SAM-to-BAM 'Failed runtime validation of Using reference genome' Error

Question: SAM-to-BAM 'Failed runtime validation of Using reference genome' Error - Local Galaxy instance

10 months ago by

nhung • 10

University of Maryland, College Park

nhung • 10 wrote:

Hi,

I'm trying to run a workflow on a local Galaxy instance that has these steps in the beginning:

Map with Bowtie for Illumina, Filter SAM, SAM-to-BAM, ...

Everything goes well up to the SAM-to-BAM step, where I get a LateValidationError:

Traceback (most recent call last):
  File "/data/galaxy/lib/galaxy/jobs/runners/__init__.py", line 157, in prepare_job
    job_wrapper.prepare()
  File "/data/galaxy/lib/galaxy/jobs/__init__.py", line 807, in prepare
    tool_evaluator.set_compute_environment( compute_environment, get_special=get_special )
  File "/data/galaxy/lib/galaxy/tools/evaluation.py", line 53, in set_compute_environment
    self.tool.handle_unvalidated_param_values( incoming, self.app )
  File "/data/galaxy/lib/galaxy/tools/__init__.py", line 2825, in handle_unvalidated_param_values
    self.handle_unvalidated_param_values_helper( self.inputs, input_values, app )
  File "/data/galaxy/lib/galaxy/tools/__init__.py", line 2844, in handle_unvalidated_param_values_helper
    self.handle_unvalidated_param_values_helper( input.cases[current].inputs, values, app, context, prefix )
  File "/data/galaxy/lib/galaxy/tools/__init__.py", line 2865, in handle_unvalidated_param_values_helper
    raise LateValidationError( message )
LateValidationError

and the following message: Failed runtime validation of Using reference genome (An invalid option was selected, please verify)

I'm using ce6 as the reference genome and setting it for SAM-to-BAM before I run the workflow (I also tried the 'Set at runtime' option but got the same result). Is there an extra step I'm missing (even though the Map with Bowtie for Illumina already recognizes ce6 and runs just fine)?

Thanks very much!

index sam genome samtools bam • 492 views

ADD COMMENT • link •

modified 10 months ago by Jennifer Hillman Jackson ♦ 25k • written 10 months ago by nhung • 10

10 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

This error can come up when there is an empty input. Check the output from the prior step to make sure it doesn't just only contain the headers (or worse, the headers were not output and/or replaced).

It can also come up when there is a missing index (this seems to be your case). Has the ce6 genome been indexed for Samtools? Indexing for Picard would be a good idea as well.

For any natively indexed reference genome, use these Data Managers: fetch the genome (creating the dbkey as needed), index for SAMtools, index for Picard, index for TwoBit. Then create additional indexes for the target tools.

Thanks! Jen, Galaxy team

ADD COMMENT • link written 10 months ago by Jennifer Hillman Jackson ♦ 25k

Thank you! It was indeed a missing index for Samtools.

However, now when I run the workflow I get

Exception: Error Setting BAM Metadata: Samtools-htslib-API: bam_index_build2() not yet implemented

I read this post: https://biostar.usegalaxy.org/p/9335/ and am using samtools ver. 0.1.19 (ver. 0.1.16 and 0.1.18 are also installed on my Galaxy instance) and ver. 1.1.4 of SAM-to-BAM.

Is there anything else I can do to try to correct this?

ADD REPLY • link written 10 months ago by nhung • 10

Go into the admin area and double check the Samtools primary install and dependencies to ensure all are intact. Also, consider uninstalling and reinstalling Samtools to see if that fixes the problem.

ADD REPLY • link written 10 months ago by Jennifer Hillman Jackson ♦ 25k

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