> Dear all,
> I am getting an error message that looks different than the
> one that was reported few days ago.

> ------------------
> [tristan@babylon 4bucky] bucky --opt-space *.t.in
> Bayesian Untangling of Concordance Knots (applied to yeast
> and other organisms)
> BUCKy version 1.4.0, 28 June 2010
> Copyright (C) 2006-2010 by Bret Larget and Cecile Ane

> This is free software; see the source for copying
> conditions.  There is NO
> warranty; not even for MERCHANTABILITY or FITNESS FOR A
> PARTICULAR PURPOSE.

> Screen output written to file run1.out
> Program initiated at Thu Dec  2 08:35:05 2010

> Reading in summary files....
> 0   10   20   30   40   50   60   70   80   90   100
> +----+----+----+----+----+----+----+----+----+----+
> ****************************************************
> ....done.
> Number of genes sequenced for each taxon:
>     1 sde   1072
>     2 spyb   1072
>     3 spy9   1072
>     4 spy6   1072
>     5 spy4   1072
>     6 spy3   1072
>     7 spyd   1072
>     8 spy5   1072
>     9 spy8   1072
>    10 spy1   1072
>    11 spyc   1072
>    12 spya   1072
>    13 spy7   1072
>    14 spy2   1072
>    15 seq   1072
>    16 sca   1072
> Read 1072 genes with a total of 37845666 different sampled
> tree topologies
> Writing input file names to file run1.input....done.
> Sorting trees by average posterior probability....done.
> Initializing random number generator....done.
> Initializing gene information....terminate called after
> throwing an instance of 'std::bad_alloc'
>    what():  std::bad_alloc
> Aborted
> ---------------

> I ran it an a 20GB memory server, and I don't think I ran
> out of memory. Any idea?

> Thanks!

On Sat, Dec 4, 2010 at 7:53 PM, Cecile Ane <a...@stat.wisc.edu> wrote:
> Hi Tristan,
> I guess this error also comes from a memory issue ('bad_alloc'). 37.8
> million different tree topologies is big... The program will need to store a
> matrix with this number of rows, unless the opt-space option is used. Did
> you try using this option? It should be particularly useful in cases with a
> very large number of trees, just like what you have.
> Cecile.

> On 12/2/2010 7:25 AM, Tristan Lefebure wrote:

>> Dear all,
>> I am getting an error message that looks different than the
>> one that was reported few days ago.

>> ------------------
>> [tristan@babylon 4bucky] bucky --opt-space *.t.in
>> Bayesian Untangling of Concordance Knots (applied to yeast
>> and other organisms)
>> BUCKy version 1.4.0, 28 June 2010
>> Copyright (C) 2006-2010 by Bret Larget and Cecile Ane

>> This is free software; see the source for copying
>> conditions.  There is NO
>> warranty; not even for MERCHANTABILITY or FITNESS FOR A
>> PARTICULAR PURPOSE.

>> Screen output written to file run1.out
>> Program initiated at Thu Dec  2 08:35:05 2010

>> Reading in summary files....
>> 0   10   20   30   40   50   60   70   80   90   100
>> +----+----+----+----+----+----+----+----+----+----+
>> ****************************************************
>> ....done.
>> Number of genes sequenced for each taxon:
>>    1 sde   1072
>>    2 spyb   1072
>>    3 spy9   1072
>>    4 spy6   1072
>>    5 spy4   1072
>>    6 spy3   1072
>>    7 spyd   1072
>>    8 spy5   1072
>>    9 spy8   1072
>>   10 spy1   1072
>>   11 spyc   1072
>>   12 spya   1072
>>   13 spy7   1072
>>   14 spy2   1072
>>   15 seq   1072
>>   16 sca   1072
>> Read 1072 genes with a total of 37845666 different sampled
>> tree topologies
>> Writing input file names to file run1.input....done.
>> Sorting trees by average posterior probability....done.
>> Initializing random number generator....done.
>> Initializing gene information....terminate called after
>> throwing an instance of 'std::bad_alloc'
>>   what():  std::bad_alloc
>> Aborted
>> ---------------

>> I ran it an a 20GB memory server, and I don't think I ran
>> out of memory. Any idea?

>> Thanks!

> Thanks Cecile. That's indeed a memory issue. In the example below I
> was already using the opt-space option. Should I try to reduce the
> tree topology space by reducing the number of samples per genes, or
> the number of genes, ... , or is Bucky more suited for smaller
> data-sets (my example is 1072genesx16taxa)?