IQTREE 1.6.6 incorrectly handles RAxML-style partition files with multiple blocks

[Alexey Kozlov]

Sorry guys,

but I have one more regression in IQTREE 1.6.6  to report:

If RAxML-style partition file contains partitions with multiple site blocks, e.g.

DNA, p1 = 1-10, 20-30, 40-60

then apparently IQTREE 1.6.6 would only use the first block (e.g. 1-10) and simply ignore the remaining parts.

Once again, this used work properly in IQTREE 1.5.5, so must be a regression bug.

The nasty aspect of this is that no error will be produced, so I discovered this problem almost by accident

when trying to find out why IQTREE 1.6.6 became 3x faster than 1.5.5 on one of my test datasets :)

Hope it will be trivial to fix, thanks in advance!

Best,

Alexey

[Minh Bui]

Hi Alexey,

Many thanks for this report and the previous email as well … Not sure why this, but I’ll have a look as soon as I’m back in August. Just a quick question for now: Does this problem happen with nexus partition file?

Cheers

Minh

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[Alexey Kozlov]

Hi Minh,

thanks! The problem seems to be present with Nexus partition file as well.

I tried the following file:

begin sets;
charset part1 = 1-1000 2001-3000;
charset part2 = 1001-2000 3001-200000;
charset part3 = 200001-394684;

charpartition mine = HKY:part1, GTR+G:part2, GTR+G: part3;
end;

iqtree -pre test -s ali.phy -q example.nex -nt 16 -te sample.treefile -blfix -redo

and got the following output:

Loading 3 partitions...
Subset Type Seqs Sites Infor Invar Model Name
1 DNA 200 1000 371 570 HKY part1
2 DNA 200 1000 416 475 GTR+G part2
3 DNA 200 194684 93507 86630 GTR+G part3


Best,
Alexey

On 18.07.2018 20:30, Minh Bui wrote:
> Hi Alexey,
>
> Many thanks for this report and the previous email as well … Not sure why this, but I’ll have a look as soon as I’m back
> in August. Just a quick question for now: Does this problem happen with nexus partition file?
>
> Cheers
> Minh
>

>> On 18 Jul 2018, at 12:35 pm, Alexey Kozlov <alexei...@gmail.com <mailto:alexei...@gmail.com>> wrote:
>>
>> Sorry guys,
>>
>> but I have one more regression in IQTREE 1.6.6  to report:
>>
>> If RAxML-style partition file contains partitions with multiple site blocks, e.g.
>>
>> DNA, p1 = 1-10, 20-30, 40-60
>>
>> then apparently IQTREE 1.6.6 would only use the first block (e.g. 1-10) and simply ignore the remaining parts.
>>
>> Once again, this used work properly in IQTREE 1.5.5, so must be a regression bug.
>>
>> The nasty aspect of this is that no error will be produced, so I discovered this problem almost by accident
>> when trying to find out why IQTREE 1.6.6 became 3x faster than 1.5.5 on one of my test datasets :)
>>
>> Hope it will be trivial to fix, thanks in advance!
>>
>> Best,
>> Alexey
>>
>> --
>> You received this message because you are subscribed to the Google Groups "IQ-TREE" group.
>> To unsubscribe from this group and stop receiving emails from it, send an email to iqtree+un...@googlegroups.com

>> <mailto:iqtree+un...@googlegroups.com>.
>> To post to this group, send email to iqt...@googlegroups.com <mailto:iqt...@googlegroups.com>.

[Minh Bui]

Hi Alexey,

I tried with an example data set here and IQ-TREE v1.6.6 loaded correctly (i.e. fragmented positions ranges are fully loaded). So I couldn’t reproduce the behaviour you described. Not sure what happened. Can you send me your input data via my personal email and I will have a look.

Cheers
Minh