problems with likelihood analisys in POY 5.1.1

[lourd...@gmail.com]

Hello, 

I am submitting the following commands:

read(prealigned:("16S.fas",tcm:(1,1)))

search(max_time:00:00:30)

select()

transform(likelihood:(gtr,rates:gamma:(4),priors:estimate))

search(max_time:00:04:00)

report("arbol.tre", trees:(branches), "reporte.txt", lkmodel)

exit()

I am running this small analysis just to test the performance of POY (in a parallel environment: 40 processors) when doing a likelihood analysis. 

I am getting the following error (right after the Wagner is finished):

poy: likelihood.c:2544: readjust_brents_gtr: Assertion `b >= x' failed.

[amazonia02:61548] *** Process received signal ***

[amazonia02:61548] Signal: Aborted (6)

[amazonia02:61548] Signal code:  (-6)

poy: newkkonen.c:1599: backtrace: Assertion `len1<=len2' failed.

poy: likelihood.c:2544: readjust_brents_gtr: Assertion `b >= x' failed.

[amazonia02:61542] *** Process received signal ***

[amazonia02:61542] Signal: Aborted (6)

[amazonia02:61542] Signal code:  (-6)

poy: newkkonen.c:1633: backtrace: Assertion `(i== -1)&&(j==-1)' failed.

poy: likelihood.c:2544: readjust_brents_gtr: Assertion `b >= x' failed.

[amazonia02:61543] *** Process received signal ***

[amazonia02:61543] Signal: Aborted (6)

[amazonia02:61543] Signal code:  (-6)

poy: newkkonen.c:1599: backtrace: Assertion `len1<=len2' failed. 

Please I would really appreciate help tot interpret this error message. 

Lourdes 

[Nicholas Lucaroni]

Shucks. I had run those functions (newkonnen and brents method) very regularly with large/small datasets and no issues ever came up like this in a long time. And since both functions failed, i'm guessing something else is going on -- well, hoping.

- What is the distribution of lengths for your sequence data? Minimum / maximum length is probably fine.

- What C compiler/toolchain are you using or are you using a distributed binary? (gcc/clang/...)

- Is this reproducible? (does every run of the script fail?)

- Does the analysis work sequentially? 

I cannot make guarantees that i'll be able to dig into this, those are both fairly subtle complicated sections of the code.