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A bioinformatics software tool for clinical interpretation of genetic variants by the 2015 ACMG-AMP guideline
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Error downloading from Annovar #2

Closed nickywhiff closed 7 years ago

nickywhiff commented 7 years ago

I am getting the following notices when trying to run the tool:

NOTICE: Downloading annotation database http://www.openbioinformatics.org/annovar/download/hg19_ALL.sites.2015_08.txt.gz ... Failed NOTICE: Downloading annotation database http://www.openbioinformatics.org/annovar/download/hg19_ALL.sites.2015_08.txt.idx.gz ... Failed

These then result in an error:

Error: the required database file ../annovar/humandbm/hg19_ALL.sites.2015_08.txt does not exist.

When I go to the above addresses I get a URL not found error.

Please can you advise how to fix this?

Many thanks, Nicky

kaichop commented 7 years ago

please read FAQ #1.

On Thu, Feb 9, 2017 at 9:10 AM, Nicky Whiffin notifications@github.com wrote:

I am getting the following notices when trying to run the tool:

NOTICE: Downloading annotation database http://www.openbioinformatics. org/annovar/download/hg19_ALL.sites.2015_08.txt.gz ... Failed NOTICE: Downloading annotation database http://www.openbioinformatics. org/annovar/download/hg19_ALL.sites.2015_08.txt.idx.gz ... Failed

These then result in an error:

Error: the required database file ../annovar/humandbm/hg19_ALL.sites.2015_08.txt does not exist.

When I go to the above addresses I get a URL not found error.

Please can you advise how to fix this?

Many thanks, Nicky

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/WGLab/InterVar/issues/2, or mute the thread https://github.com/notifications/unsubscribe-auth/AFptuMdtmIbOEHpdDL_tdLxBZplTrjTIks5rax5agaJpZM4L8LIm .

nickywhiff commented 7 years ago

As per the FAQ I have sent an email to leequan@gmail.com with the full command included

quanliustc commented 7 years ago

The web server of http://www.openbioinformatics.org/annovar was in manitenance.

Now it is ok, you can download now.

NOTICE: Downloading annotation database http://www.openbioinformatics.org/annovar/download/hg19_1000g2015aug.zip ... OK

NOTICE: Uncompressing downloaded files

Also you can try http://wintervar.wglab.org for searching when there are some downloading problems

Best,

Quan LI

leequan@gmail.com

From: Kai Wang [mailto:notifications@github.com] Sent: Thursday, February 09, 2017 10:43 AM To: WGLab/InterVar InterVar@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: Re: [WGLab/InterVar] Error downloading from Annovar (#2)

please read FAQ #1.

On Thu, Feb 9, 2017 at 9:10 AM, Nicky Whiffin <notifications@github.com mailto:notifications@github.com > wrote:

I am getting the following notices when trying to run the tool:

NOTICE: Downloading annotation database http://www.openbioinformatics. org/annovar/download/hg19_ALL.sites.2015_08.txt.gz ... Failed NOTICE: Downloading annotation database http://www.openbioinformatics. org/annovar/download/hg19_ALL.sites.2015_08.txt.idx.gz ... Failed

These then result in an error:

Error: the required database file ../annovar/humandbm/hg19_ALL.sites.2015_08.txt does not exist.

When I go to the above addresses I get a URL not found error.

Please can you advise how to fix this?

Many thanks, Nicky

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/WGLab/InterVar/issues/2, or mute the thread https://github.com/notifications/unsubscribe-auth/AFptuMdtmIbOEHpdDL_tdLxBZplTrjTIks5rax5agaJpZM4L8LIm .

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nickywhiff commented 7 years ago

Hi Quan Li,

Thank you very much for this. When I run the command the tool still tries to download 'hg19_ALL.sites.2015_08.txt.gz' - the name of the file you sent is different. How do I tell the tool to download this alternative file?

Many thanks, Nicky

From: Quan LI notifications@github.com<mailto:notifications@github.com> Reply-To: WGLab/InterVar reply@reply.github.com<mailto:reply@reply.github.com> Date: Thursday, 9 February 2017 15:09 To: WGLab/InterVar InterVar@noreply.github.com<mailto:InterVar@noreply.github.com> Cc: "Whiffin, Nicola" n.whiffin@lms.mrc.ac.uk<mailto:n.whiffin@lms.mrc.ac.uk>, Author author@noreply.github.com<mailto:author@noreply.github.com> Subject: Re: [WGLab/InterVar] Error downloading from Annovar (#2) Resent-From: n.whiffin@lms.mrc.ac.uk<mailto:n.whiffin@lms.mrc.ac.uk> Resent-Date: Thursday, 9 February 2017 15:09

The web server of http://www.openbioinformatics.org/annovar was in manitenance.

Now it is ok, you can download now.

NOTICE: Downloading annotation database http://www.openbioinformatics.org/annovar/download/hg19_1000g2015aug.zip ... OK

NOTICE: Uncompressing downloaded files

Also you can try http://wintervar.wglab.org for searching when there are some downloading problems

Best,

Quan LI

leequan@gmail.commailto:leequan@gmail.com

From: Kai Wang [mailto:notifications@github.com] Sent: Thursday, February 09, 2017 10:43 AM To: WGLab/InterVar InterVar@noreply.github.com<mailto:InterVar@noreply.github.com> Cc: Subscribed subscribed@noreply.github.com<mailto:subscribed@noreply.github.com> Subject: Re: [WGLab/InterVar] Error downloading from Annovar (#2)

please read FAQ #1.

