Error running phyluce_ncbi_prep_uce_align_files_for_ncbi_targeted_locus_db

[tomgiarla]

Hello, I hope I can get some help with the script phyluce_ncbi_prep_uce_align_files_for_ncbi_targeted_locus_db

When I try to run it, I get the following error:

(phyluce-1.7.3) s62188:~ tgiarla$ phyluce_ncbi_prep_uce_align_files_for_ncbi
Traceback (most recent call last):
File "/Users/tgiarla/opt/miniconda3/envs/phyluce-1.7.3/bin/phyluce_ncbi_prep_uce_align_files_for_ncbi", line 21, in
from Bio.Alphabet import IUPAC
File "/Users/tgiarla/opt/miniconda3/envs/phyluce-1.7.3/lib/python3.6/site-packages/Bio/Alphabet/init.py", line 21, in
"Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the molecule_type as an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabet for more information."
ImportError: Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the molecule_type as an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabet for more information.

I tried commenting out the Bio.Alphabet import command in the script, and that did get it to run. However, when I ran modified script the script, I got another error:

(phyluce-1.7.3) s62188:UCE submit tgiarla$ phyluce_ncbi_prep_uce_align_files_for_ncbi --alignments crunomys-uce-genbank-fastas/ --conf ncbi.conf --input-format fasta --output ./fsatbl_directory
2025-01-09 15:29:53,055 - phyluce_ncbi_prep_uce_align_files_for_ncbi - INFO - ====== Starting phyluce_ncbi_prep_uce_align_files_for_ncbi ======
2025-01-09 15:29:53,056 - phyluce_ncbi_prep_uce_align_files_for_ncbi - INFO - Version: 1.7.3
2025-01-09 15:29:53,056 - phyluce_ncbi_prep_uce_align_files_for_ncbi - INFO - Commit: None
2025-01-09 15:29:53,056 - phyluce_ncbi_prep_uce_align_files_for_ncbi - INFO - Argument --alignments: crunomys-uce-genbank-fastas/
2025-01-09 15:29:53,056 - phyluce_ncbi_prep_uce_align_files_for_ncbi - INFO - Argument --conf: ncbi.conf
2025-01-09 15:29:53,056 - phyluce_ncbi_prep_uce_align_files_for_ncbi - INFO - Argument --input_format: fasta
2025-01-09 15:29:53,056 - phyluce_ncbi_prep_uce_align_files_for_ncbi - INFO - Argument --log_path: None
2025-01-09 15:29:53,056 - phyluce_ncbi_prep_uce_align_files_for_ncbi - INFO - Argument --output: ./fsatbl_directory
2025-01-09 15:29:53,056 - phyluce_ncbi_prep_uce_align_files_for_ncbi - INFO - Argument --verbosity: INFO
2025-01-09 15:29:53,058 - phyluce_ncbi_prep_uce_align_files_for_ncbi - INFO - Getting alignment files
2025-01-09 15:29:53,091 - phyluce_ncbi_prep_uce_align_files_for_ncbi - WARNING - Excluding samples:
2025-01-09 15:29:53,091 - phyluce_ncbi_prep_uce_align_files_for_ncbi - WARNING - Excluding loci:
2025-01-09 15:29:53,091 - phyluce_ncbi_prep_uce_align_files_for_ncbi - INFO - Parsing alignments
Traceback (most recent call last):
File "/Users/tgiarla/opt/miniconda3/envs/phyluce-1.7.3/bin/phyluce_ncbi_prep_uce_align_files_for_ncbi", line 143, in
main()
File "/Users/tgiarla/opt/miniconda3/envs/phyluce-1.7.3/bin/phyluce_ncbi_prep_uce_align_files_for_ncbi", line 121, in main
species, uce, partial, counter, metadata, vouchers
File "/Users/tgiarla/opt/miniconda3/envs/phyluce-1.7.3/lib/python3.6/site-packages/phyluce/ncbi.py", line 68, in get_new_identifier
note = metadata["note"].format(uce)
KeyError: 'note'

[brantfaircloth]

Hi Tom,

Honestly, I've stopped bothering with the targeted_locus_db. I have a vague memory of what this needs to be... and it's something the NCBI added after a while. I think the note= attribute is meant to add an additional description to each locus, so that it looks something like:

2aph [organism=Aphelocoma wollweberi arizonae] [moltype=genomic] [location=genomic] [note=ultra conserved element locus uce-10] [specimen-voucher=FMNH:343516] [biosample=SAMN04909998] Aphelocoma wollweberi arizonae ultra-conserved element locus uce-10

which I think translates to the ncbi.conf file needing to look something like:

[metadata]
molecule:DNA
moltype:genomic
specimen_voucher:{}
bioproject:PRJNA480834
biosample:{}
note:whatever you want in note followed by the locus number which gets substituted in the braces {}

[tomgiarla]

Thanks, Brant! Honestly, I am probably not going to submit the UCEs to GenBank anymore either. Seems like Dryad or Zenodo are much easier ways to share this type of data. I'll add the Illumina reads to the SRA.

[brantfaircloth]

That's what I've been doing - just zipping up the contigs and putting them on whatever archive you want to use, then putting all the (raw) data in SRA.