Question: ANI calculation: alternatives to Jspecies
0
gravatar for fhsantanna
5.8 years ago by
fhsantanna520
Brazil
fhsantanna520 wrote:

I am trying to calculate ANI values (ANIm and ANIb) using Jspecies in Ubuntu 14.04.

For the majority of comparisons, Jspecies is not able to attribute a ANI value (instead it gives "nan" result). Funny is that sometimes it works well.

Here is the log when errors occur:

    [12:57]ERROR509909[Thread-11] - api.calculation.anim.RunANIm.calculateEMA(RunANIm.java:75) - .cluster file doesn't exist # seems to be related to nucmer
    [12:58]ERROR580395[Thread-11] - api.calculation.blast.FormatDB.runFormatDB(FormatDB.java:61) - [formatdb] FATAL ERROR: Database base name must be provided with multiple input files

Do you know an alternative software to jspecies?

Thanks.

 

 

ani jspecies • 6.1k views
ADD COMMENTlink modified 5.1 years ago by aleimba130 • written 5.8 years ago by fhsantanna520
1

I discovered this http://jspecies.ribohost.com/jspeciesws/

Apparently they moved on the web. Maybe it can help you.

ADD REPLYlink written 5.8 years ago by dago2.6k

Great! Thank you very much. I am going to give it a try.

ADD REPLYlink written 5.8 years ago by fhsantanna520

Let me understand, you submit different file in Jspecies and sometimes it works and sometimes not. Is that right?

ADD REPLYlink written 5.8 years ago by dago2.6k

Yes. I was not able to figure out what is the problem. Maybe it is a incompatibility with the new version of blast, because when I utilize an script for ani calculation, blast crashes sometimes...

ADD REPLYlink written 5.8 years ago by fhsantanna520

I had a similar problem. Are you in Linux system? Did you import the files from windows? Which blast version are you using?
 

ADD REPLYlink written 5.8 years ago by dago2.6k

Yes, I am using Linux (Ubuntu 14.04). No, I didn' t import files from windows. Blastall version 2.2.26.

ADD REPLYlink written 5.8 years ago by fhsantanna520
1

If I am not wrong ANIm uses mummer, does mummer work in your system? for the formatdb error, maybe it does not like the Ids of you seqs. You could give it a tray using one string, no space, only alphanumeric characters e.g. > MYSEQUENCE

ADD REPLYlink modified 5.8 years ago • written 5.8 years ago by dago2.6k
5
gravatar for aleimba
5.1 years ago by
aleimba130
Germany
aleimba130 wrote:

An alternative that I can highly recommend is pyani from Leighton Pritchard. No GUI just command-line, but that was one of the major drawbacks of the Java JSpecies anyway. Therefore, pyani can handle lots of microbial genomes at once.

https://github.com/widdowquinn/pyani

Additionally, pyani can also create heatmap diagrams corresponding to the ANI or Tetra values with a hierarchical clustering of the results (with additional QC graphics).

pyani relies heavily on some very common Python libraries and R or matplotlib for graphical output, but most bioinformaticians will have these installed anyway.

ADD COMMENTlink modified 5.1 years ago • written 5.1 years ago by aleimba130
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