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Importing Mothur into Phyloseqs cons.taxonomy error

Hi Everyone, I really want to use phyloseq to analyze and visualize my mothur 16s data but I cannot get the taxonomy file to import. I am using this tutorial: https://github.com/AndresICM/16S_metabarcoding_phyloseq

 sharedfile="/fwmay/fwmay_comp.opti_mcc.shared"
 taxfile="/fwmay/fwmay_comp.opti_mcc.0.03.cons.taxonomy"
mothur_data <- import_mothur(mothur_shared_file = sharedfile, mothur_constaxonomy_file = taxfile)

and I get this error:

Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  : 
  line 146 did not have 3 elements

I have checked and I see no errors in the cons.taxonomy file and I am at a loss. I am really struggling to get this to work for my analysis. Any help would be greatly appreciated

mothur phyloseq 16s
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updated by GenoMax GenoMax • written by jahlen.pinelo • jahlen.pinelo

Hi,

Can you open your taxonomy file (/fwmay/fwmay_comp.opti_mcc.0.03.cons.taxonomy) in Excel or similar and look around the line number 146 and see what differs from the above lines. If you want you can print the result of that here. The error suggests that in line number 146 the number of elements (columns) differs from the previous rows.

Best,

António

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written by antonioggsousa antonioggsousa

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