Issue with executing SNAPP.xml

[Swap90]

HI,

After installing SNAPP, I attempted to run snapp.xml with the Beast programme but received the following error. However, it run successfully with the example dataset from the tutorial. Could you please help me with this? I have also uploaded the input file.

File: snapp.xml seed: 1678760143286 threads: 1
Loading package SNAPP v1.5.2
Loading package BEAST v2.6.3
Loading package BEAST v2.6.3

Error 1017 parsing the xml input file

Class could not be found. Did you mean beast.core.MCMC?
Perhaps a package required for this class is not installed?

Error detected about here:
<beast>
<run id='mcmc' spec='MCMC'>
snapp.txt

[mmatschiner]

Hi,This is an error that occurs when updating BEAST2 to version >2.7. Can you please try again with the latest version of both BEAST2 and SNAPP?On 14 Mar 2023, at 04:32, Swap90 ***@***.***> wrote: HI, After installing SNAPP, I attempted to run snapp.xml with the Beast programme but received the following error. Could you please help me with this? File: snapp.xml seed: 1678760143286 threads: 1 Loading package SNAPP v1.5.2 Loading package BEAST v2.6.3 Loading package BEAST v2.6.3 Error 1017 parsing the xml input file Class could not be found. Did you mean beast.core.MCMC? Perhaps a package required for this class is not installed? Error detected about here: —Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[NZY1314]

Hi mmatschiner,

I found that the topology of the yielded time tree is not fully congruent with the species tree inferred by ASTRAL or SVDquartets. And the latter seems like more reliable.
Hence, could I fix the tree topology yielded by ASTRAL and only calculate the divergence time by using snapp? If it can be done, what parameters should I set in snapp_prep.rb?

Best wishes,
Zhengyang

[mmatschiner]

Hi Zhengyang,
yes, fixing the topology is possible. To do that, you need to provide a starting tree with option "-s", and you need to set the weight of the topology operator to 0 ("-w 0").
Cheers,
Michael

[NZY1314]

Hi Michael,

Thank you so much! I'll try it later.

Best wishes,

Zhengyang