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