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General Category >> Bugs and Issues >> problems with CAP3 assembler... not working!
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Message started by elmy on Oct 4th, 2012 at 4:31pm

Title: problems with CAP3 assembler... not working!
Post by elmy on Oct 4th, 2012 at 4:31pm
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 :)

Title: Re: problems with CAP3 assembler... not working!
Post by Yuriy Vaskin on Oct 4th, 2012 at 4:48pm
Hello,

thank you for the feedback.

CAP3 works on our test set. In your case it's something wrong with reading a temporary file of CAP3 output.

If it's possible to send us a file that causes the error it would be the fastest way to deal with that error.

Thanks in advance

Title: Re: problems with CAP3 assembler... not working!
Post by elmy on Oct 4th, 2012 at 4:58pm
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 :)


Title: Re: problems with CAP3 assembler... not working!
Post by Konstantin Okonechnikov on Oct 10th, 2012 at 3:41pm
Hi! Can you plz test attached files? It's a sample from MIRA package. It should work fine.

Also some questions:

- Do you have your data as multiple FASTA files or a single multifasta?
- Is it FASTA or FASTQ?
- How big is your data? (number of reads, typical read size)
https://forum.ugene.net/forum/YaBB.pl?action=downloadfile;file=U13small_m.fasta (27 KB | )

Title: Re: problems with CAP3 assembler... not working!
Post by randolf on Jun 20th, 2013 at 8:45pm
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

https://forum.ugene.net/forum/YaBB.pl?action=downloadfile;file=test_new.fa (2 KB | )

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