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mtisza1 / Cenote-Taker2

Cenote-Taker2: Discover and Annotate Divergent Viral Contigs (Please use Cenote-Taker 3 instead)
MIT License
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Unable to reproduce results of your test contigs example #27

Closed eul2021 closed 1 year ago

eul2021 commented 2 years ago

Hi Mike,

I'm having difficulties reproducing your test contig example. For instance, annotation for end features is missing for the contigs. Could you please provide what the output should look like at default or recommended for this test case parameters? Also, any tips on troubleshooting/debugging it would be helpful.

Thank you very much.

mtisza1 commented 2 years ago

Hi eul2021,

Thanks for reaching out. Did you see the wiki with the visualization of the test contigs? (you can open the .gbf files with Ugene or snapgene viewer or any other plasmid/genome map viewer).

If things are still not looking right, please run the test contigs and send me the log and the zipped output directory:

conda activate cenote-taker2_env
cd Cenote-Taker2
python run_cenote-taker2.py -c testcontigs_DNA_ct2.fasta -r test_DNA_ct -p True -m 32 -t 32 2>&1 | tee test_output.log