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.

Hello,

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 (https://ugene.dev/tracker/browse/UGENE-7783) about it and we will fix it as soon as we can.

Best regards,
Dmitrii Sukhomlinov,
The UGENE team.