This fix got me further, however I'm now getting the following error, which is now more confusing... [bam_sort_core] merging from 40 files... BGZF ERROR: unable to open file 1.0 BGZF ERROR: unable to open file 1.0 Could not open input BAM files Juan On Apr 1, 2011, at 1:53 PM, Dannon Baker wrote:
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: