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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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Only detecting 3 test viruses, and no genbank output #3

Closed pck0 closed 3 years ago

pck0 commented 3 years ago

Hey all,

I've been trying to use cenote-taker2 and ran into an issue: When analysing the testcontigs_DNA_ct2.fasta file, I only get hits for 3 elements, and no genbank file output. As far as I can tell everything has been installed correctly, although there are somehow no template files in my folder. I can run the program without the template, which might be the reason I'm not getting any genbank files, but I can't imagine why the detection would fail.

Any idea what I might be doing wrong? I have attached a log file and my output folder cheers Paul

test.zip cenote_log.txt

mtisza1 commented 3 years ago

Hi Paul,

Thanks so much for raising this issue and including the log file. I was able to determine that fastpath/fastpathz, a dependency of PHANOTATE (phage ORF caller) was not found. I was under the impression that fastpath was installed with PHANOTATE, but perhaps not always. I've added fasthpath explicitly to the install script now, so hopefully this will prevent the error for other users.

For you, I believe the problem will be resolved with the following commands:

conda activate cenote-taker2_env
pip install fastpath

Please give it a try, rerun the test contigs, and let me know if you continue to have a problem.

Best,

Mike

Here's the portion of the log file that tipped me off:

Traceback (most recent call last): File "/stor/work/POD/paul/cenote_taker/Cenote-Taker2/PHANOTATE/phanotate.py", line 7, in import fastpathz as fz ModuleNotFoundError: No module named 'fastpathz'

pck0 commented 3 years ago

A-ha, that did it! And with a quickly generated generic template file I am also getting genbank files. Thanks so much!

mtisza1 commented 3 years ago

Also, I realized that you also asked about template files. I have resisted providing a "dummy" template file, as I'm hoping people will make their own, and this will make it a bit more likely that they will deposit some genomes in GenBank. I may change my mind in the future. But, for now, please make your own template file at: https://submit.ncbi.nlm.nih.gov/genbank/template/submission/

It just takes a couple minutes. Thank you!

mtisza1 commented 3 years ago

Oh, and I see you responded already while I was drafting that response!

I'm so glad it worked out. Please let me know of any more issues that might arise. I'll close this issue now.

Cheers,

Mike