UMNFuN
commented
2 years ago Chris:
Sorry about the delay - Could you please send me the taxonomy column from your file.
Scott T. Bates, PhD @.***
From: cpbivins28 @.> Sent: Thursday, December 2, 2021 6:10 PM To: UMNFuN/FUNGuild @.> Cc: Subscribed @.***> Subject: [UMNFuN/FUNGuild] Seems like I should be getting way more OTU guild assignments (Issue #60)
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I'm trying to use Funguild to make guild assignments to an OTU table generated from NEON soil metabarcoding sequences. I've got a csv containing 22,709 OTUs, with their taxonomy specified all the way to at least the genus level. Many of these OTUs represent species whose functional guild is obvious (i.e. Amanita should be ectomycorrhizal). However, when I run the csv through the Funguild python script, I only get assignments made on 118 OTUs. When I examine the new file with the 118 guild assignments made, I notice that there are zero assignments for any of them being ectomycorrhizal, which to me is a red flag that something is not working correctly as there are a number of OTUs in the table that are obviously ectomycorrhizal genera/species. The python script is working, as it's accessing the csv and is making functional guild assignments... but it is nowhere near close to making assignments on enough of the OTUs in the csv.
Can anyone help me resolve this issue? I know I have not included a ton of information here, so please kindly let me know what other info you might need to better understand the issue.
Thanks so much in advance for your time and consideration!
-Chris
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I'm trying to use Funguild to make guild assignments to an OTU table generated from NEON soil metabarcoding sequences. I've got a csv containing 22,709 OTUs, with their taxonomy specified all the way to at least the genus level. Many of these OTUs represent species whose functional guild is obvious (i.e. Amanita should be ectomycorrhizal). However, when I run the csv through the Funguild python script, I only get assignments made on 118 OTUs. When I examine the new file with the 118 guild assignments made, I notice that there are zero assignments for any of them being ectomycorrhizal, which to me is a red flag that something is not working correctly as there are a number of OTUs in the table that are obviously ectomycorrhizal genera/species. The python script is working, as it's accessing the csv and is making functional guild assignments... but it is nowhere near close to making assignments on enough of the OTUs in the csv.
Can anyone help me resolve this issue? I know I have not included a ton of information here, so please kindly let me know what other info you might need to better understand the issue.
Thanks so much in advance for your time and consideration!
-Chris