SEA-PHAGES | Running DNA Master on a Mac using Wine

Link to this post \| posted 10 May, 2018 14:34
kbutela	I've seen this happen a few times. I have my students set up a DNA Master Archive folder somewhere on their Mac, then I have them set this folder to default in DNA Master Preferences. I discourage my students from using the WINE "DNA Master Archive" folder since sometimes files in there seem to get lost or corrupted more easily. Are the students opening files from the DNA Master "open" menu? In my experience, there is usually a brief hang time for opening files. If the program still isn't opening files, then I have the students uninstall and reinstall the program which seems to take care of the problem. Randall DeJong This will hopefully be a silly, easy-to-answer question! We don't typically use DNA Master for Mac in our course, but we have some students who wish to continue unfinished annotations into the summer. They have downloaded and installed the Wine Bottle version posted by Baylor (thanks SEA colleagues!), and it appears to run fine. However, some run into trouble in that they cannot open files - they just hang. My suspicion is that the files need to be in the DNA Master archives folder, only those files aren't 'seen' when in the Mac Finder. Is my suspicion correct or is something else? Any solutions? Thanks!

Link to this post | posted 10 May, 2018 14:34

I've seen this happen a few times. I have my students set up a DNA Master Archive folder somewhere on their Mac, then I have them set this folder to default in DNA Master Preferences. I discourage my students from using the WINE "DNA Master Archive" folder since sometimes files in there seem to get lost or corrupted more easily. Are the students opening files from the DNA Master "open" menu? In my experience, there is usually a brief hang time for opening files. If the program still isn't opening files, then I have the students uninstall and reinstall the program which seems to take care of the problem.

Randall DeJong
This will hopefully be a silly, easy-to-answer question!
We don't typically use DNA Master for Mac in our course, but we have some students who wish to continue unfinished annotations into the summer. They have downloaded and installed the Wine Bottle version posted by Baylor (thanks SEA colleagues!), and it appears to run fine. However, some run into trouble in that they cannot open files - they just hang. My suspicion is that the files need to be in the DNA Master archives folder, only those files aren't 'seen' when in the Mac Finder. Is my suspicion correct or is something else? Any solutions?

Thanks!

Link to this post \| posted 10 May, 2018 19:00
rdejong	Thanks Kristen! We'll give it a try!

Link to this post \| posted 17 Jul, 2018 17:44
smolloy123	I am running DNA Master on Wine and have been for the last two years without any problems. Until NOW! Anyone know what to do with the error message "BLOB has been modified" This error is preventing me from exporting or even saving projects on the Submit to GenBank Window. This is having on both of my computers.

Link to this post \| posted 17 Jul, 2018 17:52
delesall	Hi Sally I had the same issue two years ago. Debbie had to go to Jeffrey Lawrence for that one! Happily I still have his email response which I paste below: "That is a warning/error form the database engine. A BLOB is a "Binary Large Object"; it is a field in the database used to store large fields of information (like a BLAST alignment for a hit). That error arises when one tries to open the same record more than once; the BLOB is already open elsewhere. This warning could arise if the same sequence is loaded form the database more than once, or if the same gene is examined in more than one way that would open a BLOB field. I would need far more details to determine the actual cause, but it may not be an error. It is only an error if it persists after it is clear that the object should have been closed. One possible source is that the record for the gene may not have been save prior to opening the BLAST tab. Try to post the record first." I can't remember what I did (it was two years ago) but the problem did resolve itself…

Link to this post | posted 17 Jul, 2018 17:52

delesall

Hi Sally

I had the same issue two years ago. Debbie had to go to Jeffrey Lawrence for that one! Happily I still have his email response which I paste below:

"That is a warning/error form the database engine. A BLOB is a "Binary
Large Object"; it is a field in the database used to store large fields
of information (like a BLAST alignment for a hit). That error arises
when one tries to open the same record more than once; the BLOB is
already open elsewhere. This warning could arise if the same sequence is
loaded form the database more than once, or if the same gene is examined
in more than one way that would open a BLOB field. I would need far more
details to determine the actual cause, but it may not be an error. It is
only an error if it persists after it is clear that the object should
have been closed.

One possible source is that the record for the gene may not have been
save prior to opening the BLAST tab. Try to post the record first."

I can't remember what I did (it was two years ago) but the problem did resolve itself…

Link to this post \| posted 17 Jul, 2018 18:00
smolloy123	Hi Veronique, Thanks for getting back to me. Given that I can't even open up Submit To GenBank without getting this error, I think that I am still stuck…I think it is weird that it is happening on both versions of my DNA Master (lap top and desktop versions) Cheers Sally Veronique Delesalle Hi Sally I had the same issue two years ago. Debbie had to go to Jeffrey Lawrence for that one! Happily I still have his email response which I paste below: "That is a warning/error form the database engine. A BLOB is a "Binary Large Object"; it is a field in the database used to store large fields of information (like a BLAST alignment for a hit). That error arises when one tries to open the same record more than once; the BLOB is already open elsewhere. This warning could arise if the same sequence is loaded form the database more than once, or if the same gene is examined in more than one way that would open a BLOB field. I would need far more details to determine the actual cause, but it may not be an error. It is only an error if it persists after it is clear that the object should have been closed. One possible source is that the record for the gene may not have been save prior to opening the BLAST tab. Try to post the record first." I can't remember what I did (it was two years ago) but the problem did resolve itself…

