Hi Nic,

Yes, the program is running into a memory issue with this setting (confirmed by reviewing your bug report, thank you!).


This is not an issue that is localized to Galaxy or even our server/cluster, but seems to be with the tool itself and it comes up on different systems under different cases when deviating from a ploidy setting of 1 or 2. So, sticking with ploidy = 2 is one option.

You might try contacting the tool author at the Freebayes google group for more detailed advice, the link is:
https://groups.google.com/forum/#!forum/freebayes

Best,

Jen
Galaxy team

On 4/18/13 8:34 AM, Nicola Smith wrote:

Hi,

I am new to this and I hope someone can help. I have pooled sequencing data that I am trying to analyse using Galaxy. I've done quite a bit of online searching and it seems that FreeBayes should be able to do this, if I select "set population", click the "Assume that samples result from pooled sequencing" option and change the ploidy to nx2 (number of alleles, where n is the number of subjects and the organism is diploid).

However, whenever I do this I get an error: usually just "Killed"

I was originally setting my polidy rather high (190 as I have 95 subjects pooled), so I wondered if this was the problem, however, it fails if I do a ploidy of only 4 too. I've tried various things to try to see where I am going wrong:

All with the same BAM file:

Set population model options: Do not set à works

Set population model options: set, Assume that samples result from pooled sequencing: not ticked, Default ploidy for the analysis: 2 à works

Set population model options: set, Assume that samples result from pooled sequencing: ticked, Default ploidy for the analysis: 2 à works

Set population model options: set, Assume that samples result from pooled sequencing: ticked, Default ploidy for the analysis: 4 à fails (killed)

Set population model options: set, Assume that samples result from pooled sequencing: ticked, Default ploidy for the analysis: 10 à fails (killed)

Set population model options: set, Assume that samples result from pooled sequencing: ticked, Default ploidy for the analysis: 10 à fails (killed)

It seems that it is the ploidy part that I am doing wrong, as it works with pooled data but ploidy of 2. I'm sure I have to change the ploidy though, or else how does the program know how many subjects are in the pool? Also, everywhere that I've ready says you have to change the ploidy.

I apologise if my question is naive. As I said, I am new to Galaxy and this is the first thing I am trying to do!

Any help / suggestions would be appreciated,

Thanks,

Nic



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