arodel21
commented
3 hours ago Hi @arghya1611! Thanks for using our tool and reaching out with your question.
The warning BiopythonParserWarning: Premature end of file in sequence data indicates that the file is expected to be longer. Could you please that the end of the file is as expected? Sometimes BioPython has issues with old annotation tools.
Also, what do the predictions and test-temp/contig_1-test_bands.kar files look like? Are they empty?
The No such file or directory: 'circos.svg' error could mean that GenoVi is not processing your files due to ill-format or that the Circos installation is not recognized. Could you please check your Circos installation with which circos?
Let us know how this goes!
Hi Thanks for developing GenoVi. Looks a great tool but I was not able to use it. Please see the error message I got below.
(/data/Food/analysis/R1479_neurofoods/genovi) [arghya.mukherjee@compute07 genovi-test]$ genovi -i ../GenoVi/input_test/Corynebacterium_alimapuense_VA37.gbk -o test --status complete --colour_scheme autumn --verbose yes /data/Food/analysis/R1479_neurofoods/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
GBK file transformed into faa succesfully. File saved as test-temp/contig_1-test.faa output test-temp/contig_1-test
Deepnog prediction started
deepnog infer test-temp/contig_1-test.faa --out test-temp/contig_1-test_prediction_deepnog.csv -db cog2020 -t 1 [2024-10-31 23:35:31] deepnog.client.client - INFO - Starting deepnog [2024-10-31 23:35:32] deepnog.client.client - INFO - Loading NN-parameters from /home/arghya.mukherjee/deepnog_data/cog2020/1/deepnog.pth ... [2024-10-31 23:35:32] deepnog.client.client - INFO - Accessing dataset from test-temp/contig_1-test.faa ... [2024-10-31 23:35:32] deepnog.client.client - INFO - Starting protein sequence group/family inference ... [2024-10-31 23:35:32] deepnog.learning.inference - INFO - Inference device: cpu deepnog inference: 273seq [00:05, 47.4seq/s] [2024-10-31 23:35:38] deepnog.learning.inference - INFO - Inference complete. [2024-10-31 23:35:38] deepnog.client.client - INFO - Writing prediction to test-temp/contig_1-test_prediction_deepnog.csv [2024-10-31 23:35:38] deepnog.client.client - INFO - All done.
Deepnog prediction finished succesfully. Predictions saved as test-temp/contig_1-test_prediction_deepnog.csv
/data/Food/analysis/R1479_neurofoods/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 test-temp/contig_1-test_bands.kar created succesfully. Traceback (most recent call last): File "/data/Food/analysis/R1479_neurofoods/genovi/bin/genovi", line 8, in
sys.exit(main())
File "/data/Food/analysis/R1479_neurofoods/genovi/lib/python3.7/site-packages/scripts/GenoVi.py", line 685, in main
visualiseGenome(*get_args())
File "/data/Food/analysis/R1479_neurofoods/genovi/lib/python3.7/site-packages/scripts/GenoVi.py", line 369, in visualiseGenome
change_background("none", False)
File "/data/Food/analysis/R1479_neurofoods/genovi/lib/python3.7/site-packages/scripts/GenoVi.py", line 47, in change_background file = open(fileName)
FileNotFoundError: [Errno 2] No such file or directory: 'circos.svg'
The error is consistent for your input tests gbk or mine. I would really want to use the tool some help would be nice. Regards