Question: Cannot set metadata on .bcf output from mpileup
1
gravatar for Guy Reeves
3.0 years ago by
Guy Reeves1.0k
Germany
Guy Reeves1.0k 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

 

 

 

ADD COMMENTlink modified 2.1 years ago by rquigl0110 • written 3.0 years ago by Guy Reeves1.0k

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

 

 

ADD REPLYlink written 3.0 years ago by Guy Reeves1.0k

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.

ADD REPLYlink written 3.0 years ago by Guy Reeves1.0k

 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 

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by Guy Reeves1.0k

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)

ADD REPLYlink written 3.0 years ago by Enis Afgan690

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

 

ADD REPLYlink written 3.0 years ago by Guy Reeves1.0k

could this problem be related to?

 https://trello.com/c/fM6ambaX

ADD REPLYlink written 3.0 years ago by Guy Reeves1.0k

We used launch.usegalaxy.org beta version 

ADD REPLYlink written 3.0 years ago by Guy Reeves1.0k

Basically the same question has been posted yesterday.

mpileup metadata problem in workflow

ADD REPLYlink written 3.0 years ago by Guy Reeves1.0k
0
gravatar for Jennifer Hillman Jackson
3.0 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

Double check the output format. The tool can be used two ways: one creates bcf output and this will be labeled automatically, the other is "mpileup" format which must be assigned after the job completes. My guess is that the format is actually "mpileup" for the data you are changing. Re-run with the expanded parameters to create a bcf dataset is that is wanted instead.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 3.0 years ago by Jennifer Hillman Jackson25k

Update: the .1 and .2 versions are presenting reported problems. A Trello ticket has been created to track the resolution. Please follow it here: https://trello.com/c/cYkUbipj

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by Jennifer Hillman Jackson25k
0
gravatar for rquigl01
2.1 years ago by
rquigl0110
rquigl0110 wrote:

I had this problem as well but it fixed itself when I clicked on edit attributes and typed "bcf" in the Annotation / Notes section. Hope this helps someone.

ADD COMMENTlink written 2.1 years ago by rquigl0110
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