On Thu, Feb 9, 2017 at 9:10 AM, Nicky Whiffin notifications@github.com<mailto:notifications@github.com mailto:notifications@github.com > wrote:

I am getting the following notices when trying to run the tool:

NOTICE: Downloading annotation database http://www.openbioinformatics. org/annovar/download/hg19_ALL.sites.2015_08.txt.gz ... Failed NOTICE: Downloading annotation database http://www.openbioinformatics. org/annovar/download/hg19_ALL.sites.2015_08.txt.idx.gz ... Failed

These then result in an error:

Error: the required database file ../annovar/humandbm/hg19_ALL.sites.2015_08.txt does not exist.

When I go to the above addresses I get a URL not found error.

Please can you advise how to fix this?

Many thanks, Nicky

- You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/WGLab/InterVar/issues/2, or mute the thread https://github.com/notifications/unsubscribe-auth/AFptuMdtmIbOEHpdDL_tdLxBZplTrjTIks5rax5agaJpZM4L8LIm .

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DISCLAIMER: The information contained in this email may be subject to public disclosure under the NHS Code of Openness or the Freedom of Information Act 2000. Unless the information is legally exempt from disclosure, the confidentiality of this email, and your reply cannot be guaranteed. The information and material in this email is intended for the use of the intended addressee or the person responsible for delivering it to the intended addressee. It may contain privileged or confidential information and/or copyright material. If you receive this email by mistake please advise the sender immediately by using the reply facility in your email software or notify Royal Brompton & Harefield NHS Foundation Trust Help Desk on +44(0) 20 7351 8696 Communication is not sent through a secure server; Royal Brompton & Harefield NHS Foundation Trust cannot accept responsibility for the accuracy of outgoing electronic mail. Any views or opinions expressed are solely those of the author and do not represent the view of Royal Brompton & Harefield NHS Foundation Trust unless specifically stated.

kaichop commented 7 years ago

Nicky, You are not supposed to download this file hg19_ALL.sites.2015_08.txt.gz, which is why I asked you to provide your command. This file never existed. -Kai

On Thu, Feb 9, 2017 at 10:44 AM, Nicky Whiffin notifications@github.com wrote:

Hi Quan Li,

Thank you very much for this. When I run the command the tool still tries to download 'hg19_ALL.sites.2015_08.txt.gz' - the name of the file you sent is different. How do I tell the tool to download this alternative file?

Many thanks, Nicky

From: Quan LI notifications@github.com<mailto:notifications@github.com> Reply-To: WGLab/InterVar <reply@reply.github.com<mailto: reply@reply.github.com>> Date: Thursday, 9 February 2017 15:09 To: WGLab/InterVar <InterVar@noreply.github.com<mailto:InterVar@noreply. github.com>> Cc: "Whiffin, Nicola" <n.whiffin@lms.mrc.ac.uk<mailto: n.whiffin@lms.mrc.ac.uk>>, Author <author@noreply.github.com<mailto: author@noreply.github.com>> Subject: Re: [WGLab/InterVar] Error downloading from Annovar (#2) Resent-From: n.whiffin@lms.mrc.ac.uk<mailto:n.whiffin@lms.mrc.ac.uk> Resent-Date: Thursday, 9 February 2017 15:09

The web server of http://www.openbioinformatics.org/annovar was in manitenance.

Now it is ok, you can download now.

NOTICE: Downloading annotation database http://www.openbioinformatics. org/annovar/download/hg19_1000g2015aug.zip ... OK

NOTICE: Uncompressing downloaded files

Also you can try http://wintervar.wglab.org for searching when there are some downloading problems

Best,

Quan LI

leequan@gmail.commailto:leequan@gmail.com

From: Kai Wang [mailto:notifications@github.com] Sent: Thursday, February 09, 2017 10:43 AM To: WGLab/InterVar <InterVar@noreply.github.com<mailto:InterVar@noreply. github.com>> Cc: Subscribed <subscribed@noreply.github.com<mailto:subscribed@noreply. github.com>> Subject: Re: [WGLab/InterVar] Error downloading from Annovar (#2)

please read FAQ #1.

On Thu, Feb 9, 2017 at 9:10 AM, Nicky Whiffin <notifications@github.com< mailto:notifications@github.com> mailto:notifications@github.com > wrote:

I am getting the following notices when trying to run the tool:

NOTICE: Downloading annotation database http://www.openbioinformatics. org/annovar/download/hg19_ALL.sites.2015_08.txt.gz ... Failed NOTICE: Downloading annotation database http://www.openbioinformatics. org/annovar/download/hg19_ALL.sites.2015_08.txt.idx.gz ... Failed

These then result in an error:

Error: the required database file ../annovar/humandbm/hg19_ALL. sites.2015_08.txt does not exist.

When I go to the above addresses I get a URL not found error.

Please can you advise how to fix this?

Many thanks, Nicky

- You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/WGLab/InterVar/issues/2, or mute the thread https://github.com/notifications/unsubscribe-auth/AFptuMdtmIbOEHpdDL_ tdLxBZplTrjTIks5rax5agaJpZM4L8LIm .

- You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/WGLab/ InterVar/issues/2#issuecomment-278651797 , or mute the thread < https://github.com/notifications/unsubscribe-auth/APD6JNBdfeiNDSICTyoNc- pUiRDAI-Skks5rax7cgaJpZM4L8LIm> . https://github.com/ notifications/beacon/APD6JNkWr63Yece7VM7qXsiXJaMSnR 13ks5rax7cgaJpZM4L8LIm.gif

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  1. Unless the information is legally exempt from disclosure, the confidentiality of this email, and your reply cannot be guaranteed. The information and material in this email is intended for the use of the intended addressee or the person responsible for delivering it to the intended addressee. It may contain privileged or confidential information and/or copyright material. If you receive this email by mistake please advise the sender immediately by using the reply facility in your email software or notify Royal Brompton & Harefield NHS Foundation Trust Help Desk on +44(0) 20 7351 8696 <+44%2020%207351%208696> Communication is not sent through a secure server; Royal Brompton & Harefield NHS Foundation Trust cannot accept responsibility for the accuracy of outgoing electronic mail. Any views or opinions expressed are solely those of the author and do not represent the view of Royal Brompton & Harefield NHS Foundation Trust unless specifically stated.

