Closed Kelzor closed 3 years ago
Hello Kelly,
Thank you for using haystac
and apologies for the super delayed response !
I noticed that in your command you are using a query for the genus Yersinia, but in the haystac
output a query for the genus Mycobacterium pops up, which is odd.
Just in case I ran two database builds, one with Yersinia and one with Mycobacterium, and both of them were completed without any errors.
Would it be possible that you are using an output folder, that contains the outputs from a previous database you tried to build ? I did a test run for such a scenario but a validation error was raised.
It would be really helpful if you could please provide a few more details on how you tried to run this command. In the meantime I will try to reproduce the error you are getting, and of course update you if I come across the cause of the problem.
Let me know what you think and thank you for your help !
Best, Antony
Hello Kelly,
I hope you are doing great and apologies for the delayed response !
I actually managed to reproduce your error. It was caused due to an issue related to the latest version of snakemake
.
If you would like please follow the updated installation instructions, and install the latest version of haystac
through github
. Of course please do not hesitate to contact us if you face any new issues.
Thank you for all your patience !
Best, Antony
Hi, Antony!
Apologies for my delayed response too. I hadn't circled back to this yet. Great news!
To clarify, I should re-install haystac via mamba or conda, as stated on the github page?
Thanks, Kelly
Hello Kelly,
I hope you are doing great and apologies for the late response !
I have uploaded an executable on my personal conda
channel. Could you please install haystac
in a fresh conda
environment with the following command:
mamba install -c antonisdim haystac
Please let me know how it goes and thank you for your patience !
Best, Antony
Hello!
database --mode build fails for me with the following error. Snakemake doesn't successfully remove entrez-selected-seqs.tsv though, and the file seems to be intact. Also, the .snakemake directory and log are missing. I appreciate any suggestions for what could be mucking things up!
Thanks, Kelly