Closed BenjaminGuinet closed 9 months ago
Hello Benjamin,
I hope you are doing great and thank you for reporting this !
I will have a look at this issue this week and get back to you ASAP.
Thank you for your patience !
Best, Antony
Hello Benjamin,
I hope you are doing great and thank you for your patience !
I ran a few tests on both an Ubuntu and a MacOS machine using the command you provided and each time haystac
ran to completion, so unfortunately I was not able to reproduce your error.
After looking into the error message you provided, it seems that this is a bgzip
/htslib
build related error. More specifically quoting the developers from https://github.com/samtools/htslib/issues/1684
Protocol not supported" ususally means htslib was built without libcurl. While this is possible to do, it generally causes more confusion downstream such as this, so it's best to get it building complete.
and from https://github.com/samtools/htslib/issues/1515
It looks like htslib has been compiled without finding a working copy of curl, so it has no access to fetching references via https. That'll be where the "Protocol not supported" line comes from.
Would you happen to be running haystac
on a Debian machine ?
Two possible solutions to that would be:
conda
to install all the dependencies needed by haystac
in the environment you are running the program from, and then run haystac config --use-conda False
to stop haystac
from using the incomplete build of samtools
installed in your cache directory. For that you can use this yaml file: https://github.com/antonisdim/haystac_paper/blob/main/performance_tests/environment.yaml haystac
cache directory '/home/grendel/haystac/cache/conda/e18f9b8a5c397a3d990a9b7c0a4d94ce'
, and do a full re-installation of samtools
with libcurl
included. I will keep looking into this in case a more explicit solution can be found. Of course please let me know if any of the above works, or if any other issues arise.
I hope this helps !
Best, Antony
Hello thanks for the reply, the first idea solved the issue. Thanks for your help. Benjamin
Dear Haystac developers, I tried to use Haystac on a cluster but unfortunately I got the following error message : "Protocol not supported" in the bgzip command part, do you have any idea what is going on please?
Here is the command I used (it is the same if I put Yersina).
haystac database --mode build --query '"Clostridium"[Organism] AND "complete genome"[All Fields]' --output Clostridium_db --cores 20
Thanks for your time.
Here are the messages :