fang9319
commented
10 months ago Hi Fabio,
It happened to me after I updated the crabs to v0.1.8 too. Try add seqcount=0 at line 102, it will fix the problem roughly.
Best regards, Zifang
On Sat, 25 Nov 2023 at 00:29, FabioGAmaral @.***> wrote:
It's happening the same to me, crabs version: 0.1.8
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System: MacOS Ventura, Python version:3.9.1 crabs:0.1.4
Code: crabs db_download --source ncbi --database nucleotide --query '12S[All Fields] AND ("1"[SLEN] : "50000"[SLEN])' --species zhuangjiang_fish.csv --output zhujiang_fish_ncbi.fasta --keep_original yes --email myemail --batchsize 500000
error report: Traceback (most recent call last): File "/Users/liuzifang/reference_database_creator/crabs", line 1428, in
main()
File "/Users/liuzifang/reference_database_creator/crabs", line 1425, in main
args.func(args)
File "/Users/liuzifang/reference_database_creator/crabs", line 80, in db_download
speciesTempFileList = wget_ncbi_species(QUERY, DATABASE, EMAIL, BATCHSIZE, OUTPUT, speciesName)
File "/Users/liuzifang/reference_database_creator/function/module_db_download.py", line 111, in wget_ncbi_species
print(f'downloading {seqcount} sequences from NCBI using the searchterm: {speciesSearchTerm}')
UnboundLocalError: local variable 'seqcount' referenced before assignment
I changed the script in module_db_download.py by adding seqcount=0 at line 102, also tried seqcount='', and both worked. When I used the newest version of Crabs on an Ubuntu desktop, I didn't encounter the same error. So I guess it's possibly just happened in the older version of crabs, but I just think it could be helpful for people who encounter similar problems using the old versions.