search

aitgon / vtam

MIT License
3 stars 3 forks source link

Getting ValueError when running taxassign with NCBI db #32

Open MarionDFO opened 1 year ago

MarionDFO commented 1 year ago

Hi,

I got an error message when running the vtam taxassign command with a freshly downloaded NCBI db, I am working with Blast v2.13.0. Do you know what is the issue here? Thank you!

(vtam3) genpop@Genpop:~/anaconda3/envs/vtam3/12S_SG_2021$ vtam taxassign --db run1/db.sqlite --asvtable run1/asvtable_default.tsv --output run1/asvtable_default_taxa.tsv --taxonomy taxonomy.tsv --blastdbdir /media/genpop/My_Book/Marion/NCBI_db2 --blastdbname nt -v --log run1/vtam.log

Traceback (most recent call last): File "/home/genpop/anaconda3/envs/vtam3/bin/vtam", line 8, in sys.exit(main()) File "/home/genpop/anaconda3/envs/vtam3/lib/python3.7/site-packages/vtam/init.py", line 308, in main VTAM(sys.argv[1:]) File "/home/genpop/anaconda3/envs/vtam3/lib/python3.7/site-packages/vtam/init.py", line 237, in init blastdbname_str=blastdbname_str, params=params, num_threads=num_threads) File "/home/genpop/anaconda3/envs/vtam3/lib/python3.7/site-packages/vtam/CommandTaxAssign.py", line 180, in main params = None) File "/home/genpop/anaconda3/envs/vtam3/lib/python3.7/site-packages/vtam/utils/RunnerTaxAssign.py", line 73, in init blast_output_df = RunnerBlast.process_blast_result(blast_output_tsv) File "/home/genpop/anaconda3/envs/vtam3/lib/python3.7/site-packages/vtam/utils/RunnerBlast.py", line 96, in process_blast_result expand=True) File "/home/genpop/anaconda3/envs/vtam3/lib/python3.7/site-packages/pandas/core/generic.py", line 5516, in setattr self[name] = value File "/home/genpop/anaconda3/envs/vtam3/lib/python3.7/site-packages/pandas/core/frame.py", line 3602, in setitem self._set_item_frame_value(key, value) File "/home/genpop/anaconda3/envs/vtam3/lib/python3.7/site-packages/pandas/core/frame.py", line 3729, in _set_item_frame_value raise ValueError("Columns must be same length as key") ValueError: Columns must be same length as key

meglecz commented 1 year ago

Hi Marion,

Have you created the taxonomy file from new ?

vtam taxonomy --output taxonomy.tsv

There are probably new taxids in the newly dowloaded ncbi database that are not in the precomputed taxonomy.tsv file.

Which marker are you using ?

Emese

MarionDFO commented 1 year ago

Hi Emese,

Yes I've created the taxonomy file from new with your taxonomy function from VTAM after downloading NCBI nt db (not a specific marker, all the db). Thanks, Marion