Queries regarding -megax(Multiplesequencealignment tool)

Question

[asharuthra]

Hi people!

I am newbie in Bioinformatics. I have problem in doing multiple sequence alignment of my genome sequences in megax tool. My genome size is 2.8 Mbp, when I tried aligning three sequences using muscle alignment option (default parameter) in megax.

I got the following error

Error Alignment failed: Muscle logfile didn't end properly, suggesting an unhandled exception.

I also tried doing multiple sequence alignment using other option like clustal W, but nothing worked as I expected. I have no idea how to rectify this error. Can someone help me to figure out this problem?

[griffinwhy]

Did you ever figure out what was wrong? I got the exact same error and this is the only question about this error on the internet.

Answer 1

[griffinwhy]

Did you ever figure out what was wrong? I got the exact same error and this is the only question about this error on the internet.

[s.labuschagne96]

I am also getting this error, did you manage to figure it out? No matter the number of sequences I run, I still get the error!

[kittychase13]

I am also getting that error every time, no matter how many sequences or length. Any help?

Answer 2

[s.labuschagne96]

The only thing I know is it has something to do with your computer running out of RAM while doing the alignment. I just used less sequences to fix the problem, my computer didnt seem to be able to go past 500. I know some people just deleted things and made sure there was enough space and tried again.