Link to this post | posted 11 Mar, 2019 16:34
cristian2	Hi, I am trying to make a genome comparison to calculate the ANI values, but when I run the analyses DNA Master shows a warning message "pair analysis exception". Could someone please help me with this error?? Thanks in advance Cristian

Link to this post | posted 11 Mar, 2019 19:07
cdshaffer	cristian, I have my students use this online tool for ANI calculations, sorry it doesn't answer your question but a work around is better than nothing: http://enve-omics.ce.gatech.edu/ani/

Link to this post | posted 11 Mar, 2019 19:22
scaruso	Christian, We use that one as well, and also OrthoANI, here: https://www.ezbiocloud.net/tools https://www.ezbiocloud.net/tools/ani Steve

Link to this post | posted 11 Mar, 2019 21:51
cristian2	Thanks cdshaffer and Steven, I need to compare 80 genomes all-vs-all to build a double entry matriz with the ANI values. Do you know if these programs are suitable for this task? Thanks!! Cristian.-

Link to this post | posted 11 Mar, 2019 22:40
scaruso	I know you can run OrthoANI as a stand alone program and do so. I let Ivan do that, though, since it's command line. The GUI based one has a limit of 10 genomes. It didn't seem to be particularly challenging for him. Might give him a shout if you run into any trouble. Steve

Link to this post | posted 13 Mar, 2019 11:21
cristian2	Thank you very much Steven. I ran the stand alone version of OrthoANI without any problem. The only thing is that some value of ANI was -1.0 (negative).Do you know what could be the reason? Thank you again

Link to this post | posted 13 Mar, 2019 16:24
scaruso	I don't know. I wouldn't be surprised it that wasn't an error code or below the measurable threshold code, but I don't know offhand, I'm afraid.

Link to this post | posted 13 Mar, 2019 16:34
welkin	Hi Cristian, I've never seen the error that you are describing, but I can tell you that I've had difficulty performing simultaneous comparisons with 80 phages. I had to do it in smaller chunks (like 20 at a time) and then collect the answers in a spreadsheet. So it is possible you are maxing it out. Best, Welkin

Link to this post | posted 13 Mar, 2019 18:54
cristian2	Thanks Steven and Welkin, I have tried to compare with a set of 20 phages and the negative values was still there. Then I ran the online version of the program with the sequences of two phages with -1.0% ANI and the result was the same. I don`t know what is the problem with these phages.. Thanks! Cristian.-

Link to this post | posted 03 Dec, 2020 01:10

anders

Hi, I'm having new problems with Genome Comparison in DNA Master. When I use it to look at map comparison and ANIs, the results show zero alignments were found: every gene in the map comparison is black and all the ANIs read 0.000. Genomes previously analyzed are fine, as if the results had been stored. But adding new genomes for analysis throws "File read" and "FASTA error" warnings. I found that this problem does not happen when I use an older version (5.23.3, build 2657), which is the current state of DNA Master on most of our lab computers because we didn't use DNA Master in class this fall. But when a lab computer version gets updated (now 5.23.6, build 2674), the above problem is recreated. I know that doing a fresh installation on my home computer does not help, and I have confirmed the Watson release code is set in preferences. Are there any other troubleshooting things I can do, or is something broken in the most recent update? thanks, Kirk