Question: SAM-to-BAM 'Failed runtime validation of Using reference genome' Error - Local Galaxy instance
gravatar for nhung
4 months ago by
University of Maryland, College Park
nhung0 wrote:


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/", line 157, in prepare_job
  File "/data/galaxy/lib/galaxy/jobs/", line 807, in prepare
    tool_evaluator.set_compute_environment( compute_environment, get_special=get_special )
  File "/data/galaxy/lib/galaxy/tools/", line 53, in set_compute_environment
    self.tool.handle_unvalidated_param_values( incoming, )
  File "/data/galaxy/lib/galaxy/tools/", line 2825, in handle_unvalidated_param_values
    self.handle_unvalidated_param_values_helper( self.inputs, input_values, app )
  File "/data/galaxy/lib/galaxy/tools/", 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/", line 2865, in handle_unvalidated_param_values_helper
    raise LateValidationError( message )

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 • 220 views
ADD COMMENTlink modified 4 months ago by Jennifer Hillman Jackson25k • written 4 months ago by nhung0
gravatar for Jennifer Hillman Jackson
4 months ago by
United States
Jennifer Hillman Jackson25k wrote:


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 COMMENTlink written 4 months ago by Jennifer Hillman Jackson25k

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: 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 REPLYlink written 4 months ago by nhung0

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 REPLYlink written 4 months ago by Jennifer Hillman Jackson25k
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