File upload issue

[cmariencheck]

Hi,

Apologies if this post is repetitive or unclear. I am having some issues getting Datamonkey to work with uploaded files. When I upload an aligned file, even after checking for and fixing split codons in any sequence, I keep getting the message that "an unexpected error occurred when parsing the sequence alignment!" I have used Datamonkey a bit in the past and have never run into this issue, so I am confused as to how to go about resolving this issue if it's an error with the file I'm uploading.

Thanks!

[spond]

Dear @cmariencheck,

My guess is that HyPhy doesn't recognize the sequence format / alignment following editing. Would you mind sharing the file you are trying to upload so I can take a quick look? Can also e-mail it to me if you don't feel comfortable posting the file here.

Best, Sergei

[cmariencheck]

@spond
Of course, here it is attached. Thank you so much for your help! TLR7_24_aligned_tree_edited.txt

[spond]

Dear @cmariencheck,

The tool that generated your NEXUS file did a very poor job of it. For example, it misstates the length of the sequences as 75624 but in reality they are 3150 (this prevents HyPhy from reading the file correctly)

BEGIN CHARACTERS; 
    DIMENSIONS NCHAR = 75624;
    FORMAT 
        DATATYPE = DNA 

        GAP=- 
        MISSING=N

In addition, the DATA block is missing a ; at the end of the matrix and the END; statement at the end of DATA. It mixes up TAXA and CHARACTERS blocks (see https://plewis.github.io/nexus/)

In other words, this is a severely broken NEXUS file. You may want to follow up with the data generators. I attached a version in FASTA format that you should be able to use.,

Best, Sergei

TLR7_24_aligned_tree_edited.fas.txt

[cmariencheck]

@spond Thank you so much for this help--I will look into using a different tool for the future.

[cmariencheck]

@spond

I went through the file you attached and tried to upload it to HyPhy, but got a new/different error message (see text file attached). It says that there is an issue with leaf and sequence names matching, but I went through the file myself and the names all seem to match, so I am unsure of where to go from here. log (1).txt

Thank you again for your help!

[spond]

Dear @cmariencheck,

Ah, I missed one more NEXUS issue. The species 12 is mapped to a non-existent taxon (Cercocebus_torquatus_atys). Try the attached .fas

TLR7_24_aligned_tree_edited.fas.txt

Best, Sergei

[cmariencheck]

Oh I see it now. Thank you so much!

[spond]

Dear @cmariencheck,

No problem. I am glad you brought this to my attention because HyPhy was crashing (ungracefully) on the NEXUS example (malformed as it may be) you sent me!

Best, Sergei