Hi everyone,
i'm a new user of UGENE and i'm trying to use the CAP3 tool for contig assembly...

I've tryed many imput, fasta and multifasta, of different lenght but in any case the program give me this error after a few seconds:

'CAP3SupportTask' task failed: Subtask {CAP3 run task} is failed: CAP3 tool exited with code 1

and rarely this one:


'CAP3SupportTask' task failed: Subtask {Read document: '11t_c72.cap.ace'} is failed: Bad sequence data
Sent at 11:29 AM on




Thank you for any help you'll be able to provide me

we installed UGENE on two computer, one with windows XP and the other with windows 7 and on both systems we encountered the same problems...

We tryed with MIRA unpadded fasta output (that we usualy assemble with SeqMan software), to create test multifastas with small sequence overlapping, to create single fasta files etc... but nothing worked...

Unfortunately we aren't allowed to share our data but if you can give us a test multifasta we can try and give you feedback

Hi, I have the same problem.
The problem occurs in version 1.11.5 and also the latest 1.12 from the 16.6.2013.
@Konstantin: The file you attached worked for me, but my own sequencing results gave an error:

[ERROR][15:41] Task {CAP3SupportTask} finished with error: Subtask {Read document: 'test_new.cap.ace'} is failed: Bad sequence data

My sequencing results are attached, so you can test them. With another program SeqMan the reads were assembled nicely into a contig. So the file should be all right.

Hope this can be fixed!
Thomas