Issue with pre-msa.bf

[lakshsesh97]

Hi,

I am trying to use the codon-msa pipeline to make my alignment more codon aware. I am encountering this issue when I run the pre-msa.bf it starts the analysis but then throws errors like below:

I am a bit confused with what to do in this case? my alignment is fairly short, it has 42 taxa with 201 nucleotides each.
I would really appreciate some help.

Thanks a bunch!

[spond]

Dear @lakshsesh97,

I have not seen this error before! Not sure what it indicates.
Would you mind sharing your input file and the command line you used to call pre-msa.bf?

You can either post them here, or email me at spond at temple dot edu

Best,
Sergei

[lakshsesh97]

Dear Sergei,
Thanks for getting back so quickly. I have emailed you yesterday with all the requested details.
Best,
Lakshmi

[spond]

Dear @lakshsesh97,

I was not able to locate your e-mail. Could you resend, or alternatively drop your files here: https://www.dropbox.com/request/8tvfcvj8R6yZLqbLN7Pq

Best,
Sergei

[lakshsesh97]

Dear Sergei,
I have uploaded the fasta file to the drop box. The command I used was: hyphy pre-msa.bf --input all.lin.fa

Thank,
Best,
Lakshmi

[spond]

Dear @lakshsesh97,

I think the error you see is because you are running pre-msa.bf using an older version of HyPhy (check with hyphy --version). Please update to a more recent version to resolve that particular issue. When I run your file with the current HyPhy build, I get the following

...
code: Universal
[Data QC] Loaded 42 sequences on 201 sites from **/Users/sergei/Dropbox/File requests/FUBAR alignment/all.fa**
Load reference sequences from : reference: /dev/null
Maximum acceptable fraction of N's (permissible range = [0,1], default value = 0.05): N-fraction: 1.0
[Data QC] Will write unaligned protein sequences for MSA to **/Users/sergei/Dropbox/File requests/FUBAR alignment/all.fa_protein.fas**, and the corresponding nucleotide sequences to **/Users/sergei/Dropbox/File requests/FUBAR alignment/all.fa_nuc.fas**
[Data QC] Found 0 unique sequences that were in frame
Error:
There were no sequences that were in frame and had no stop codons in call to assert(filter.longest_seq_L>0, error_msg);
...

Please check the input file to ensure that at least ONE sequence is in frame.

Best,
Sergei