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I got error when I run the tool #20

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Sam131992 opened this issue Aug 9, 2024 · 1 comment
Open

I got error when I run the tool #20

Sam131992 opened this issue Aug 9, 2024 · 1 comment

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@Sam131992
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The following error I received when I run the tutorial

(genovi) sam@DESKTOP-QP6LGUS:~$ genovi -i Paenibacillus.gbff -cs paradise --scale linear --alignment '<' -s complete
/home/sam/miniconda3/envs/genovi/lib/python3.7/site-packages/Bio/GenBank/Scanner.py:1219: BiopythonParserWarning: Premature end of file in sequence data
"Premature end of file in sequence data", BiopythonParserWarning
'locus_tag'
Error when transforming gbk to faa.
genovi-temp/contig_1-genovi_bands.kar created succesfully.
genovi-temp/contig_1-genovi_tRNA_pos.txt created succesfully.
genovi-temp/contig_1-genovi_tRNA_neg.txt created succesfully.
genovi-temp/contig_1-genovi_rRNA_pos.txt created succesfully.
genovi-temp/contig_1-genovi_rRNA_neg.txt created succesfully.
Traceback (most recent call last):
File "/home/sam/miniconda3/envs/genovi/bin/genovi", line 8, in
sys.exit(main())
File "/home/sam/miniconda3/envs/genovi/lib/python3.7/site-packages/scripts/GenoVi.py", line 685, in main
visualiseGenome(*get_args())
File "/home/sam/miniconda3/envs/genovi/lib/python3.7/site-packages/scripts/GenoVi.py", line 341, in visualiseGenome
sizes, cogs_p, cogs_n, lengths, chrms, hist, wanted_cogs = base(file, temp_folder + "/" + output_file_part, output_file + "/" + output_file, True, True, cogs_classified, cogs_classified, False, True, deepnog_confidence_threshold, verbose, wanted_cogs=wanted_cogs)
File "/home/sam/miniconda3/envs/genovi/lib/python3.7/site-packages/scripts/create_raw.py", line 507, in base
_ , _, chrms_cp, chrms_cn, hist = create_feature(gbk_file, tmp, output, sizes, "CDS", cogs_dict, verbose = verbose, complete=complete)
File "/home/sam/miniconda3/envs/genovi/lib/python3.7/site-packages/scripts/create_raw.py", line 321, in create_feature locus_tag = feature.qualifiers.get("locus_tag")[0]
TypeError: 'NoneType' object is not subscriptable

@vsaona
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vsaona commented Sep 4, 2024

It looks like there's some kind of incompatibility between the file you are trying to read and the application.
Did you try with the files in "input_test" and did it work properly?
The Paenibacillus annotated genome is public? May I see it? If not, where did you get this file from? (Which tool did you use for annotation?)

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