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De novo assembly (with CAP3) error (Read 240 times)
Oct 12th, 2023 at 1:27pm

Sunisa   Offline
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Hello!

I want to upload my fasta file to do contig assembly with CAP3 but it always show the error:  Subtask {Load document: 'HC00796079_ITS2_annotated.cap_1.ace'} is failed: There is no AF note.
What is AF note?
What should I fix this problem?

Thank you in advance!
 
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Reply #1 - Oct 12th, 2023 at 3:00pm

Dmitrii Sukhomlinov   Offline
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Hello,

This line means missing of special file part. The description from the ACE specification says:

AF <read name> <C or U> <padded start consensus position>

This line replaces the 'AssembledFrom*' line in the previous ace file
format. C or U means complemented or uncomplemented. The <read name>
is the true read name (no .comp on it as with the previous ace file
format.)

But, also, it could be, that the ACE file formats parsing algorihm has some problems, but we have never met the ACE file this problem could be reproduced. It would be great, if you send us your ACE file and we will try to figure the problem out. If this file is confedential, you can send it to ugene@unipro.ru - I can assume you, that we will not use this file anywhere but handling this problem.

Best regards,
Dmitrii Sukhomlinov,
The UGENE team.
 

Best regards,
Dmitrii Sukhomlinov,
The UGENE team.
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Reply #2 - Oct 13th, 2023 at 10:22am

Sunisa   Offline
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Hi Dmitrii Sukhomlinov,

Thank you very much for your reply!
Actually the file I upload is only fasta file but ACE file is created automatically, am I understand right?

I attached my fasta file and ACE file the was created automatically and also the capture of UGENE window.

Here is an error report:
[INFO][10:11] UGENE started
[INFO][10:11] UGENE version: 46.0 64-bit
[INFO][10:11] Starting {Check for updates} task
[INFO][10:11] Task {Check for updates} finished
[ERROR][10:12] Subtask {Load document: 'Sunisa_test.cap.ace'} is failed: There is no AF note
[ERROR][10:12] Task {CAP3 run and open result task} finished with error: Subtask {Loading documents} is failed: Subtask {Opening view for document: Sunisa_test.cap.ace} is failed: Subtask {Load document: 'Sunisa_test.cap.ace'} is failed: There is no AF note

Best regards,
Sunisa
 

Sunisa_test.fasta (1 KB | 12 )
Capture.JPG (40 KB | 10 )
Capture.JPG
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Reply #3 - Oct 13th, 2023 at 1:14pm

Dmitrii Sukhomlinov   Offline
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Russia

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Posts: 75
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Hello,

Thank you for you files. I investigated the problem - CAP3 produces the result file, which are not fully fit to the ACE format parcing algorithm, which is used in UGENE. Actually, the original problem is that the file, generated by CAP3 not fully fit to the ACE Format specification. Some ACE specification fragments could be interpreted in two ways and UGENE appeared to be not very flexible in these thin moments. THe general solution is, of cource, to fix the algorithm. We will do it, I hope, up to the closes release. If you are interested, you may watch the status of the task https://ugene.dev/tracker/browse/UGENE-7956

About you very case - I may suggest you to open you ACE file in some text editor (Notepad++, BBEdit or just any OS implemented editor) and that to fix some fragments of this file, which allow UGENE to open it:

- Find all lines started with "AF". The line after this line looks like " U 1" (in all places you see "AF"). The point is this " U 1" should be at the same line as "AF". So just remove the new line and all "AF"-start lines will look like "AF A U 1"
- Find all lines started with "RD". It has the same problem than "AF". Just remove the new line on the end of "RD" line.
- Find all lines started with "QA" and look at it. The filst appearens looks like "QA 1 327 1 327". Replace each large number (327, in this case) to "small number + 1". So, this line should look like "QA 1 2 1 2"

After you do that, you may open this file as Alignmetn or Assembly in UGENE. I attached the example of the fixed file, just compare this file to your if you doubt. I described the fixing mechanism in case you have another input data.

This is an importand bug, so wi will fix it as soon as we can. For now, please, just edit the result file on your own.

Best regards,
Dmitrii Sukhomlinov,
The UGENE team.
 

Best regards,
Dmitrii Sukhomlinov,
The UGENE team.
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