Hello all,

 I am new to UGENE. I've tried running a 5000 sequence alignment using MUSCLE. Somewhere in the process I end up with this error:

[ERROR][13:50] Task {MUSCLE align 'KS_in_cluster.aln'} finished with error: Subtask {Workflow wrapper 'MUSCLE align 'KS_in_cluster.aln''} is failed: Subtask {Run workflow: align} is failed: Subtask {Read document: 'Co6348.fasta'} is failed: Document is empty.

I've tried this on three computers OS X running Lion on a MacBook Air, and two separate Windows 7 machines (32 bit and 64 bit).

In UGENE I open the fasta file and then export as an alignment file. I've tried both the fasta format and clustalw format. I end up with the same error.

I ran a smaller subset of the sequences and it aligned with no problem.

I was wondering if this error message means by original fasta in not formatted correctly somewhere in the file.

Thanks!
ara

Thanks for the report!

It has nothing to do with your file's format it's just our internal error.
I've created an issue in our bug-tracker(https://ugene.unipro.ru/tracker/browse/UGENE-854) and it will be fixed asap in the next versions of UGENE.

If you have other problems using UGENE, please, feel free to contact us.