Hello,
it is the second time that sequence and annotations can no more be openned in Ugene which displays this mesage in the Log :
[11:09][ERROR] Task {Load document: 'EZ no repeat Venus_copy1.gb'} finished with error: Record is truncated.
Lot of work lost.
Is there a way to rescues these files?
Thanks
Philippe
(by the way, I really like Ugene!)

Hi, Philippe.
Don't panic.


Quote:

Is there a way to rescues these files?

Of course it depends in what means "truncated" in this case, but you can manually inspect the files. You can just open this files with any text editor and try to see if the structure is correct (open a .gb from GenBank as reference). I you want, you can attach one of the corrupted files here to have a look.

> Is there a way to rescues these files?

Yes, genbank is a plain text file, so information is easily accessible with any text editor, as Agu already said.

Could you provide more details here:
1) was file UGENE fails to open created with UGENE?
2) could you share one the problem files with us, so we we can reproduce the problem locally?

Thank you very much for your answer.
Under Word one of the files has lost the sequence part and the other looks normal.
Files were initially serial cloner, then exported in genbank format and opened in Ugene, then cut, past, clone, delete, annotate etc etc

The files may not be rescued, but I would like to no reproduce this problem with all my Ugene annotation work

Thank you for your help

Philippe / Yunus
(Mohammad Yunus : Bangladeshi Nobel Peace Price who invented microcredit and more recently social buziness. Apparently a Great Man.
Such ideas could drag us-earthlings out of trouble)

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Ups, those are really truncated. Not much saved, one feature in the first file and two in the other...

Try to remember what was the las step before the crash (if any?) ant try to reproduce it. Is the only way to find the bug and fix it.

Just in case, in the panel on the left you can press right button on any modified document and select "Save selected documents".

Thanks for looking at.
Nothing special occured, apparently. But when I  someday tried to load the file, it was truncated. Incidentally, both files have a piece in common which was inserted using the "edit-replace/insert subsequence" function.

Philippe
(long life to Mohammad Yunus!)
8-)

Philippe,
could you please provide the initial file that you created with Serial Cloner?

I assume in UGENE you made a copy of it and then started to edit. Perhaps the copy wasn't saved properly due to some Genbank parser error. I tried creating some file in SC and then using in UGENE - and was unable to reproduce the bug.

Also, as Agu mentioned it would be very helpful if you repeat all the steps that lead to the truncation.

Dear Konstantin,

thanks for your help.

I imported a large BAC DNA genebank file and a plamid genebank file using Serial cloner (I could nod do it with Ugene, don't know why, probably my mistake since both files had different origins). Then I re-exported these files in Genbank format from SC. Then I imported in Ugene. I "cloned" a fragment of the plasmid into the BAC. I did a lot of annotation. I removed most of the BAC DNA using Edit/remove subsequence. Did some Restriction Enzyme search. Saved always using the "Save all" function and "save project as" function. One day, at the loading command of one file I had the "error truncation" message. Few days latter the same happened to another file which had been created the same way with another BAC file and the same plasmid file. We will see if all my Ugene files dye one by one...

plasmid SC file is attached. BAC file was rejected because too big

Cheers
Philippe
(Social business aims at providing a specific service to a selected population which really needs it (example : cheap safe yoghurt to be sold to poors of Bangladesh). Capitalistic and rational methods are used. Investors get their money back but make no profit. Sounds better than charity where nobody sees money back).
;D

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