Amptk summarize ValueError: not enough values to unpack (expected 2, got 1) about amptk

[nextgenusfs]

The taxonomy string is not formatted the way it is expecting. Compare the taxonomy columns between your two results.

[Alenap26]

Hi thanks for your time, I compared the two files, but I really don't know where is the problem.
I'm attaching you an extract of the taxonomy column for both.

Taxonomy for the file that does't work:

Taxonomy
GS|98.9|JX036083|SH1553429.08FU;k:Fungi,p:Ascomycota,c:Lecanoromycetes,o:Lecanorales,f:Catillariaceae,g:Austrolecia
GS|98.8|JQ689430|NA;k:Fungi,p:Ascomycota,c:Sordariomycetes
GS|99.1|KJ576704|NA;k:Viridiplantae,p:Chlorophyta,c:Trebouxiophyceae,o:Trebouxiales,f:Trebouxiaceae,g:Trebouxia
GS|99.4|JX036043|SH1176515.08FU;k:Fungi,p:Ascomycota,c:Lecanoromycetes,o:Caliciales,f:Caliciaceae,g:Buellia
GS|98.9|JQ689440|NA;k:Fungi,p:Ascomycota,c:Sordariomycetes
GSL|100.0|AF353997|SH1646182.08FU;k:Fungi,p:Ascomycota,c:Sordariomycetes
US|0.8882|JX848589|NA;k:Fungi,p:Glomeromycota,c:Glomeromycetes,o:Diversisporales
GS|98.0|KY608888|NA;k:Fungi,p:Ascomycota,c:Dothideomycetes,o:Botryosphaeriales,f:Phyllostictaceae,g:Guignardia,s:Guignardia laricina
GS|100.0|MH660418|SH1566856.08FU;k:Fungi,p:Chytridiomycota,c:Spizellomycetes,o:Spizellomycetales,f:Powellomycetaceae,g:Powellomyces,s:Powellomyces hirtus
GS|99.5|KJ599551|NA;k:Viridiplantae,p:Chlorophyta,c:Trebouxiophyceae,o:Trebouxiales,f:Trebouxiaceae,g:Trebouxia
US|0.9426|AB219231|NA;k:Fungi,p:Ascomycota,c:Sordariomycetes

Taxonomy for the file that works:

Taxonomy
SS|0.8400|None;d:Bacteria
SS|0.8900|None;d:Bacteria
SS|1.0000|DQ422812_S001020357;d:Bacteria,p:Cyanobacteria/Chloroplast
SS|0.9300|None;d:Bacteria
GS|98.4|KF245634_S003920711;d:Bacteria,p:"Acidobacteria",c:Acidobacteria_Gp4,o:Aridibacter;
SS|1.0000|KC560021_S003719248;d:Bacteria,p:"Bacteroidetes",c:Sphingobacteriia,o:"Sphingobacteriales",f:Chitinophagaceae
SS|0.9500|KF459924_S004053537;d:Bacteria,p:"Actinobacteria",c:Actinobacteria,o:Rubrobacteridae,f:Solirubrobacterales
SS|1.0000|None;d:Bacteria

[nextgenusfs]

The error says there is a taxonomy string that doesn’t have a colon separating the taxonomy level from the name. Looks like might be a single or a few strings that are causing the problem. Are there any that are empty?

[Alenap26]

Hi,
No one raw is empty, I also checked if same raw of column taxonomy dosen't have ":" necessary for the w.split(":"), but al raws have the ":"

[Alenap26]

Ok, If I do :

a=pd.read_csv(path+"miseq.otu_table.taxonomy.txt",sep="\t")
for i in a.Taxonomy:
    print(i.split(":")[0])
    print(i.split(":")[1])

I obtain the same error, I'm trying to fix the wrong raw ! But why these happened ? if I performed just the classic commands ?

[Alenap26]

Ok I fixed the problem adding ":Unknown" in the raw GDL|100.0|KY932470|NA;.
Now summarize works !

[nextgenusfs]

Is this the database packaged with AMPtk or one that you made? The taxonomy string in the fasta file used to create the database is the underlying problem.

[Alenap26]

Yes it is, I used the database packaged with AMPTK.

[nextgenusfs]

Okay. Let’s leave this open so I remember to fix the underlying issue as well as patch the code in summarize to not error out but alert user of which taxonomy strings are empty.

[nextgenusfs]

fixed in v1.4.1