We have deployed a local server Galaxy and we plan to execute some workflows. One of them include FreeBayes tool latest version. We want to execute FreeBayes with a built-in genome that we have uploaded to Galaxy. We have checked that the built-in genome is working with the BWA-MEM2 tool. We have executed the SAM fasta index builder, 2bit builder, picard builder and BWA-MEM2 index builder with the built-in genome.
The problem is that when we try to execute FreeBayes with all the parameters set and the built-in genome selected, it denies the execution with the following error:
Parameter input_bams: Unspecified genome build, click the pencil icon in the history item to set the genome build
There is no problem when we execute FreeBayes with a genome from the history but we prefer the other method. What could be the problem?
P.S. We have installed older versions of FreeBayes to test the error and it is the same in all versions
The message from the tool is about the database assignment on the input BAMs.
What happens if the input dataset BAM has the correct database assigned? One that matches the built-in index that you are using for all of the other steps?
When mapping against a native index on the server, the resulting BAM should automatically be assigned the correct database key. But if you are doing something else and the key was lost, it can be added back again.
If you can reproduce this at a public server, I would be interested in reviewing it. Some tools do check the database across inputs but I didn’t think Freebayes did that anymore. Maybe I am wrong or maybe there is another small corner case issue we can explore to make sure it is all working as expected.
Thank you so much for the response. I have changed the dbkey and this error is solved but a new error appears:
Parameter input_bams: Sequences are not currently available for the specified build.
I hope i could test this in the future in a public server, but now I am too busy to configure it. In this tool, I have tried with a history ingested genome and it works in a reasonable time (~5mins) so I can continue with this configuration if this is not solved.
Hi @fcasnun ,
now, of course, your built-in genome needs to have that same dbkey that you set for your bam datasets. The genome dbkey should have been set when you uploaded the genome and should have been inherited by the various indices and the 2bit format.
In the Admin panel, you can check this setting by going to “Local Data” and then selecting the data table you want to inspect under “Tool Data Tables”. The one relevant for Freebayes will be “fasta_indexes”.