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nickywhiff commented 7 years ago

Sorry Kai I might be being very stupid but when I run my command the script automatically tries to download this file. Full output is:

./Intervar.py -c config.ini --table_annovar=../annovar/table_annovar.pl --convert2annovar=../annovar/convert2annovar.pl --annotate_variation=../annovar/annotate_variation.pl --database_locat=../annovar/humandbm

=============================================================================

InterVar

Interpretation of Pathogenic/Benign for variants using python scripts of InterVar.

=============================================================================

%prog 0.1

Written by Quan LI,leequan@gmail.com.

InterVar is free for non-commercial use without warranty.

Please contact the authors for commercial use.

Copyright (C) 2016 Wang Genomic Lab

============================================================================

Notice: Your command of InterVar is ['./Intervar.py', '-c', 'config.ini', '--table_annovar=../annovar/table_annovar.pl', '--convert2annovar=../annovar/convert2annovar.pl', '--annotate_variation=../annovar/annotate_variation.pl', '--database_locat=../annovar/humandbm']

INFO: The options are {'pp2_genes': 'intervardb/PP2.genes', 'inputfile': 'example/ex1.avinput', 'exclude_snps': 'intervardb/ext.variants.hg19', 'annotate_variation': '../annovar/annotate_variation.pl', 'ps4_snps': 'intervardb/PS4.variants.hg19', 'mim_recessive': 'intervardb/mim_recessive.txt', 'current_version': 'Intervar_20151116', 'bs2_snps': 'intervardb/BS2_hom_het.hg19', 'evidence_file': 'None', 'public_dev': 'https://github.com/WGLab/InterVar/releases', 'otherinfo': 'FALSE', 'database_names': 'refGene esp6500siv2_all 1000g2015aug avsnp144 dbnsfp30a clinvar_20160302 exac03 dbscsnv11 dbnsfp31a_interpro rmsk ensGene knownGene', 'mim_pheno': 'intervardb/mim_pheno.txt', 'table_annovar': '../annovar/table_annovar.pl', 'buildver': 'hg19', 'inputfile_type': 'AVinput', 'onetranscript': 'FALSE', 'mim2gene': 'intervardb/mim2gene.txt', 'orpha': 'intervardb/orpha.txt', 'ps1_aa': 'intervardb/PS1.AA.change.patho.hg19', 'mim_adultonset': 'intervardb/mim_adultonset.txt', 'morbidmap': 'intervardb/morbidmap', 'outfile': 'example/myanno', 'csvout': 'FALSE', 'knowngenecanonical': 'intervardb/knownGeneCanonical.txt', 'dot2underline': 'TRUE', 'convert2annovar': '../annovar/convert2annovar.pl', 'database_locat': '../annovar/humandbm', 'database_intervar': 'intervardb', 'lof_genes': 'intervardb/PVS1.LOF.genes', 'disorder_cutoff': '0.01', 'mim_domin': 'intervardb/mim_domin.txt', 'pm1_domain': 'intervardb/PM1_domains_with_benigns', 'mim_orpha': 'intervardb/mim_orpha.txt', 'bp1_genes': 'intervardb/BP1.genes'}

Warning: the folder of ../annovar/humandbm is already created!

Warning: The Annovar dataset file of 1000g2015aug is not in ../annovar/humandbm,begin to download this ../annovar/humandbm/hg19_ALL.sites.2015_08.txt ...

perl ../annovar/annotate_variation.pl -buildver hg19 -downdb -webfrom annovar ALL.sites.2015_08 ../annovar/humandbm

NOTICE: Web-based checking to see whether ANNOVAR new version is available ... Done

NOTICE: Downloading annotation database http://www.openbioinformatics.org/annovar/download/hg19_ALL.sites.2015_08.txt.gz ... Failed

NOTICE: Downloading annotation database http://www.openbioinformatics.org/annovar/download/hg19_ALL.sites.2015_08.txt.idx.gz ... Failed

WARNING: Some files cannot be downloaded, including http://www.openbioinformatics.org/annovar/download/hg19_ALL.sites.2015_08.txt.idx.gz, http://www.openbioinformatics.org/annovar/download/hg19_ALL.sites.2015_08.txt.gz

perl ../annovar/table_annovar.pl example/ex1.avinput ../annovar/humandbm -buildver hg19 -remove -out example/myanno -protocol refGene,esp6500siv2_all,1000g2015aug_all,avsnp144,dbnsfp30a,clinvar_20160302,exac03,dbscsnv11,dbnsfp31a_interpro,rmsk,ensGene,knownGene -operation g,f,f,f,f,f,f,f,f,r,g,g -nastring .

Error: the required database file ../annovar/humandbm/hg19_ALL.sites.2015_08.txt does not exist.

Error: can't read the OMIM morbidmap disorder file intervardb/morbidmap

Error: Please download it from http://www.omim.org/downloads

Best wishes,

Nicky

From: Kai Wang notifications@github.com<mailto:notifications@github.com> Reply-To: WGLab/InterVar reply@reply.github.com<mailto:reply@reply.github.com> Date: Thursday, 9 February 2017 15:47 To: WGLab/InterVar InterVar@noreply.github.com<mailto:InterVar@noreply.github.com> Cc: "Whiffin, Nicola" n.whiffin@lms.mrc.ac.uk<mailto:n.whiffin@lms.mrc.ac.uk>, Author author@noreply.github.com<mailto:author@noreply.github.com> Subject: Re: [WGLab/InterVar] Error downloading from Annovar (#2) Resent-From: n.whiffin@lms.mrc.ac.uk<mailto:n.whiffin@lms.mrc.ac.uk> Resent-Date: Thursday, 9 February 2017 15:48

Nicky, You are not supposed to download this file hg19_ALL.sites.2015_08.txt.gz, which is why I asked you to provide your command. This file never existed. -Kai

On Thu, Feb 9, 2017 at 10:44 AM, Nicky Whiffin notifications@github.com<mailto:notifications@github.com> wrote:

Hi Quan Li,

Thank you very much for this. When I run the command the tool still tries to download 'hg19_ALL.sites.2015_08.txt.gz' - the name of the file you sent is different. How do I tell the tool to download this alternative file?

