Failed ANNOVAR

[PriyankaMaripuri]

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]

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

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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 <#88>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNG3OA54F3P53OITFJ7Q53W2RCTTANCNFSM6AAAAAAVQAWEWQ> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[PriyankaMaripuri]

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

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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 > <#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 <#88 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AISKIA6U5ONJ6EHWRTBU2BLW2SWUFANCNFSM6AAAAAAVQAWEWQ> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[kaichop]

why do you specify -skip_annovar? On Sun, Mar 5, 2023 at 5:21 PM Priyanka Maripuri ***@***.***> wrote:

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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 > > <#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 > <#88 (comment)>, or > unsubscribe > < https://github.com/notifications/unsubscribe-auth/AISKIA6U5ONJ6EHWRTBU2BLW2SWUFANCNFSM6AAAAAAVQAWEWQ > > . > You are receiving this because you authored the thread.Message ID: > ***@***.***> > — Reply to this email directly, view it on GitHub <#88 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNG3OGRMIXJHRNWBAAJOHDW2UGWDANCNFSM6AAAAAAVQAWEWQ> . You are receiving this because you commented.Message ID: ***@***.***>

[PriyankaMaripuri]

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!

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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 > > > <#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 > > <#88 (comment)>, > or > > unsubscribe > > < > https://github.com/notifications/unsubscribe-auth/AISKIA6U5ONJ6EHWRTBU2BLW2SWUFANCNFSM6AAAAAAVQAWEWQ > > > > . > > You are receiving this because you authored the thread.Message ID: > > ***@***.***> > > > > — > Reply to this email directly, view it on GitHub > <#88 (comment)>, or > unsubscribe > < https://github.com/notifications/unsubscribe-auth/ABNG3OGRMIXJHRNWBAAJOHDW2UGWDANCNFSM6AAAAAAVQAWEWQ > > . > You are receiving this because you commented.Message ID: > ***@***.***> > — Reply to this email directly, view it on GitHub <#88 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AISKIA5FQK4UVVYT4SGGE2LW2VA5TANCNFSM6AAAAAAVQAWEWQ> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[manburst]

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]

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