Geeting error when trying to run the select_taxa.py script

[robert-ervin-jones]

^{Originally posted by **shahed30** July 12, 2023} Hi all I encountered an error while attempting to run the select_taxa script. My input command was "select_taxa.py --to_exclude exclude.txt --to_include include.txt". In order to build my dataset, I utilized two .txt file containing single column taxa information to include and exclude taxa. Please refer to the attached image.  ``` Traceback (most recent call last): File "/opt/anaconda/envs/fisher/bin/select_taxa.py", line 174, in matrix = update_df_ortho(matrix) File "/opt/anaconda/envs/fisher/bin/select_taxa.py", line 92, in update_df_ortho gene, _, include = line.split() ValueError: too many values to unpack (expected 3) ``` I am using phylofisher ver. 1.2.9. I would greatly appreciate any assistance you can provide. Thank you. Best Shahed

[robert-ervin-jones]

Hi @shahed30,

Can you please provide the command you ran?

Thanks, Robert

[shahed30]

My input command was

select_taxa.py --to_exclude exclude.txt --to_include include.txt

[robert-ervin-jones]

Did you run select_orthologs.py first? If so, did you edit select_orthologs.tsv?

[shahed30]

I ran select_taxa.py before select_orthologs.py

[robert-ervin-jones]

Can you try removing select_orthologs.tsv and re-running select_taxa.py?

[robert-ervin-jones]

Hi @shahed30,

I am just checking in to see if this has been resolved.

Best, Robert

[shahed30]

After removing the old select_orthologs.tsv file, I re-ran the select_taxa.py, now it's working fine. Thank you.

Best SHAHED

On Mon, Aug 14, 2023 at 10:54 AM Robert E. Jones @.***> wrote:

Hi @shahed30 https://github.com/shahed30,

I am just checking in to see if this has been resolved.

Best, Robert

— Reply to this email directly, view it on GitHub https://github.com/TheBrownLab/PhyloFisher/issues/87#issuecomment-1677485296, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALFDLQPX4R5DQKJNANN6EDDXVI33BANCNFSM6AAAAAA2QD4SF4 . You are receiving this because you were mentioned.Message ID: @.***>