Loading Fasta Failed: Expected sequence of length 29866 instead of 29885 for taxon ......

[PRINCE KUMAR SAH]

Hi all,

My name is Prince Kumar Sah. I am a new BEAST user.

While loading my fasta file in beauti, I get this error: "Loading of 10.sequence.fasta failed: Expected sequence of length 29866 instead of 29885 for taxon hCoV-19/India/HR-MDU-IGIB1210607500611313/2022". 

I have attached my fasta file which I downloaded from GISAID with this mail and also picture of the Message I got from Beauti.

Thank You in Advance.

link to fasta file

[Pawan Kr. Gupta]

Hi, Prince 

Try converting FASTA format to .nex ( nexus file) using MEGA and then try to load the file. 

I believe this might resolve the problem. 

Thank you 

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[PRINCE KUMAR SAH]

Thank You for your help. 

But sequences length are not equal. I tried to convert it but it shows sequence must be same length. The data is downloaded from GISAID.

Can I delete the N values of the sequence to match the length of the sequence. But, here also, the problem if I have 5000 sequence then how will I do the same? 

[Pawan Kr. Gupta]

You should align the sequence 1st 

Using MEGA. 

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[Pawan Kr. Gupta]

Hi, prince 

For alignment you can use online tools also 

Like MUSCLE or MAFFT

[Jordan Douglas]

Hi Prince,

Yes, you'll need to align the genomes first. In the case of covid genomes, I recommend you make the alignments with NextAlign

https://docs.nextstrain.org/projects/nextclade/en/stable/user/nextalign-cli.html

It takes a little more work to get it installed than MAFFT or MUSCLE for example, but it generates much more high quality alignments, which don't need as much manual correction, and also runs a lot faster (by incorporating known information about the viral genome)

Jordan

[PRINCE KUMAR SAH]

Thanks, Jordan, the Nextalign thing works. 

Thanks, Pawan for your help. 

[PRINCE KUMAR SAH]

Hello,

I have one more question. How to add lineages and clade information in the Tree which we get from FigTree after many steps. 

Thank You, in Advance.

On Friday, 8 July 2022 at 02:00:58 UTC+5:30 Jordan Douglas wrote:

[Omar Mejía]

You can load the sequences in seaview, align and export as Nexus file

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