Many thanks, Nicky

From: Quan LI notifications@github.com<mailto:notifications@github.commailto:notifications@github.com> Reply-To: WGLab/InterVar reply@reply.github.com<mailto:reply@reply.github.com<mailto: reply@reply.github.commailto:reply@reply.github.com>> Date: Thursday, 9 February 2017 15:09 To: WGLab/InterVar InterVar@noreply.github.com<mailto:InterVar@noreply.github.com<mailto:InterVar@noreply. github.com>> Cc: "Whiffin, Nicola" n.whiffin@lms.mrc.ac.uk<mailto:n.whiffin@lms.mrc.ac.uk<mailto: n.whiffin@lms.mrc.ac.ukmailto:n.whiffin@lms.mrc.ac.uk>>, Author author@noreply.github.com<mailto:author@noreply.github.com<mailto: author@noreply.github.commailto:author@noreply.github.com>> Subject: Re: [WGLab/InterVar] Error downloading from Annovar (#2) Resent-From: n.whiffin@lms.mrc.ac.uk<mailto:n.whiffin@lms.mrc.ac.ukmailto:n.whiffin@lms.mrc.ac.uk> Resent-Date: Thursday, 9 February 2017 15:09

The web server of http://www.openbioinformatics.org/annovar was in manitenance.

Now it is ok, you can download now.

NOTICE: Downloading annotation database http://www.openbioinformatics. org/annovar/download/hg19_1000g2015aug.zip ... OK

NOTICE: Uncompressing downloaded files

Also you can try http://wintervar.wglab.org for searching when there are some downloading problems

Best,

Quan LI

leequan@gmail.commailto:leequan@gmail.commailto:leequan@gmail.com

From: Kai Wang [mailto:notifications@github.com] Sent: Thursday, February 09, 2017 10:43 AM To: WGLab/InterVar InterVar@noreply.github.com<mailto:InterVar@noreply.github.com<mailto:InterVar@noreply. github.com>> Cc: Subscribed subscribed@noreply.github.com<mailto:subscribed@noreply.github.com<mailto:subscribed@noreply. github.com>> Subject: Re: [WGLab/InterVar] Error downloading from Annovar (#2)

please read FAQ #1.

On Thu, Feb 9, 2017 at 9:10 AM, Nicky Whiffin notifications@github.com<mailto:notifications@github.com< mailto:notifications@github.com> mailto:notifications@github.com > wrote:

I am getting the following notices when trying to run the tool:

NOTICE: Downloading annotation database http://www.openbioinformatics. org/annovar/download/hg19_ALL.sites.2015_08.txt.gz ... Failed NOTICE: Downloading annotation database http://www.openbioinformatics. org/annovar/download/hg19_ALL.sites.2015_08.txt.idx.gz ... Failed

These then result in an error:

Error: the required database file ../annovar/humandbm/hg19_ALL. sites.2015_08.txt does not exist.

When I go to the above addresses I get a URL not found error.

Please can you advise how to fix this?

Many thanks, Nicky

- You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/WGLab/InterVar/issues/2, or mute the thread https://github.com/notifications/unsubscribe-auth/AFptuMdtmIbOEHpdDL_ tdLxBZplTrjTIks5rax5agaJpZM4L8LIm .

- You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/WGLab/ InterVar/issues/2#issuecomment-278651797 , or mute the thread < https://github.com/notifications/unsubscribe-auth/APD6JNBdfeiNDSICTyoNc- pUiRDAI-Skks5rax7cgaJpZM4L8LIm> . https://github.com/ notifications/beacon/APD6JNkWr63Yece7VM7qXsiXJaMSnR 13ks5rax7cgaJpZM4L8LIm.gif

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kaichop commented 7 years ago

you can run below to fix the problem for now so that you can run intervar perl ../annovar/annotate_variation.pl -buildver hg19 -downdb -webfrom annovar 1000g2015aug ../annovar/humandbm

It looks like a bug in intervar to download the file below, which Quan will fix.

On Thu, Feb 9, 2017 at 10:55 AM, Nicky Whiffin notifications@github.com wrote:

Sorry Kai I might be being very stupid but when I run my command the script automatically tries to download this file. Full output is:

./Intervar.py -c config.ini --table_annovar=../annovar/table_annovar.pl --convert2annovar=../annovar/convert2annovar.pl --annotate_variation=../ annovar/annotate_variation.pl --database_locat=../annovar/humandbm

============================================================

InterVar

Interpretation of Pathogenic/Benign for variants using python scripts of InterVar.

============================================================

%prog 0.1

Written by Quan LI,leequan@gmail.com.

InterVar is free for non-commercial use without warranty.

Please contact the authors for commercial use.

