General Category >> Help and How-to >> Reads de novo assembly with CAP3

Message started by andr_ on Jan 25th, 2023 at 9:49pm

Title: Reads de novo assembly with CAP3
Post by andr_ on Jan 25th, 2023 at 9:49pm
I exported reads mapped in the BAM files as a FASTQ archive and tried to de novo assembly the reads using CAP3 o UGENE, but it always results in this error

'CAP3 run and open result task' task failed: Subtask {Loading documents} is failed: Subtask {Opening view for document: Trma-DQBreads.cap.ace} is failed: Subtask {Adding document to project: Trma-DQBreads.cap.ace} is failed: Subtask {ACE file import: Trma-DQBreads.cap.ace} is failed: Subtask {Convert ACE to UGENE database (Trma-DQBreads.cap.ace)} is failed: A name is duplicated: 20247412Document was removed

Not sure what name is duplicated and how it would be so.

Title: Re: Reads de novo assembly with CAP3
Post by Dmitrii Sukhomlinov on Jan 27th, 2023 at 12:31pm

This error message means, that your result ACE file contains several sequences with the same name "20247412". Unfortunately, the current version of UGENE doesn't support ACE format with same-name sequences, so the only solution I can suggest you is to fix these names in the FASTQ file they were inherited from. So:
1. Open your input FASTQ file in some text editor (Notepad, Notepad++, etc.).
2. Find "20247412" in this file using the context search (Ctrl + F).
3. Rename it (e.g. to "20247412_2").
4. Do "CAP3" alignment again.
5. If you have the error like " A name is duplicated: %NAME% Document was removed" again repeat steps 1-4, but with the sequence name %NAME%.

I have created an issue in our bug-tracking system ( about it and we will fix it as soon as we can.

Best regards,
Dmitrii Sukhomlinov,
The UGENE team.

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