Juan,

What version of freebayes are you running?  The freebayes configuration in the 
galaxy repository was written with the .4 series in mind, and it appears that 
the options have changed with the .6 series.  We'll update the tool config, but 
in the meanwhile you could probably get it working again for your local use by 
editing the tools/human_genome_variation/freebayes.xml file to comment out the 
no-longer-valid parameter in line 34:

  -Y $params.postIntegBanddepth


Let me know if this doesn't get things moving again for you,

Dannon


On Apr 1, 2011, at 1:17 PM, Juan Carlos Perin wrote:

> I'm trying to run Freebayes SNP calling on a bam file from a BWA alignment of 
> solid data.  I keep getting the following error:
> 
> [bam_sort_core] merging from 40 files...
> freebayes: invalid option -- Y
> did you mean --bam ?
> 
> 
> I'm not sure where this is set in the code to try to debug things.  I'm 
> wondering if anyones had this error, and how to fix it?  Just to note, I'm 
> running Brad Chapmans branch of galaxy for the LIMS functionality.  But it 
> appears to be an issue with either galaxy-dist or this one. 
> 
> Thanks in advance for any advice. 
> 
> Juan Perin
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
> 
>  http://lists.bx.psu.edu/

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Reply via email to