Welcome to the MapMan Family of Software Forum

Please do not hesitate to register and post your question.

Don't forget to subscribe to your posted message so you get notified on updates.
Every question you post will help others and or enhance the software!

Post a question,   post a bug!

Welcome to the MapMen Family of Software Forum Welcome to the MapMen Family of Software Forum

MapMan Bugs

RE: FATAL ERROR: The input contains both nucleotide and protein sequences.

FATAL ERROR: The input contains both nucleotide and protein sequences.
error message proteins
Answer
1/20/17 5:20 PM
Hello!

I have submitted a job to Mercator (Mercator26d0193ce6a1fc05b1aa30c4e58e6fbd). I was trying to annotate the protein fasta file, but It failed with the following error message.

: FATAL ERROR: The input contains both nucleotide and protein sequences. Please make sure the input only contains data of a single type. Number of sequence types found in input: Protein : 171596 Nucleotide: null Ambigous nucleotides: 3

I have checked all the document but I could not see these ambiguos nucleotides.

Thanks for your help.

Best,
Monica

RE: FATAL ERROR: The input contains both nucleotide and protein sequences.
Answer
1/23/17 8:18 AM as a reply to Monica Escandon.
Hi Monica,

You can validate your fasta file using this tool:-

http://www.plabipd.de/portal/mercator-fasta-validator

It will give you a list of 'Mercator invalid' records and also allow you to generate a fasa file with the invalid records removed.

Regards

RE: FATAL ERROR: The input contains both nucleotide and protein sequences.
Answer
1/23/17 12:30 PM as a reply to Marie Bolger.
Hi Marie,


I validated my fasta file using the tool that you recomend me. The file was valid for Mercator according to this tool.
Mercator Fasta Validator Message : ""The fasta file contained 171599 records. 171599 were valid for Mercator""

Even so, I created a Mercator-valid Fasta file with this tool. I tried to run this file in Mercator but this new file gave the same error (3 ambigous nucleotides) that the previous one.

FATAL ERROR: The input contains both nucleotide and protein sequences. Please make sure the input only contains data of a single type. Number of sequence types found in input: Protein : 171596 Nucleotide: null Ambigous nucleotides: 3

How could I solve that?

Thanks for your help,

Monica

RE: FATAL ERROR: The input contains both nucleotide and protein sequences.
Answer
1/23/17 12:58 PM as a reply to Monica Escandon.
Hi Monica.

I have just check the sequences, and it seems that there are three records in your fasta file which are causing Mercator an issue:-

Contig_24728_5_2
Contig_33058_6_16
Contig_58322_6_1

Although these are indeed valid protein sequences, the mercator tool has determined that they are valid 'AMBIGUOUS NUCLEOTIDES' and therefore becomes confused as it believes that there are two different types of sequences in the fasta file.

This is a Mercator bug which is currently been worked on, but if you could manage without these three records then I would advise removing them (or I can send you the file with them removed) for now. I can inform you when this bug has been fixed.
Sorry for the inconvenience.

RE: FATAL ERROR: The input contains both nucleotide and protein sequences.
i
Answer
1/23/17 2:10 PM as a reply to Marie Bolger.
Thanks for your quick reply Marie.
I could manage without these three records.

I have another Mercator job (GeneralMercator4f61abb3310679e7ddb81b2eaf64b205) with the same fatal error (Ambigous nucleotides: 2). Could you say me which are the ambigous records?


I look forward to hearing from you when this bug has been fixed.

Thank you again for the information.

Monica