RAxML partition file format error in CIPRES

[Sheila Rodríguez Machado]

Hello,

Thank you for developing and maintaining RAxMLit's great.

Now, when I was trying to run a ML analysis using the tool RAxML-HPC2 Workflow on XSEDE in CIPRES, I got the error highlighted below.. 

I'm using the partition file phyluce generates plus the partition model for each loci.

My alignment has 92 species and 1024 loci.

Hope you can help,

Thanks,

Sheila

CIPRES_NP=1 CIPRES_THREADSPP=128 running: raxmlHPC-PTHREADS-AVX -T 128 -s infile.txt -N 1000 -m GTRGAMMA -p 12345 -q part -b 12345 -o Ana_dowei_2563,Jen_lineata_14775 -n testR 

Partition file parsing error!

Each line must contain a "=" character 

Offending line: #nexus 

 RAxML will exit now.

[Pfeiffer, Wayne]

You need to delete the line with #nexus from your partition file part.

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[Sheila Rodríguez Machado]

Hello and thanks for your prompt reply.

The file I have with partitions and model per partitions (loci) is a nexus file. Given than RAxML is not recognizing common lines in a nexus file (ex., #nexus, begin sets, end; ), does this mean that I should just provide a nexus file with only lines including "=" characters?

Thanks again,

Sheila

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[Pfeiffer, Wayne]

Hi Sheila,

Yes. In addition, the partition file needs to be in the format that RAxML expects.

The user manual lists the following as an example for a DNA alignment with two partitions:

DNA, gene1 = 1­500

DNA, gene2 = 501­1000

Good luck!

Wayne

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[Alexey Kozlov]

Hi Sheila,

for standard/old RAxML, please see here:

https://cme.h-its.org/exelixis/resource/download/NewManual.pdf#page=36

for raxml-ng, please see here:

https://github.com/amkozlov/raxml-ng/wiki/Input-data#multiple-models

Best,
Alexey

On 22.09.22 20:57, Pfeiffer, Wayne wrote:
> Hi Sheila,
>
> Yes. In addition, the partition file needs to be in the format that RAxML expects.
>
> The user manual lists the following as an example for a DNA alignment with two partitions:
>
> DNA, gene1 = 1­500
> DNA, gene2 = 501­1000
>
> Good luck!
>
> Wayne
>
>> On Sep 22, 2022, at 10:07 AM, Sheila Rodríguez Machado <sheila...@gmail.com

>> <mailto:sheila...@gmail.com>> wrote:
>>
>> Hello and thanks for your prompt reply.
>> The file I have with partitions and model per partitions (loci) is a nexus file. Given than RAxML
>> is not recognizing common lines in a nexus file (ex., #nexus, begin sets, end; ), does this mean
>> that I should just provide a nexus file with only lines including "=" characters?
>> Thanks again,
>> Sheila
>>

>> On Thu, Sep 22, 2022 at 10:37 AM Pfeiffer, Wayne <pfei...@sdsc.edu <mailto:pfei...@sdsc.edu>> wrote:
>>
>> You need to delete the line with #nexus from your partition file part.
>>
>>> On Sep 22, 2022, at 6:55 AM, Sheila Rodríguez Machado <sheila...@gmail.com

>>> <mailto:sheila...@gmail.com>> wrote:
>>>
>>> Hello,
>>> Thank you for developing and maintaining RAxMLit's great.

>>> Now, when I was trying to run a ML analysis using the tool *RAxML-HPC2 Workflow on XSEDE* in

>>> CIPRES, I got the error highlighted below..

>>> I'm using the partition file *phyluce* generates plus the partition model for each loci.

>>> My alignment has 92 species and 1024 loci.
>>> Hope you can help,
>>> Thanks,
>>> Sheila
>>>
>>> CIPRES_NP=1 CIPRES_THREADSPP=128 running: raxmlHPC-PTHREADS-AVX -T 128 -s infile.txt -N 1000
>>> -m GTRGAMMA -p 12345 -q part -b 12345 -o Ana_dowei_2563,Jen_lineata_14775 -n testR
>>>
>>> Partition file parsing error!
>>> Each line must contain a "=" character
>>> Offending line: #nexus
>>>  RAxML will exit now.
>>>
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>>
>>
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[Sheila Rodríguez Machado]

Thank y'all for your answers!

Have a great weekend. Will let you know if it works.

Best,

Sheila