Link to this post | posted 17 Jul, 2018 18:00

smolloy123

Hi Veronique,
Thanks for getting back to me. Given that I can't even open up Submit To GenBank without getting this error, I think that I am still stuck…I think it is weird that it is happening on both versions of my DNA Master (lap top and desktop versions)
Cheers
Sally

Veronique Delesalle
Hi Sally

I had the same issue two years ago. Debbie had to go to Jeffrey Lawrence for that one! Happily I still have his email response which I paste below:

"That is a warning/error form the database engine. A BLOB is a "Binary
Large Object"; it is a field in the database used to store large fields
of information (like a BLAST alignment for a hit). That error arises
when one tries to open the same record more than once; the BLOB is
already open elsewhere. This warning could arise if the same sequence is
loaded form the database more than once, or if the same gene is examined
in more than one way that would open a BLOB field. I would need far more
details to determine the actual cause, but it may not be an error. It is
only an error if it persists after it is clear that the object should
have been closed.

One possible source is that the record for the gene may not have been
save prior to opening the BLAST tab. Try to post the record first."

I can't remember what I did (it was two years ago) but the problem did resolve itself…

Link to this post \| posted 17 Jul, 2018 18:30
smolloy123	I fixed it by deleting all the projects in GenBank submission window. There were two or three projects that were causing the error. It wouldn't let me delete the files directly but somehow as I deleted the others it eventually allowed me to delete the problem files. I still don't know what was going on but managed to export the project. smolloy123 Hi Veronique, Thanks for getting back to me. Given that I can't even open up Submit To GenBank without getting this error, I think that I am still stuck…I think it is weird that it is happening on both versions of my DNA Master (lap top and desktop versions) Cheers Sally Veronique Delesalle Hi Sally I had the same issue two years ago. Debbie had to go to Jeffrey Lawrence for that one! Happily I still have his email response which I paste below: "That is a warning/error form the database engine. A BLOB is a "Binary Large Object"; it is a field in the database used to store large fields of information (like a BLAST alignment for a hit). That error arises when one tries to open the same record more than once; the BLOB is already open elsewhere. This warning could arise if the same sequence is loaded form the database more than once, or if the same gene is examined in more than one way that would open a BLOB field. I would need far more details to determine the actual cause, but it may not be an error. It is only an error if it persists after it is clear that the object should have been closed. One possible source is that the record for the gene may not have been save prior to opening the BLAST tab. Try to post the record first." I can't remember what I did (it was two years ago) but the problem did resolve itself…

Link to this post | posted 17 Jul, 2018 18:30

smolloy123

I fixed it by deleting all the projects in GenBank submission window. There were two or three projects that were causing the error. It wouldn't let me delete the files directly but somehow as I deleted the others it eventually allowed me to delete the problem files. I still don't know what was going on but managed to export the project.

smolloy123
Hi Veronique,
Thanks for getting back to me. Given that I can't even open up Submit To GenBank without getting this error, I think that I am still stuck…I think it is weird that it is happening on both versions of my DNA Master (lap top and desktop versions)
Cheers
Sally

Veronique Delesalle
Hi Sally

I had the same issue two years ago. Debbie had to go to Jeffrey Lawrence for that one! Happily I still have his email response which I paste below:

"That is a warning/error form the database engine. A BLOB is a "Binary
Large Object"; it is a field in the database used to store large fields
of information (like a BLAST alignment for a hit). That error arises
when one tries to open the same record more than once; the BLOB is
already open elsewhere. This warning could arise if the same sequence is
loaded form the database more than once, or if the same gene is examined
in more than one way that would open a BLOB field. I would need far more
details to determine the actual cause, but it may not be an error. It is
only an error if it persists after it is clear that the object should
have been closed.

One possible source is that the record for the gene may not have been
save prior to opening the BLAST tab. Try to post the record first."

I can't remember what I did (it was two years ago) but the problem did resolve itself…

Link to this post \| posted 19 Jul, 2018 12:37
welkin	Please note— this thread was too long and covered too many different topics over a number of years, so we have closed it and restarted it as a separate forum under DNA Master. please start new threads here: https://seaphages.org/forums/forum/160/ Thanks! Welkin

Link to this post \| posted 07 Dec, 2018 23:39
DrCatalase	Trying to set up DNA Master on Wine for the upcoming Bioinformatics workshop and after I hit auto annotate I only get one sequence in the features tab of the Extracted from FASTA Library Shubert.FASTA window. Please help.

Link to this post \| posted 10 Dec, 2018 00:11
MSMC	DrCatalase Trying to set up DNA Master on Wine for the upcoming Bioinformatics workshop and after I hit auto annotate I only get one sequence in the features tab of the Extracted from FASTA Library Shubert.FASTA window. Please help. Have you done the update to access GeneMark and Glimmer (attached)? 166Kb

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Running DNA Master on a Mac using Wine