SEA-PHAGES | All posts created by c.sunnen

Link to this post \| posted 10 Sep, 2022 17:36
c.sunnen	For anyone that may be helped by this, installing that library worked like a charm!

Posted in: DNA Master → DNAMaster BLAST failure

Link to this post \| posted 10 Sep, 2022 16:30
c.sunnen	Hmmmm. I wonder if I'm having this issue. I've tried BLASTing a single gene, and now I get the error "Could not load SSL library." I'll try the fix below, and let everyone know if it works. Nikki 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 Sep, 2022 16:30

c.sunnen

Hmmmm. I wonder if I'm having this issue. I've tried BLASTing a single gene, and now I get the error "Could not load SSL library."

I'll try the fix below, and let everyone know if it works.

Nikki

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!

Posted in: DNA Master → DNAMaster BLAST failure

Link to this post \| posted 10 Sep, 2022 12:52
c.sunnen	Veronique, Did this ever fix for you? It looks like I might be having the same issue. It's almost as if DNA Master just didn't even start sending queries. It stayed at 0% overnight with no progress. Is this what happened for you? Nikki

Posted in: DNA Master → DNAMaster BLAST failure

Link to this post \| posted 03 Jun, 2022 21:08
c.sunnen	Thank-you, Christian! I see that now in my flat file. It's weird though, because the DNA Master file has "tRNA-Ile2(cat)" in the product field (and properly in the Documentation), so I don't know why it's getting changed in the flat file. Maybe I can just edit the flat file directly and resubmit; the sub file appears accurate. Thank-you! Nikki

Posted in: tRNAs → Met vs Ile2

Link to this post \| posted 03 Jun, 2022 13:53
c.sunnen	I am attempting to submit C1 phage Jedediah, but when it goes through the file checker, I get the following error: ERROR: Evaluation ID: TRNA-EVAL-011. Status: error. Definition: Check that the annotated amino acid is consistent with the prediction(s) made by Aragorn and/or tRNAscan-SE for SEA_JEDEDIAH_180 (Jedediah_TRNA_24). The tRNA feature is expected to have a correct isotype (amino acid) prediction. Result: The annotated isotype (Ile) is inconsistent with Aragorn (Met) and tRNAscan-SE (Ile2). Status was changed from 'warning' to 'error' automatically due to no interactivity. The problem is, it IS annotated as Ile2, not Ile. I even re-typed it to be sure. The Bioinformatics Guide says to annotate this as Ile2 (tRNAScan's call, not Aragorn's call of Met), but I also see that other C1s, such as Khaleesi, TinyTim, and McWolfish all call this Met. I re-ran Khaleesi through tRNAScan-SE, and it also calls this Ile2, even though the final GenBank version calls it Met. What am I missing? Should I call this Met?

Link to this post | posted 03 Jun, 2022 13:53

c.sunnen

I am attempting to submit C1 phage Jedediah, but when it goes through the file checker, I get the following error:

ERROR: Evaluation ID: TRNA-EVAL-011. Status: error. Definition: Check that the annotated amino acid is consistent with the prediction(s) made by Aragorn and/or tRNAscan-SE for SEA_JEDEDIAH_180 (Jedediah_TRNA_24). The tRNA feature is expected to have a correct isotype (amino acid) prediction. Result: The annotated isotype (Ile) is inconsistent with Aragorn (Met) and tRNAscan-SE (Ile2). Status was changed from 'warning' to 'error' automatically due to no interactivity.

The problem is, it IS annotated as Ile2, not Ile. I even re-typed it to be sure. The Bioinformatics Guide says to annotate this as Ile2 (tRNAScan's call, not Aragorn's call of Met), but I also see that other C1s, such as Khaleesi, TinyTim, and McWolfish all call this Met. I re-ran Khaleesi through tRNAScan-SE, and it also calls this Ile2, even though the final GenBank version calls it Met.

What am I missing? Should I call this Met?

Posted in: tRNAs → Met vs Ile2

Link to this post \| posted 22 Feb, 2022 22:46
c.sunnen	Oops! Thanks Eric. I updated the sharing settings. Try it now. Also, a FANTASTIC TA of mine, Mayra Rosales (who also works in IT part-time), found a great resource for those of us that had issues uninstalling DNA Master (in order to reinstall into the correct place). You can access it here: http://www.uninstallhelps.com/how-to-uninstall-dna-master-5-22-1-build-2307.html There are 7 different methods to try, one of which is an "Auto-uninstall" button at the bottom that you can also try. She also recommends going into the Control Panel to uninstall from there. Edited 22 Feb, 2022 22:51

Link to this post | posted 22 Feb, 2022 22:46

c.sunnen

Oops! Thanks Eric. I updated the sharing settings. Try it now.

Also, a FANTASTIC TA of mine, Mayra Rosales (who also works in IT part-time), found a great resource for those of us that had issues uninstalling DNA Master (in order to reinstall into the correct place). You can access it here: http://www.uninstallhelps.com/how-to-uninstall-dna-master-5-22-1-build-2307.html There are 7 different methods to try, one of which is an "Auto-uninstall" button at the bottom that you can also try. She also recommends going into the Control Panel to uninstall from there.

Edited 22 Feb, 2022 22:51

Posted in: DNA Master → DNA Master on M1 Mac

Link to this post \| posted 22 Feb, 2022 22:30
c.sunnen	Update! I created a little protocol for how to download and install DNA Master on Windows 11 (in Parallels). I've found it's critical not to make a shortcut and to download it directly to the Program Files (x86) location. These instructions can be found here: https://docs.google.com/document/d/1YNqYrnjzNkVGNv-gjxvrX_8_sIWuxDqXc_ZPLREhYfI/edit?usp=sharing I hope this is helpful to others! Let me know if it does/doesn't work for you.

Link to this post | posted 22 Feb, 2022 22:30

c.sunnen

Update!

I created a little protocol for how to download and install DNA Master on Windows 11 (in Parallels). I've found it's critical not to make a shortcut and to download it directly to the Program Files (x86) location. These instructions can be found here:
https://docs.google.com/document/d/1YNqYrnjzNkVGNv-gjxvrX_8_sIWuxDqXc_ZPLREhYfI/edit?usp=sharing

I hope this is helpful to others! Let me know if it does/doesn't work for you.

Posted in: DNA Master → DNA Master on M1 Mac

Link to this post \| posted 22 Feb, 2022 17:14
c.sunnen	Thanks everyone. It is now working on my end. I have no idea why you'd be getting a message that you don't have WiFi. Nikki

Posted in: Phamerator → Phamerator not loading

Link to this post \| posted 21 Feb, 2022 19:17
c.sunnen	Thank-you both! Hopefully someone will post soon with a solution! I wonder if I could access it the old-fashioned way in Ubuntu. If I get the chance, I'll try it and let you all know if it worked.

Posted in: Phamerator → Phamerator not loading

Link to this post \| posted 21 Feb, 2022 13:30
c.sunnen	Hi all, Is anyone else having trouble accessing Phamerator? It started for me on Friday, and I figured it was just updating, but I still can't access this morning. Tried 2 different browsers, and it just doesn't load. I get "HTTP ERROR 502." Is it just me? I wanted to teach translational frameshifts this week, which will be tricky without Phamerator! Thanks! Nikki @ USciences

Posted in: Phamerator → Phamerator not loading

Recent Activity

All posts created by c.sunnen