Question: Cannot set metadata on .bcf output from mpileup
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Guy Reeves • 1.0k wrote:
Hi
I am trying to use mpileup> bcf tools view to call variants on a cloudman instance.
If I set mpileup up to output a .vcf there is no problem but if I select all the same settings but select .bcf format the job runs and goes green but there is a yellow flag stating 'An error occurred setting the metadata for this dataset
Set it manually or retry auto-detection' .
I have tried auto detect and the same error flag remains.The database build is correct and so is the datatype (bcf). If I change the data type to another arbitrary type the yellow flag disappears but returns if 'bcc' is re-specfied.
bcf tools will not recognise the dataset as valid input with this flag present.
Do you have ideas what is going wrong? Thanks Guy
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modified 2.4 years ago
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rquigl01 • 10
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written
3.3 years ago by
Guy Reeves • 1.0k
Hi Jen
If I understand correctly I do not have that problem as I am using the following 2 options
Genotype Likelihood Computation
Perform genotype likelihood computation (--VCF, --BCF options)
Choose the output format
BCF
The version of Mpileup I am using on the cloudman instance is'MPileup call variants (Galaxy Tool Version 2.0)' . However I think the much earlier version of this tool on usegalaxy.org also generates the same metadata flag (and it does not have any .vcf output options.
Thanks Guy
I have tried using an earlier version of mpileup 0.0.1 but contrary to the description this only outputs a .vcf file rather than the expected .bcf file, so does not have this metadata problem.
I get the same error on both usegalaxy.org and a cloudman instance regardless of what version of mpileup I use ( I tried 0.0.01, 0.0.02 and 2.0). But I have found a galaxy instance where everything works. So I suspect this is related to a recent galaxy update.
By the way bcftools viewer is installed
For the CloudMan case - did you launch it using usegalaxy.org/cloudlaunch or launch.usegalaxy.org? (different versions get launched from these each of these sites atm so would be good to know for tracking this down)
Hi Enis
To be honest I do not know how it was launched, but I will find out from the administrator. Though, the same error occurs on use galaxy.org, so I don´t think it is a cloudman specific thing. Thanks Guy
could this problem be related to?
https://trello.com/c/fM6ambaX
We used launch.usegalaxy.org beta version
Basically the same question has been posted yesterday.
mpileup metadata problem in workflow