Dear Mauve users,
I am trying to export orthologs from an alignment of annotated genomes.
Mauve created 2 files (one that is a “file”-type and the other is
“ALIGNMENTS file”-type). Initially both files were at 0 kb but after a
while, the size of the “file” was a few kb. The “alignments file” remained
at 0 kb.
I tried to open the “file” with Mauve and it did not work. I then opened it
with Notepad ++ and got something like this:
0:SSYM_0331:192-500
0:SSYM_0332:688-1260
0:SSYM_0333:1404-2648
0:SSYM_0334:3163-4237
0:SSYM_0335:4601-5191
0:SSYM_0336:5188-6592
0:SSYM_0337:6719-7558
0:SSYM_0338:7630-8672
0:SSYM_0339:8968-9834
0:SSYM_0340:10253-11707
0:SSYM_0341:12211-12429
0:SSYM_0342:12419-13231
0:SSYM_0343:13449-15235
0:SSYM_0344:16874-17467
0:SSYM_0345:17589-17780
0:SSYM_0346:17911-18615
0:SSYM_0347:20504-21223
0:SSYM_0348:21228-22829
0:SSYM_0349:23497-23829
0:SSYM_0350:24012-24305
0:SSYM_0351:24684-26492
0:SSYM_0352:26495-27259
0:SSYM_0353:29758-30390
0:SSYM_0354:30625-30966
0:SSYM_0355:31256-31672
0:SSYM_0356:31669-31899
0:SSYM_0357:32576-32881
0:SSYM_0358:33551-33643
0:SSYM_0359:33660-34304
0:SSYM_0360:34478-34669
0:SSYM_0361:34874-35128
0:SSYM_0362:35125-35547
0:SSYM_0363:35612-36505
0:SSYM_0364:36702-37955
I have no idea what this means!
My biggest concern is that the software doesn’t tell me about the progress
of the work on the exportation of orthologs (the console doesn’t show
anything like when it created the alignment). Thus, I have no idea how much
time I should wait before checking those files. I also have no idea of how
the information should look like when orthologs are exported correctly.
So I would like to ask you: is there a way to check the progress of Mauve?
How do I know when it is done exporting? Also: how should I open the files
created (with Mauve or with any text editor)? Last but not least: how can I
know if Mauve works correctly on this or if it has problems with the
exportation?
Any help is highly appreciated.
Thanks much,
Alina
--
Alina Grigorescu, PhD
[email protected]
[email protected]
Postodctoral Researcher
Centre Wallon de Biologie Industrielle
Universite de Liege
Sart-Tilman, B40
Tel: +3243663997
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