the bug after you view it, just go back and review the format for the inputs.

For this case, start with the fasta dataset. You want the data to be in "fastqsanger" format. Here is a wiki page that explains how to check the initial format and convert/assign to this type.
http://wiki.galaxyproject.org/Support#FASTQ_Datatype_QA

Hopefully that helps. If not, double check other inputs.

The BAM and any reference genomes specified in Galaxy must be an exact match. How to check: https://wiki.galaxyproject.org/Support#Reference_genomes, and perhaps see Custom Genomes on the same page if you are using one.
BAM must have read groups assigned (use Picard)

There can be other details, but start there, the above are the most common issues with this tool.

Thanks, Jen, Galaxy team

ADD COMMENT • link written 3.9 years ago by Jennifer Hillman Jackson ♦ 25k

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