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WGLab / InterVar

A bioinformatics software tool for clinical interpretation of genetic variants by the 2015 ACMG-AMP guideline
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Failed ANNOVAR #88

Open PriyankaMaripuri opened 1 year ago

PriyankaMaripuri commented 1 year ago

image

Hello!

I've been trying to run InterVar but ANNOVAR seems to be failing. It shows the following errors: ERROR: The InterVar did not find the annotation result file from ANNOVAR! ERROR: The name of annotation result file should be like wes_intervar*.hg38__multianno.txt. Thank you!

kaichop commented 1 year ago

you need to rename "VCF files" directory to "VCF_files" so there is no space.

On Sun, Mar 5, 2023 at 3:07 AM Priyanka Maripuri @.***> wrote:

[image: image] https://user-images.githubusercontent.com/35955715/222949129-b2d48803-5a7e-4436-ad1f-59780cae0cbe.png

Hello!

I've been trying to run InterVar but ANNOVAR seems to be failing. It shows the following errors: ERROR: The InterVar did not find the annotation result file from ANNOVAR! ERROR: The name of annotation result file should be like wes_intervar*.hg38__multianno.txt. Thank you!

— Reply to this email directly, view it on GitHub https://github.com/WGLab/InterVar/issues/88, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNG3OA54F3P53OITFJ7Q53W2RCTTANCNFSM6AAAAAAVQAWEWQ . You are receiving this because you are subscribed to this thread.Message ID: @.***>

PriyankaMaripuri commented 1 year ago

Thank you Kai for your quick response. I've made some edits and having been getting this error when running multiple files image

On Sun, Mar 5, 2023 at 8:31 AM Kai Wang @.***> wrote:

you need to rename "VCF files" directory to "VCF_files" so there is no space.

On Sun, Mar 5, 2023 at 3:07 AM Priyanka Maripuri @.***> wrote:

[image: image] < https://user-images.githubusercontent.com/35955715/222949129-b2d48803-5a7e-4436-ad1f-59780cae0cbe.png

Hello!

I've been trying to run InterVar but ANNOVAR seems to be failing. It shows the following errors: ERROR: The InterVar did not find the annotation result file from ANNOVAR! ERROR: The name of annotation result file should be like wes_intervar*.hg38__multianno.txt. Thank you!

— Reply to this email directly, view it on GitHub https://github.com/WGLab/InterVar/issues/88, or unsubscribe < https://github.com/notifications/unsubscribe-auth/ABNG3OA54F3P53OITFJ7Q53W2RCTTANCNFSM6AAAAAAVQAWEWQ

. You are receiving this because you are subscribed to this thread.Message ID: @.***>

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kaichop commented 1 year ago

why do you specify -skip_annovar?

On Sun, Mar 5, 2023 at 5:21 PM Priyanka Maripuri @.***> wrote:

Thank you Kai for your quick response. However, I am still getting the same error message. Please see below:

[image: image.png]

On Sun, Mar 5, 2023 at 8:31 AM Kai Wang @.***> wrote:

you need to rename "VCF files" directory to "VCF_files" so there is no space.

On Sun, Mar 5, 2023 at 3:07 AM Priyanka Maripuri @.***> wrote:

[image: image] <

https://user-images.githubusercontent.com/35955715/222949129-b2d48803-5a7e-4436-ad1f-59780cae0cbe.png

Hello!

I've been trying to run InterVar but ANNOVAR seems to be failing. It shows the following errors: ERROR: The InterVar did not find the annotation result file from ANNOVAR! ERROR: The name of annotation result file should be like wes_intervar*.hg38__multianno.txt. Thank you!

— Reply to this email directly, view it on GitHub https://github.com/WGLab/InterVar/issues/88, or unsubscribe <

https://github.com/notifications/unsubscribe-auth/ABNG3OA54F3P53OITFJ7Q53W2RCTTANCNFSM6AAAAAAVQAWEWQ

. You are receiving this because you are subscribed to this thread.Message ID: @.***>

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PriyankaMaripuri commented 1 year ago

Hello Kai,

I was trying different options to see where the error was coming from. No matter what I do, this is the same error for my wes file. Please see attached

[image: image.png]

Surprisingly, I have a wgs file and it seems to be running okay for the same command. I'm not sure what is happening with this particular file. Thank you!

On Sun, Mar 5, 2023 at 7:05 PM Kai Wang @.***> wrote:

why do you specify -skip_annovar?

On Sun, Mar 5, 2023 at 5:21 PM Priyanka Maripuri @.***> wrote:

Thank you Kai for your quick response. However, I am still getting the same error message. Please see below:

[image: image.png]

On Sun, Mar 5, 2023 at 8:31 AM Kai Wang @.***> wrote:

you need to rename "VCF files" directory to "VCF_files" so there is no space.

On Sun, Mar 5, 2023 at 3:07 AM Priyanka Maripuri @.***> wrote:

[image: image] <

https://user-images.githubusercontent.com/35955715/222949129-b2d48803-5a7e-4436-ad1f-59780cae0cbe.png

Hello!

I've been trying to run InterVar but ANNOVAR seems to be failing. It shows the following errors: ERROR: The InterVar did not find the annotation result file from ANNOVAR! ERROR: The name of annotation result file should be like wes_intervar*.hg38__multianno.txt. Thank you!

— Reply to this email directly, view it on GitHub https://github.com/WGLab/InterVar/issues/88, or unsubscribe <

https://github.com/notifications/unsubscribe-auth/ABNG3OA54F3P53OITFJ7Q53W2RCTTANCNFSM6AAAAAAVQAWEWQ

. You are receiving this because you are subscribed to this thread.Message ID: @.***>

— Reply to this email directly, view it on GitHub https://github.com/WGLab/InterVar/issues/88#issuecomment-1455123609, or unsubscribe <

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manburst commented 1 year ago

Dear Priyanka

Could I ask about how to run/download intervar build hg38? because the instruction manual is based on hg19. And the input file is the filtered VCF file?

Thank you

JK

kaichop commented 1 year ago

PriyankaMaripuri, I cannot see the image that you posted in your message in github.