Copyright (C) 2016 Wang Genomic Lab

============================================================

Notice: Your command of InterVar is ['./Intervar.py', '-c', 'config.ini', '--table_annovar=../annovar/table_annovar.pl', '--convert2annovar=../annovar/convert2annovar.pl', '--annotate_variation=../annovar/annotate_variation.pl', '--database_locat=../annovar/humandbm']

INFO: The options are {'pp2_genes': 'intervardb/PP2.genes', 'inputfile': 'example/ex1.avinput', 'exclude_snps': 'intervardb/ext.variants.hg19', 'annotate_variation': '../annovar/annotate_variation.pl', 'ps4_snps': 'intervardb/PS4.variants.hg19', 'mim_recessive': 'intervardb/mim_recessive.txt', 'current_version': 'Intervar_20151116', 'bs2_snps': 'intervardb/BS2_hom_het.hg19', 'evidence_file': 'None', 'public_dev': 'https://github.com/WGLab/InterVar/releases', 'otherinfo': 'FALSE', 'database_names': 'refGene esp6500siv2_all 1000g2015aug avsnp144 dbnsfp30a clinvar_20160302 exac03 dbscsnv11 dbnsfp31a_interpro rmsk ensGene knownGene', 'mim_pheno': 'intervardb/mim_pheno.txt', 'table_annovar': '../annovar/table_annovar.pl', 'buildver': 'hg19', 'inputfile_type': 'AVinput', 'onetranscript': 'FALSE', 'mim2gene': 'intervardb/mim2gene.txt', 'orpha': 'intervardb/orpha.txt', 'ps1_aa': 'intervardb/PS1.AA.change.patho.hg19', 'mim_adultonset': 'intervardb/mim_adultonset.txt', 'morbidmap': 'intervardb/morbidmap', 'outfile': 'example/myanno', 'csvout': 'FALSE', 'knowngenecanonical': 'intervardb/knownGeneCanonical.txt', 'dot2underline': 'TRUE', 'convert2annovar': '../annovar/convert2annovar.pl', 'database_locat': '../annovar/humandbm', 'database_intervar': 'intervardb', 'lof_genes': 'intervardb/PVS1.LOF.genes', 'disorder_cutoff': '0.01', 'mim_domin': 'intervardb/mim_domin.txt', 'pm1_domain': 'intervardb/PM1_domains_with_benigns', 'mim_orpha': 'intervardb/mim_orpha.txt', 'bp1_genes': 'intervardb/BP1.genes'}

Warning: the folder of ../annovar/humandbm is already created!

Warning: The Annovar dataset file of 1000g2015aug is not in ../annovar/humandbm,begin to download this ../annovar/humandbm/hg19_ALL.sites.2015_08.txt ...

perl ../annovar/annotate_variation.pl -buildver hg19 -downdb -webfrom annovar ALL.sites.2015_08 ../annovar/humandbm

NOTICE: Web-based checking to see whether ANNOVAR new version is available ... Done

NOTICE: Downloading annotation database http://www.openbioinformatics. org/annovar/download/hg19_ALL.sites.2015_08.txt.gz ... Failed

NOTICE: Downloading annotation database http://www.openbioinformatics. org/annovar/download/hg19_ALL.sites.2015_08.txt.idx.gz ... Failed

WARNING: Some files cannot be downloaded, including http://www.openbioinformatics.org/annovar/download/hg19_ALL. sites.2015_08.txt.idx.gz, http://www.openbioinformatics. org/annovar/download/hg19_ALL.sites.2015_08.txt.gz

perl ../annovar/table_annovar.pl example/ex1.avinput ../annovar/humandbm -buildver hg19 -remove -out example/myanno -protocol refGene,esp6500siv2_all,1000g2015aug_all,avsnp144, dbnsfp30a,clinvar20160302,exac03,dbscsnv11,dbnsfp31a interpro,rmsk,ensGene,knownGene -operation g,f,f,f,f,f,f,f,f,r,g,g -nastring .

Error: the required database file ../annovar/humandbm/hg19_ALL.sites.2015_08.txt does not exist.

Error: can't read the OMIM morbidmap disorder file intervardb/morbidmap

Error: Please download it from http://www.omim.org/downloads

Best wishes,

Nicky

From: Kai Wang notifications@github.com<mailto:notifications@github.com> Reply-To: WGLab/InterVar <reply@reply.github.com<mailto: reply@reply.github.com>> Date: Thursday, 9 February 2017 15:47 To: WGLab/InterVar <InterVar@noreply.github.com<mailto:InterVar@noreply. github.com>> Cc: "Whiffin, Nicola" <n.whiffin@lms.mrc.ac.uk<mailto: n.whiffin@lms.mrc.ac.uk>>, Author <author@noreply.github.com<mailto: author@noreply.github.com>> Subject: Re: [WGLab/InterVar] Error downloading from Annovar (#2) Resent-From: n.whiffin@lms.mrc.ac.uk<mailto:n.whiffin@lms.mrc.ac.uk> Resent-Date: Thursday, 9 February 2017 15:48

Nicky, You are not supposed to download this file hg19_ALL.sites.2015_08.txt.gz, which is why I asked you to provide your command. This file never existed. -Kai

On Thu, Feb 9, 2017 at 10:44 AM, Nicky Whiffin <notifications@github.com< mailto:notifications@github.com>> wrote:

Hi Quan Li,

Thank you very much for this. When I run the command the tool still tries to download 'hg19_ALL.sites.2015_08.txt.gz' - the name of the file you sent is different. How do I tell the tool to download this alternative file?

Many thanks, Nicky

From: Quan LI <notifications@github.com<mailto:notifications@github.com mailto:notifications@github.com> Reply-To: WGLab/InterVar <reply@reply.github.com<mailto: reply@reply.github.com><mailto: reply@reply.github.commailto:reply@reply.github.com>> Date: Thursday, 9 February 2017 15:09 To: WGLab/InterVar <InterVar@noreply.github.com<mailto:InterVar@noreply. github.com><mailto:InterVar@noreply. github.com>> Cc: "Whiffin, Nicola" <n.whiffin@lms.mrc.ac.uk<mailto: n.whiffin@lms.mrc.ac.uk><mailto: n.whiffin@lms.mrc.ac.ukmailto:n.whiffin@lms.mrc.ac.uk>>, Author < author@noreply.github.commailto:author@noreply.github.com<mailto: author@noreply.github.commailto:author@noreply.github.com>> Subject: Re: [WGLab/InterVar] Error downloading from Annovar (#2) Resent-From: <n.whiffin@lms.mrc.ac.uk<mailto:n.whiffin@lms.mrc.ac.uk mailto:n.whiffin@lms.mrc.ac.uk> Resent-Date: Thursday, 9 February 2017 15:09

The web server of http://www.openbioinformatics.org/annovar was in manitenance.

