veg/hivtrace

The results included the distances between sequence and itself

Closed this issue · 4 comments

Huanchang-Yan commented

Dear @stevenweaver ,

Hello.

I ran the following command line without any error reported:

hivtrace -i XX.fasta -a resolve -r HXB2_pol -t .015 -m 500 -g .05

However, the results in the csv file included the distance between every sequence and itself.

When viewing the JSON file, it failed.
捕获

The fasta file includes 66 sequences without any duplicates.

I have no clue so I am writing to ask for your favor.

Many thanks.

Best wishes,
Huanchang

spond commented

Dear @Huanchang-Yan,

This behavior simply means that you have no clusters in your dataset. The visualization module is showing you an empty network. Switch over to the Statistics tab and confirm.

Best,
Sergei

Huanchang-Yan commented

Dear @spond ,

Thanks for your response.

Actually, there are some pairwise distances below the threshold of 0.015.
I think, the failure of the network visualization might be due to the results that contains pairwise distance between every sequence and itself, just like this in output.csv:
1 (2)
Also, I tried other methods such as Hyphy and MicrobeTrace, and used the same threshold, and I did find some clusters. But I have no clue to get it correctly in HIVTRACE.

Best wishes,
Huanchang

spond commented

Dear @Huanchang-Yan,

Would you mind sharing the JSON file produced by HIV-TRACE? You can e-mail it to me (spond.at.temple.edu)

Best,
Sergei

Huanchang-Yan commented

Dear @spond ,

Just now, I tried to load the file on https://veg.github.io/hivtrace-viz/ instead of using the command hivtrace_viz <path_to_json_file>, and then it worked well.

Thank you a lot.

Best wishes,
Huanchang