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can't get ecoprimers to work
#1
I am trying to run ecoprimers, an after countless hours of trying to figure it out I am still at a loss. I have obitools installed and am trying to convert my sequences from fasta to ecopcrdb format with the code:
obiconvert --fasta --ecopcrdb-output=sequencesDB sequences.fast 

Then I get the error message:
TypeError: object of type 'NoneType' has no len()

How do I fix this? Any help is appreciated!
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#2
Hi hglass,

It's difficult to kwon exactly what is wrong with so few information. But at least there is one big mistake. For building an ecopcr or ecoprimer database you need taxonomically annotated sequences and a taxonomy database. I can't know if you have taxids associated to your fasta sequences but you are not specifying taxonomy.

You can have a look to this page for more explanations.

http://metabarcoding.org/IMG/html/primerdesign.html

all the best

Eric
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#3
(05-06-2016, 06:19 AM)coissac Wrote: Hi hglass,

It's difficult to kwon exactly what is wrong with so few information. But at least there is one big mistake. For building an ecopcr or ecoprimer database you need taxonomically annotated sequences and a taxonomy database. I can't know if you have taxids associated to your fasta sequences but you are not specifying taxonomy.

You can have a look to this page for more explanations.

  http://metabarcoding.org/IMG/html/primerdesign.html

all the best

Eric


Hi Eric,

I tried to follow the tutorial on the website you sent, but when I do the command 
wget 'ftp://ftp.ncbi.nlm.nih.gov/genomes/MITOCHONDRIA/Metazoa/*.gbk'
it says:
No such directory ‘genomes/MITOCHONDRIA/Metazoa’.

I ended up going directly to the NCBI genomes website and none of my species of interest are in the genomes folder anyways. I did manually look up the taxid's for the species and include them in the first line of the fast file, as you showed in the tutorial (>AC_000022 organism=Rattus norvegicus; taxid=10116; Rattus norvegicus strain Wistar mitochondrion, complete genome)
I tried to run obiconvert with the specific taxi's in the fastq file with the command: 
obiconvert --sanger --ecopcrdb-output=sequences sequences.fastq
But I still get the message "Exception: Taxonomy error for 1: taxonomy is missing"
How to I get around this problem? Is there another way to get a mitochondrial genome database that includes my species of interest? Thanks for your help!

Haley
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