Now it is ok, you can download now.

NOTICE: Downloading annotation database http://www.openbioinformatics. org/annovar/download/hg19_1000g2015aug.zip ... OK

NOTICE: Uncompressing downloaded files

Also you can try http://wintervar.wglab.org for searching when there are some downloading problems

Best,

Quan LI

leequan@gmail.commailto:leequan@gmail.commailto:leequan@gmail.com

From: Kai Wang [mailto:notifications@github.com] Sent: Thursday, February 09, 2017 10:43 AM To: WGLab/InterVar <InterVar@noreply.github.com<mailto:InterVar@noreply. github.com><mailto:InterVar@noreply. github.com>> Cc: Subscribed <subscribed@noreply.github.com<mailto:subscribed@noreply. github.com><mailto:subscribed@noreply. github.com>> Subject: Re: [WGLab/InterVar] Error downloading from Annovar (#2)

please read FAQ #1.

On Thu, Feb 9, 2017 at 9:10 AM, Nicky Whiffin <notifications@github.com< mailto:notifications@github.com>< mailto:notifications@github.com> mailto:notifications@github.com > wrote:

I am getting the following notices when trying to run the tool:

NOTICE: Downloading annotation database http://www.openbioinformatics. org/annovar/download/hg19_ALL.sites.2015_08.txt.gz ... Failed NOTICE: Downloading annotation database http://www.openbioinformatics. org/annovar/download/hg19_ALL.sites.2015_08.txt.idx.gz ... Failed

These then result in an error:

Error: the required database file ../annovar/humandbm/hg19_ALL. sites.2015_08.txt does not exist.

When I go to the above addresses I get a URL not found error.

Please can you advise how to fix this?

Many thanks, Nicky

- You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/WGLab/InterVar/issues/2, or mute the thread https://github.com/notifications/unsubscribe-auth/AFptuMdtmIbOEHpdDL_ tdLxBZplTrjTIks5rax5agaJpZM4L8LIm .

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kaichop commented 7 years ago

Also see below, which you need to take care of yourself. We cannot include omim in intervar distribution.

Error: can't read the OMIM morbidmap disorder file intervardb/morbidmap

Error: Please download it from http://www.omim.org/downloads

On Thu, Feb 9, 2017 at 10:58 AM, Kai Wang kaichop@gmail.com wrote:

you can run below to fix the problem for now so that you can run intervar perl ../annovar/annotate_variation.pl -buildver hg19 -downdb -webfrom annovar 1000g2015aug ../annovar/humandbm

It looks like a bug in intervar to download the file below, which Quan will fix.

On Thu, Feb 9, 2017 at 10:55 AM, Nicky Whiffin notifications@github.com wrote:

Sorry Kai I might be being very stupid but when I run my command the script automatically tries to download this file. Full output is:

./Intervar.py -c config.ini --table_annovar=../annovar/table_annovar.pl --convert2annovar=../annovar/convert2annovar.pl --annotate_variation=../annovar/annotate_variation.pl --database_locat=../annovar/humandbm

============================================================

InterVar

Interpretation of Pathogenic/Benign for variants using python scripts of InterVar.

============================================================

%prog 0.1

Written by Quan LI,leequan@gmail.com.

InterVar is free for non-commercial use without warranty.

Please contact the authors for commercial use.

Copyright (C) 2016 Wang Genomic Lab

============================================================

Notice: Your command of InterVar is ['./Intervar.py', '-c', 'config.ini', '--table_annovar=../annovar/table_annovar.pl', '--convert2annovar=../annovar/convert2annovar.pl', '--annotate_variation=../annovar/annotate_variation.pl', '--database_locat=../annovar/humandbm']

INFO: The options are {'pp2_genes': 'intervardb/PP2.genes', 'inputfile': 'example/ex1.avinput', 'exclude_snps': 'intervardb/ext.variants.hg19', 'annotate_variation': '../annovar/annotate_variation.pl', 'ps4_snps': 'intervardb/PS4.variants.hg19', 'mim_recessive': 'intervardb/mim_recessive.txt', 'current_version': 'Intervar_20151116', 'bs2_snps': 'intervardb/BS2_hom_het.hg19', 'evidence_file': 'None', 'public_dev': 'https://github.com/WGLab/InterVar/releases', 'otherinfo': 'FALSE', 'database_names': 'refGene esp6500siv2_all 1000g2015aug avsnp144 dbnsfp30a clinvar_20160302 exac03 dbscsnv11 dbnsfp31a_interpro rmsk ensGene knownGene', 'mim_pheno': 'intervardb/mim_pheno.txt', 'table_annovar': '../annovar/table_annovar.pl', 'buildver': 'hg19', 'inputfile_type': 'AVinput', 'onetranscript': 'FALSE', 'mim2gene': 'intervardb/mim2gene.txt', 'orpha': 'intervardb/orpha.txt', 'ps1_aa': 'intervardb/PS1.AA.change.patho.hg19', 'mim_adultonset': 'intervardb/mim_adultonset.txt', 'morbidmap': 'intervardb/morbidmap', 'outfile': 'example/myanno', 'csvout': 'FALSE', 'knowngenecanonical': 'intervardb/knownGeneCanonical.txt', 'dot2underline': 'TRUE', 'convert2annovar': '../annovar/ convert2annovar.pl', 'database_locat': '../annovar/humandbm', 'database_intervar': 'intervardb', 'lof_genes': 'intervardb/PVS1.LOF.genes', 'disorder_cutoff': '0.01', 'mim_domin': 'intervardb/mim_domin.txt', 'pm1_domain': 'intervardb/PM1_domains_with_benigns', 'mim_orpha': 'intervardb/mim_orpha.txt', 'bp1_genes': 'intervardb/BP1.genes'}

Warning: the folder of ../annovar/humandbm is already created!

