An error message

[Paulo Oliveira]

Hello,

I did my first run of bali-phy in an WSL environment, using a command

bali-phy --iter=10000 -c ITSops.txt &

the ITSops.txt starts by asking to align three partitions

Everything seems fine, but there is an error message (attached picture).

I would like to have a reason for this. Thanks in advance!

Paulo

[Benjamin Redelings]

Hi Paulo,

Thank you for the bug report.  In order to figure out the reason, I need
more information.

Can you send me the ITSops.txt file?  Can you also send me the sequence
files for the tree partitions?

-BenRI

> bali-phy error.png
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[Benjamin Redelings]

Sorry, I meant "for the THREE partitions".

[Benjamin Redelings]

Hi Paulo,

Thanks for sending me the files.

The underlying problem is that the three files do not have the same
sequence names. For example, the 5.8S file contains a sequence that is
not the ITS1 file, and the ITS2 file is missing a sequence from the ITS1
file.

The current error message is not very good -- I will try and improve it
for the next release.

-BenRI

On 4/8/26 3:37 PM, Benjamin Redelings wrote:

[oliveira]

I see, thanks. So, the solution is to remove the ones in such situations, that's fairly simple to do. 

Best wishes, 

Paulo

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