Submitting phage sequences to NCBI
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3.5 years ago

Hello, I'm trying to submit all genome sequences of phages with bankit, however I continue to have the same problem with the feature annotation.

>Feature ID                 
<974     >1096  CDS     
                                product hypothetical protein

<1376   >1825   1825    CDS     
                                product hypothetical protein

However I continue to have this error from ncbi: The following lines in the feature table have an incorrect format for nucleotide intervals How can I do a correct feature table? Thanks

ncbi sequencing • 1.1k views
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Ideally you should contact NCBI help desk since they can probably see what is going on with your submission and help.

Otherwise you will need to provide more detail than

I continue to have the same problem with the feature annotation

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I already altered the question, can you please help?

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Make you submission compliant with the required format

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I submitted in that format however, when I passed the table here, it lost the format

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If you continue having the error, then clearly there is a problem with your file. Check with e.g. cat -vet that the tabs are how they're supposed to be, and really go through your file line by line and make sure that it's compliant with the required format

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2.3 years ago
al-ash ▴ 200

I encountered a similar problem ("The following lines in the feature table have an incorrect format for nucleotide intervals") for features with ">" and "<" indicating incomplete genes.

Notably, I had tens of such incomplete features in my large batch submission and only two of the features were reported by BankIt as erroneous.

I did not identify anything specific to these features that should make them invalid (e.g. formatting problems as suggested above) so I defined manually that the two features are incomplete (via their web-based feature editing tool) and such revised features were accepted. Not elegant but perhaps acceptable workaround when the number of "erroneous" features is very low.

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