Warning: The Annovar dataset file of 1000g2015aug is not in ../annovar/humandbm,begin to download this ../annovar/humandbm/hg19_ALL.sites.2015_08.txt ...

perl ../annovar/annotate_variation.pl -buildver hg19 -downdb -webfrom annovar ALL.sites.2015_08 ../annovar/humandbm

NOTICE: Web-based checking to see whether ANNOVAR new version is available ... Done

NOTICE: Downloading annotation database http://www.openbioinformatics. org/annovar/download/hg19_ALL.sites.2015_08.txt.gz ... Failed

NOTICE: Downloading annotation database http://www.openbioinformatics. org/annovar/download/hg19_ALL.sites.2015_08.txt.idx.gz ... Failed

WARNING: Some files cannot be downloaded, including http://www.openbioinformatics.org/annovar/download/hg19_ALL. sites.2015_08.txt.idx.gz, http://www.openbioinformatics. org/annovar/download/hg19_ALL.sites.2015_08.txt.gz

perl ../annovar/table_annovar.pl example/ex1.avinput ../annovar/humandbm -buildver hg19 -remove -out example/myanno -protocol refGene,esp6500siv2_all,1000g2015aug_all,avsnp144,dbnsfp30a, clinvar_20160302,exac03,dbscsnv11,dbnsfp31a_interpro,rmsk,ensGene,knownGene -operation g,f,f,f,f,f,f,f,f,r,g,g -nastring .

Error: the required database file ../annovar/humandbm/hg19_ALL.sites.2015_08.txt does not exist.

Error: can't read the OMIM morbidmap disorder file intervardb/morbidmap

Error: Please download it from http://www.omim.org/downloads

Best wishes,

Nicky

From: Kai Wang <notifications@github.com<mailto:notifications@github.com

Reply-To: WGLab/InterVar <reply@reply.github.com<mailto: reply@reply.github.com>> Date: Thursday, 9 February 2017 15:47 To: WGLab/InterVar <InterVar@noreply.github.com<mailto: InterVar@noreply.github.com>> Cc: "Whiffin, Nicola" <n.whiffin@lms.mrc.ac.uk<mailto: n.whiffin@lms.mrc.ac.uk>>, Author <author@noreply.github.com<mailto: author@noreply.github.com>> Subject: Re: [WGLab/InterVar] Error downloading from Annovar (#2) Resent-From: n.whiffin@lms.mrc.ac.uk<mailto:n.whiffin@lms.mrc.ac.uk> Resent-Date: Thursday, 9 February 2017 15:48

Nicky, You are not supposed to download this file hg19_ALL.sites.2015_08.txt.gz, which is why I asked you to provide your command. This file never existed. -Kai

On Thu, Feb 9, 2017 at 10:44 AM, Nicky Whiffin <notifications@github.com mailto:notifications@github.com> wrote:

Hi Quan Li,

Thank you very much for this. When I run the command the tool still tries to download 'hg19_ALL.sites.2015_08.txt.gz' - the name of the file you sent is different. How do I tell the tool to download this alternative file?

Many thanks, Nicky

From: Quan LI <notifications@github.com<mailto:notifications@github.com mailto:notifications@github.com> Reply-To: WGLab/InterVar <reply@reply.github.com<mailto: reply@reply.github.com><mailto: reply@reply.github.commailto:reply@reply.github.com>> Date: Thursday, 9 February 2017 15:09 To: WGLab/InterVar <InterVar@noreply.github.com<mailto: InterVar@noreply.github.com><mailto:InterVar@noreply. github.com>> Cc: "Whiffin, Nicola" <n.whiffin@lms.mrc.ac.uk<mailto: n.whiffin@lms.mrc.ac.uk><mailto: n.whiffin@lms.mrc.ac.ukmailto:n.whiffin@lms.mrc.ac.uk>>, Author < author@noreply.github.commailto:author@noreply.github.com<mailto: author@noreply.github.commailto:author@noreply.github.com>> Subject: Re: [WGLab/InterVar] Error downloading from Annovar (#2) Resent-From: n.whiffin@lms.mrc.ac.uk<mailto:n.whiffin@lms.mrc.ac.uk< mailto:n.whiffin@lms.mrc.ac.uk>> Resent-Date: Thursday, 9 February 2017 15:09

The web server of http://www.openbioinformatics.org/annovar was in manitenance.

Now it is ok, you can download now.

NOTICE: Downloading annotation database http://www.openbioinformatics. org/annovar/download/hg19_1000g2015aug.zip ... OK

NOTICE: Uncompressing downloaded files

Also you can try http://wintervar.wglab.org for searching when there are some downloading problems

Best,

Quan LI

leequan@gmail.commailto:leequan@gmail.commailto:leequan@gmail.com

From: Kai Wang [mailto:notifications@github.com] Sent: Thursday, February 09, 2017 10:43 AM To: WGLab/InterVar <InterVar@noreply.github.com<mailto: InterVar@noreply.github.com><mailto:InterVar@noreply. github.com>> Cc: Subscribed <subscribed@noreply.github.com<mailto: subscribed@noreply.github.com><mailto:subscribed@noreply. github.com>> Subject: Re: [WGLab/InterVar] Error downloading from Annovar (#2)

please read FAQ #1.

