SEA-PHAGES | Corrupt DNAM5 File - Features not visible in table

Link to this post \| posted 02 Jun, 2020 21:29
GregFrederick@letu.edu	Hi all. I just ran into a DNA Master error that I've not seen in the five plus years we have been in the program. I searched the forums, but did not find a solution. PROBLEM: A newly saved DNAM5 file when reopened did not list the features in the feature table. The documentation appeared correct. I could see all the features listed correctly with coordinates and functions in the documentation. I went through the process described in the Annotation Guide to "Parse the Documentation". That is linked here: https://seaphagesbioinformatics.helpdocsonline.com/article-93 However, this did not resolve the problem on the original DNAM5 file. SOLUTION: I watched this video where Welkin Pope describes how to repair a corrupted DNAM5 file. https://vimeo.com/277487017 I went through all the steps that she included. When I opened the repacked file, I still could not see any features listed in the feature list. Then I went back to the documentation tab and could see the features listed there. One more reparse recreated the features in the feature tab. Now everything has been restored EXCEPT that the Blast Data appears to have been lost. There were two blast file in the directory. (QBlastHit0.MB and QBlastHSP0.MB) However, that data was apparently not pulled in on the repackaging. I'll rerun the Blast analysis tonight. FINAL COMMENT: The one step I needed to add beyond Welkin's video was to reprase the documentation after the repackaged file was created. Good luck! Edited 02 Jun, 2020 22:07

Link to this post | posted 02 Jun, 2020 21:29

Hi all.

I just ran into a DNA Master error that I've not seen in the five plus years we have been in the program. I searched the forums, but did not find a solution.

PROBLEM: A newly saved DNAM5 file when reopened did not list the features in the feature table. The documentation appeared correct. I could see all the features listed correctly with coordinates and functions in the documentation. I went through the process described in the Annotation Guide to "Parse the Documentation". That is linked here: https://seaphagesbioinformatics.helpdocsonline.com/article-93 However, this did not resolve the problem on the original DNAM5 file.

SOLUTION: I watched this video where Welkin Pope describes how to repair a corrupted DNAM5 file. https://vimeo.com/277487017

I went through all the steps that she included. When I opened the repacked file, I still could not see any features listed in the feature list.

Then I went back to the documentation tab and could see the features listed there.

One more reparse recreated the features in the feature tab.

Now everything has been restored EXCEPT that the Blast Data appears to have been lost. There were two blast file in the directory. (QBlastHit0.MB and QBlastHSP0.MB) However, that data was apparently not pulled in on the repackaging. I'll rerun the Blast analysis tonight.

FINAL COMMENT: The one step I needed to add beyond Welkin's video was to reprase the documentation after the repackaged file was created. Good luck!

Edited 02 Jun, 2020 22:07

Link to this post \| posted 02 Jun, 2020 21:33
welkin	Thanks Greg!

Link to this post \| posted 02 Jun, 2020 22:07
GregFrederick@letu.edu	No problem. Hopefully this will keep someone else from banging their head! ha! gf

Link to this post \| posted 02 Jun, 2020 22:08
GregFrederick@letu.edu	No problem. Hopefully this will keep someone else from banging their head! ha! gf

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Corrupt DNAM5 File - Features not visible in table