SEA-PHAGES | DNAMaster BLAST failure

Link to this post \| posted 05 Aug, 2021 22:20
vbrownk	vbrownk I am getting this same error now, just like Tamarah's. Error (16) retrieving results for RID … OK WELL … this resolved when I switched from university wifi to ethernet. Whew! -VBK

Link to this post \| posted 25 Aug, 2021 12:41
CCSNH-NHTI	Hi. I'm getting a Blast error: "Error sending requests to QBlast server". The one thing I see in Preferences that the Guide doesn't specify is on the Secure Connections page, I have drop down boxes next to what is checked and it is defaulted to TLS 1.2. Should it be SSL 2 or 3 instead? Or any other suggestions are very welcome. Thanks

Link to this post \| posted 10 Dec, 2021 00:26
hgavin90	CCSNH-NHTI Hi. I'm getting a Blast error: "Error sending requests to QBlast server". The one thing I see in Preferences that the Guide doesn't specify is on the Secure Connections page, I have drop down boxes next to what is checked and it is defaulted to TLS 1.2. Should it be SSL 2 or 3 instead? Or any other suggestions are very welcome. Thanks I second this inquiry! Same error & same thought re: specifying the dropdown secure connection type…

Link to this post | posted 10 Dec, 2021 00:26

hgavin90

CCSNH-NHTI
Hi. I'm getting a Blast error: "Error sending requests to QBlast server". The one thing I see in Preferences that the Guide doesn't specify is on the Secure Connections page, I have drop down boxes next to what is checked and it is defaulted to TLS 1.2. Should it be SSL 2 or 3 instead? Or any other suggestions are very welcome.
Thanks

I second this inquiry! Same error & same thought re: specifying the dropdown secure connection type…

Link to this post \| posted 10 Dec, 2021 00:49
hgavin90	DanRussell Hi Katie, I think this error is due to not having a certain library installed on the particular version of Windows that's running. That library wasn't required until after the update earlier this year to use secure NCBI servers. I think I came across that error myself, and in my notes I have that I went to the link below and installed the Visual C++ package there, then restarted and it worked. ~~https://www.microsoft.com/en-us/download/details.aspx?id=5555~~ UPDATE Sep 2021: The link above no longer works, but the file can be found at the link below now. Download it from within Windows and then run it, and make sure you close DNA Master and restart Windows before trying to BLAST again. https://phagesdb.org/static/vcredist_x86.exe Hopefully that helps, –Dan Nevermind – changing secure connection did not work but this installation recommended by Dann has. Woo!

Link to this post | posted 10 Dec, 2021 00:49

hgavin90

DanRussell
Hi Katie,

I think this error is due to not having a certain library installed on the particular version of Windows that's running. That library wasn't required until after the update earlier this year to use secure NCBI servers. I think I came across that error myself, and in my notes I have that I went to the link below and installed the Visual C++ package there, then restarted and it worked.

~~https://www.microsoft.com/en-us/download/details.aspx?id=5555~~

UPDATE Sep 2021: The link above no longer works, but the file can be found at the link below now. Download it from within Windows and then run it, and make sure you close DNA Master and restart Windows before trying to BLAST again.

https://phagesdb.org/static/vcredist_x86.exe

Hopefully that helps,
–Dan

Nevermind – changing secure connection did not work but this installation recommended by Dann has. Woo!

Link to this post \| posted 07 Apr, 2022 14:29
engstrom	Hey Folks, We are experiencing trouble Blasting in DNA Master. When BLASTing all genes, it can run for days with 0% progress. When BLASTing a single gene, we see an error message "HTTP/1.1 403 Forbidden" I have updated DNA Master. Tied ethernet and wireless. I have tried to ensure that our preferences are set correctly, according to the directions in the Bioinformatics Guidelines, but I do not even have a "secure connections" box as an option under PREFERENCES–> Internet. Any ideas would be greatly appreciated.

Link to this post | posted 07 Apr, 2022 14:29

engstrom

Hey Folks,

We are experiencing trouble Blasting in DNA Master. When BLASTing all genes, it can run for days with 0% progress. When BLASTing a single gene, we see an error message "HTTP/1.1 403 Forbidden" I have updated DNA Master. Tied ethernet and wireless. I have tried to ensure that our preferences are set correctly, according to the directions in the Bioinformatics Guidelines, but I do not even have a "secure connections" box as an option under PREFERENCES–> Internet. Any ideas would be greatly appreciated.

Link to this post \| posted 07 Apr, 2022 17:06
debbie	Eric, Your version of DNA Master needs to be updated. You must update to get that "secure connections" box in preferences. I believe the problem is that you must run DNA Master as administrator even when you are updating. Check on that and try again. My latest version is 5.23.6, Build 2705, 14 October 2021.

Link to this post \| posted 14 Jul, 2022 18:17
afreise	Hi all, I'm also running into issues with BLAST. My version of DNAM is 5.23.6, Build 2705, 14 October 2021.I did install the file that Dan shared above using his directions. When I tried to re-BLAST the entire genome last night, it did seem to send all the queries and read results, but I did get some errors like the following: Error (4) retrieving results for RID FA02Z622015 for feature 280 I'm also getting errors called "Error sending results to QBlast server" Unfortunately when I woke up and checked the results this morning, DNA master had completely crashed so I don't know if that BLAST search worked or not. I tried to BLAST a single gene, and it doesn't seem to be doing anything at all. The window has displayed "Sending BLAST request" for 5 minutes and no other updates are coming through. I also tried to blast a subset (the first 5) genes and I am getting the same "error retrieving results". Any thoughts on what I can try next? Thanks, Amanda Edited 14 Jul, 2022 18:49

Link to this post | posted 14 Jul, 2022 18:17

afreise

Hi all,

I'm also running into issues with BLAST.
My version of DNAM is 5.23.6, Build 2705, 14 October 2021.I did install the file that Dan shared above using his directions.

When I tried to re-BLAST the entire genome last night, it did seem to send all the queries and read results, but I did get some errors like the following:

Error (4) retrieving results for RID FA02Z622015 for feature 280

I'm also getting errors called "Error sending results to QBlast server"

Unfortunately when I woke up and checked the results this morning, DNA master had completely crashed smile

so I don't know if that BLAST search worked or not.

I tried to BLAST a single gene, and it doesn't seem to be doing anything at all. The window has displayed "Sending BLAST request" for 5 minutes and no other updates are coming through.

I also tried to blast a subset (the first 5) genes and I am getting the same "error retrieving results".

Any thoughts on what I can try next?

Thanks,
Amanda

Edited 14 Jul, 2022 18:49

Link to this post \| posted 14 Jul, 2022 18:28
afreise	*One other note: We did all our annotations in PECAAN, which I think does re-BLAST automatically if a different start site is chosen. I then exported the annotation and used it to parse genes in the FASTA file in DNAM in preparation for the minimal file. With that in mind, do I need to do the re-BLAST within DNA Master?

Link to this post \| posted 14 Jul, 2022 19:22
debbie	Hi Amanda, Here is thought, that may help. You can BLAST a subset of genes at a time in DNA Master. Here is the Bioinformatics Guide entry that explains: https://seaphagesbioinformatics.helpdocsonline.com/article-70

Link to this post \| posted 14 Jul, 2022 19:31
afreise	Thanks, Debbie - I did try BLASTing a subset (the first five genes) and got the same issue.

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DNAMaster BLAST failure