taxonomy_nexus.txt file empty

mgarl-10 commented 6 months ago

Hello,

Thanks for this tool. I am running the pipeline using blast and the nr database. The pipeline seems to work but all my HGT candidates are classified as UNKNOWN. It seems there is an error with the avp prepare module because the file taxonomy_nexus.txt is empty. Do you know what might be the issue?

Thanks

GDKO commented 6 months ago

Hi @mgarl-10,

Can you send me the input files of the avp prepare command by email?

mgarl-10 commented 6 months ago

Sure. I just did.

GDKO commented 6 months ago

Hi @mgarl-10,

I find no problems on my end. Can you check the following on your environment?

You have the latest avp version.
The file tmp/setblast.fa inside the output folder should contain sequences with headers like >CAD0201461.1@689277.
Run the following pyton3 code snippet on your environment to update the local ete3 ncbi taxonomy database.
```
from ete3 import NCBITaxa
ncbi = NCBITaxa()
ncbi.update_taxonomy_database()
```
Cheers, Georgios

mgarl-10 commented 6 months ago

Hello,

I have updated it but still not working :( The setblast.fa is formatted accordingly. No error message.

GDKO commented 5 months ago

Can you send me the fasttree_tree_results.txt and the fasttree file that contains the protein with id 000059?

GDKO commented 5 months ago

Send both files to my email if possible.

Thanks

GDKO commented 3 weeks ago

Hi Bastion,

Please send me all your input files for the avp prepare command.

Cheers, Georgios

On Thu, 13 Jun 2024 at 16:00, bheimbu @.***> wrote:

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

it's me again, Bastian. I have a related issue. My taxonomy_nexus.txt is also empty, and I get following error, while running avp prepare:

$ ../avp prepare \
-a @.@@.@1.out_ai.out \ -o @.@1 -f @.@@.@1.fas \ -b @.@@.***@1.out \ -x groups.yaml \ -c config.yaml [+] Setting up [!] Selected 233 HGT candidates [+] Parsing hits file and grouping similar queries [!] Formed 165 groups [+] Extracting hits from DB [+] Writing fasta files Traceback (most recent call last): File "/scratch1/users/bheimbu/avp/latest/../avp", line 7, in main() File "/scratch1/users/bheimbu/avp/depot/interface.py", line 29, in main prepare.main() File "/scratch1/users/bheimbu/avp/depot/prepare.py", line 313, in main fw_gp.write('>' + q + orgtag + '\n' + str(record_dict[q].seq) + '\n')
File "/home/uni08/bheimbu/miniforge3/envs/avp/lib/python3.12/site-packages/Bio/File.py", line 238, in __getitem__
record = self._proxy.get(self._offsets[key])
~~~~~~~~~~~~~^^^^^
KeyError: 'scaffold2157_size9494'
Any thoughts on this? I can send you more files if you want to?

Cheers Bastian

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taxonomy_nexus.txt file empty #17