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PoonLab / OpenRDP

An open-source re-implementation of the RDP4 recombination detection program
GNU General Public License v3.0
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Create a distance matrix between query sequences and reference sequences #97

Closed GopiGugan closed 1 week ago

GopiGugan commented 2 weeks ago
GopiGugan commented 1 week ago

Unable to test on RDP4. Program crashed when trying to do the query vs reference analysis after loading sequences.

Merging into dev

darrenpmartin commented 1 week ago

Hi Gopi - could you send me the alignment that crashed in RDP5. I'll try figure out what went wrong

On Tue, Jun 25, 2024 at 3:42 PM Gopi Gugan @.***> wrote:

Unable to test on RDP5. Program crashed after loading sequences.

Merging into dev

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GopiGugan commented 1 week ago

Hi @darrenpmartin - I just tried on RDP v5.57 and got the following error when doing the "full query vs reference recombination scan":

image

I've attached the alignment. Thanks!

test.fasta.zip

darrenpmartin commented 1 week ago

THanks for this.

On Wed, Jun 26, 2024 at 2:10 PM Gopi Gugan @.***> wrote:

Hi @darrenpmartin https://github.com/darrenpmartin - I just tried on RDP v5.57 and got the following error when doing the "full query vs reference recombination scan":

image.png (view on web) https://github.com/PoonLab/OpenRDP/assets/35086217/2af547d0-3894-4b72-9574-a5c68852cf65

I've attached the alignment. Thanks!

test.fasta.zip https://github.com/user-attachments/files/15987934/test.fasta.zip

— Reply to this email directly, view it on GitHub https://github.com/PoonLab/OpenRDP/pull/97#issuecomment-2191532232, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADEJ3TUQL7UVMLGF3M6TN7LZJKVTDAVCNFSM6AAAAABJKM7IT2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCOJRGUZTEMRTGI . You are receiving this because you were mentioned.Message ID: @.***>

darrenpmartin commented 6 days ago

Hi Gopi - did you get the error during the scan or when you started clicking on events in the table on the top right panel? I fixed a bug that caused a crash when you click on event 2 in the table but not sure if thats the one you encountered.

On Wed, Jun 26, 2024 at 2:10 PM Gopi Gugan @.***> wrote:

Hi @darrenpmartin https://github.com/darrenpmartin - I just tried on RDP v5.57 and got the following error when doing the "full query vs reference recombination scan":

image.png (view on web) https://github.com/PoonLab/OpenRDP/assets/35086217/2af547d0-3894-4b72-9574-a5c68852cf65

I've attached the alignment. Thanks!

test.fasta.zip https://github.com/user-attachments/files/15987934/test.fasta.zip

— Reply to this email directly, view it on GitHub https://github.com/PoonLab/OpenRDP/pull/97#issuecomment-2191532232, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADEJ3TUQL7UVMLGF3M6TN7LZJKVTDAVCNFSM6AAAAABJKM7IT2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCOJRGUZTEMRTGI . You are receiving this because you were mentioned.Message ID: @.***>

GopiGugan commented 6 days ago

Hi Gopi - did you get the error during the scan or when you started clicking on events in the table on the top right panel? I fixed a bug that caused a crash when you click on event 2 in the table but not sure if thats the one you encountered.

Hi @darrenpmartin, I got the error during the scan

darrenpmartin commented 6 days ago

OK then I assume you must be using different program settings t me - could you send the file rdp.ini to me (it is in the directory where you have rdp5 installed)

Darren

On Thu, Jun 27, 2024 at 6:14 AM Gopi Gugan @.***> wrote:

Hi Gopi - did you get the error during the scan or when you started clicking on events in the table on the top right panel? I fixed a bug that caused a crash when you click on event 2 in the table but not sure if thats the one you encountered.

Hi @darrenpmartin https://github.com/darrenpmartin, I got the error during the scan

— Reply to this email directly, view it on GitHub https://github.com/PoonLab/OpenRDP/pull/97#issuecomment-2193631682, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADEJ3TRXGTHMN2MZ67MX453ZJOGTTAVCNFSM6AAAAABJKM7IT2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCOJTGYZTCNRYGI . You are receiving this because you were mentioned.Message ID: @.***>

darrenpmartin commented 6 days ago

OK no worries found the problem (tt was related to the progress bar during the bootscan part of the analysis). if you'd like you can download a fixed version of the RDP5.exe here: https://web.cbio.uct.ac.za/~darren/rdp5.exe

Use it to the replace the one that you currently have installed (likely in the c:/program files x86/rdp5 directory)

Darren

On Thu, Jun 27, 2024 at 9:54 AM Darren Martin @.***> wrote:

OK then I assume you must be using different program settings t me - could you send the file rdp.ini to me (it is in the directory where you have rdp5 installed)

Darren

On Thu, Jun 27, 2024 at 6:14 AM Gopi Gugan @.***> wrote:

Hi Gopi - did you get the error during the scan or when you started clicking on events in the table on the top right panel? I fixed a bug that caused a crash when you click on event 2 in the table but not sure if thats the one you encountered.

Hi @darrenpmartin https://github.com/darrenpmartin, I got the error during the scan

— Reply to this email directly, view it on GitHub https://github.com/PoonLab/OpenRDP/pull/97#issuecomment-2193631682, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADEJ3TRXGTHMN2MZ67MX453ZJOGTTAVCNFSM6AAAAABJKM7IT2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCOJTGYZTCNRYGI . You are receiving this because you were mentioned.Message ID: @.***>