Keyerror: taxonomy

[maracashay]

Hi everyone,

I am working with an ASV table from dada2 output in R. I did some data wrangling to make a 'taxonomy' column as similar as I could to the example asv table provided. I also changed 'ASV' to 'OTU' in case that was important. The taxonomy column in the ASV table looks like this:

|Vishniacozyma_victoriae|kFungi;pBasidiomycota;cTremellomycetes;oTremellales;fBulleribasidiaceae;gVishniacozyma;s__victoriae

Here is the error message: FUNGuild % python FUNGuild.py taxa -otu /Users/maraslaptop/Downloads/Fungal-Steam-ASV-Table.txt -format tsv -column taxonomy -classifier unite Taxa parser initiated. Loading OTU table: /Users/maraslaptop/Downloads/Fungal-Steam-ASV-Table.txt Table format: tsv Taxonomic column: taxonomy Taxonomic style: unite Traceback (most recent call last): File "/opt/anaconda3/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 2897, in get_loc return self._engine.get_loc(key) File "pandas/_libs/index.pyx", line 107, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/index.pyx", line 131, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/hashtable_class_helper.pxi", line 1607, in pandas._libs.hashtable.PyObjectHashTable.get_item File "pandas/_libs/hashtable_class_helper.pxi", line 1614, in pandas._libs.hashtable.PyObjectHashTable.get_item KeyError: 'taxonomy'

I'm attaching a shortened version of my asv file. Fungal-ASV-Funguild.txt

[sandipansamaddar]

Hi, I am trying to format the dada2 ASV table to a format which is supported by FUNGuild but I am unable to do it. Can you please help me with that? I can also try after that to see if I get same error while running FUNGuild.

Thanks,

Sandipan

[ZeweiSong]

Can you specify the error you encountered? Please also provide with us the format you are using.

Zewei

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From: Sandipan @.> Sent: 2021年6月22日 5:23 To: @.> Cc: @.***> Subject: Re: [UMNFuN/FUNGuild] Keyerror: taxonomy (#56)

Hi, I am trying to format the dada2 ASV table to a format which is supported by FUNGuild but I am unable to do it. Can you please help me with that? I can also try after that to see if I get same error while running FUNGuild.

Thanks,

Sandipan

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://apac01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FUMNFuN%2FFUNGuild%2Fissues%2F56%23issuecomment-865354424&data=04%7C01%7C%7Cf93978290fa046adbee608d934fad442%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637599074170979166%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=3Xhrbn%2B7jrgMmQkLFc906fxsa7B7MPyp0LbbZEqwW6E%3D&reserved=0, or unsubscribehttps://apac01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAB3EDWZ7M3EHYECPC7DR653TT6UVPANCNFSM43KZB46Q&data=04%7C01%7C%7Cf93978290fa046adbee608d934fad442%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637599074170989126%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=ULMdHIREvNSPG8I%2Ft1c9eZ2hjUiVpowzh0DpQZ31ziU%3D&reserved=0.

[sandipansamaddar]

Hi Zewei, I didnot try funguild yet. I just outputted the ASV table (attached) from dada2 and want to format it as an input for Funguild. So I am wondering can I get some help on how to format a normal ASV table to a funguild format? After I have that file I will try Funguild and can let you know fi that works.

Thanks and any help will be appreciated.

Thanks again. dada2ASVtable.xlsx

Sandipan

[ZeweiSong]

There is an example table file in the “example/” folder for your reference. Take a look and make sure your taxonomic string is in the right format (usually we follow UNITE).

Cheers,

Zewei

-- 宋泽伟 Zewei Song 华大生命科学研究院 宏基因组研究所 BGI-Shenzhen Institute of Metagenomics 电话 Tel: +86 13632929180 邮件 Email: @. 邮件 Email: @.

发件人: Sandipan @.> 发送时间: Friday, June 25, 2021 3:20 AM 收件人: @.> 抄送: Zewei @.>; @.> 主题: Re: [UMNFuN/FUNGuild] Keyerror: taxonomy (#56)

Hi Zewei, I didnot try funguild yet. I just outputted the ASV table (attached) from dada2 and want to format it as an input for Funguild. So I am wondering can I get some help on how to format a normal ASV table to a funguild format? After I have that file I will try Funguild and can let you know fi that works.

Thanks and any help will be appreciated.

Thanks again. dada2ASVtable.xlsxhttps://apac01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FUMNFuN%2FFUNGuild%2Ffiles%2F6711640%2Fdada2ASVtable.xlsx&data=04%7C01%7C%7Cb0f21eaf2c1f4983b36b08d937450e12%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637601591993297036%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=yoww57SRG%2BzLT3Izm44nPBp0XECE%2FdI2lBKI7Stttro%3D&reserved=0

Sandipan

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[merytouceda]

Hi! I had the same error as @maracashay here. Did anyone find a solution to it?