vsaona
commented
2 months ago 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?)
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/createraw.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