On Thu, Feb 9, 2017 at 9:10 AM, Nicky Whiffin <notifications@github.com mailto:notifications@github.com< mailto:notifications@github.com> mailto:notifications@github.com > wrote:

I am getting the following notices when trying to run the tool:

NOTICE: Downloading annotation database http://www.openbioinformatics . org/annovar/download/hg19_ALL.sites.2015_08.txt.gz ... Failed NOTICE: Downloading annotation database http://www.openbioinformatics . org/annovar/download/hg19_ALL.sites.2015_08.txt.idx.gz ... Failed

These then result in an error:

Error: the required database file ../annovar/humandbm/hg19_ALL. sites.2015_08.txt does not exist.

When I go to the above addresses I get a URL not found error.

Please can you advise how to fix this?

Many thanks, Nicky

- You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/WGLab/InterVar/issues/2, or mute the thread https://github.com/notifications/unsubscribe-auth/ AFptuMdtmIbOEHpdDL_ tdLxBZplTrjTIks5rax5agaJpZM4L8LIm .

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  1. Unless the information is legally exempt from disclosure, the confidentiality of this email, and your reply cannot be guaranteed. The information and material in this email is intended for the use of the intended addressee or the person responsible for delivering it to the intended addressee. It may contain privileged or confidential information and/or copyright material. If you receive this email by mistake please advise the sender immediately by using the reply facility in your email software or notify Royal Brompton & Harefield NHS Foundation Trust Help Desk on +44(0) 20 7351 8696 <+44%2020%207351%208696> Communication is not sent through a secure server; Royal Brompton & Harefield NHS Foundation Trust cannot accept responsibility for the accuracy of outgoing electronic mail. Any views or opinions expressed are solely those of the author and do not represent the view of Royal Brompton & Harefield NHS Foundation Trust unless specifically stated.

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quanliustc commented 7 years ago

Hi, Nivky

Please redownload the InterVar, the download file problem for 1000g2015aug has been fixed.

Best,

Quan LI

leequan@gmail.com

From: Nicky Whiffin [mailto:notifications@github.com] Sent: Thursday, February 09, 2017 12:25 PM To: WGLab/InterVar InterVar@noreply.github.com Cc: Quan LI leequan@gmail.com; Comment comment@noreply.github.com Subject: Re: [WGLab/InterVar] Error downloading from Annovar (#2)

Sorry Kai I might be being very stupid but when I run my command the script automatically tries to download this file. Full output is:

./Intervar.py -c config.ini --table_annovar=../annovar/table_annovar.pl --convert2annovar=../annovar/convert2annovar.pl --annotate_variation=../annovar/annotate_variation.pl --database_locat=../annovar/humandbm

=============================================================================

InterVar

Interpretation of Pathogenic/Benign for variants using python scripts of InterVar.

=============================================================================

%prog 0.1

Written by Quan LI,leequan@gmail.com.

InterVar is free for non-commercial use without warranty.

Please contact the authors for commercial use.

Copyright (C) 2016 Wang Genomic Lab

============================================================================

Notice: Your command of InterVar is ['./Intervar.py', '-c', 'config.ini', '--table_annovar=../annovar/table_annovar.pl', '--convert2annovar=../annovar/convert2annovar.pl', '--annotate_variation=../annovar/annotate_variation.pl', '--database_locat=../annovar/humandbm']

INFO: The options are {'pp2_genes': 'intervardb/PP2.genes', 'inputfile': 'example/ex1.avinput', 'exclude_snps': 'intervardb/ext.variants.hg19', 'annotate_variation': '../annovar/annotate_variation.pl', 'ps4_snps': 'intervardb/PS4.variants.hg19', 'mim_recessive': 'intervardb/mim_recessive.txt', 'current_version': 'Intervar_20151116', 'bs2_snps': 'intervardb/BS2_hom_het.hg19', 'evidence_file': 'None', 'public_dev': 'https://github.com/WGLab/InterVar/releases', 'otherinfo': 'FALSE', 'database_names': 'refGene esp6500siv2_all 1000g2015aug avsnp144 dbnsfp30a clinvar_20160302 exac03 dbscsnv11 dbnsfp31a_interpro rmsk ensGene knownGene', 'mim_pheno': 'intervardb/mim_pheno.txt', 'table_annovar': '../annovar/table_annovar.pl', 'buildver': 'hg19', 'inputfile_type': 'AVinput', 'onetranscript': 'FALSE', 'mim2gene': 'intervardb/mim2gene.txt', 'orpha': 'intervardb/orpha.txt', 'ps1_aa': 'intervardb/PS1.AA.change.patho.hg19', 'mim_adultonset': 'intervardb/mim_adultonset.txt', 'morbidmap': 'intervardb/morbidmap', 'outfile': 'example/myanno', 'csvout': 'FALSE', 'knowngenecanonical': 'intervardb/knownGeneCanonical.txt', 'dot2underline': 'TRUE', 'convert2annovar': '../annovar/convert2annovar.pl', 'database_locat': '../annovar/humandbm', 'database_intervar': 'intervardb', 'lof_genes': 'intervardb/PVS1.LOF.genes', 'disorder_cutoff': '0.01', 'mim_domin': 'intervardb/mim_domin.txt', 'pm1_domain': 'intervardb/PM1_domains_with_benigns', 'mim_orpha': 'intervardb/mim_orpha.txt', 'bp1_genes': 'intervardb/BP1.genes'}

Warning: the folder of ../annovar/humandbm is already created!

Warning: The Annovar dataset file of 1000g2015aug is not in ../annovar/humandbm,begin to download this ../annovar/humandbm/hg19_ALL.sites.2015_08.txt ...

perl ../annovar/annotate_variation.pl -buildver hg19 -downdb -webfrom annovar ALL.sites.2015_08 ../annovar/humandbm

NOTICE: Web-based checking to see whether ANNOVAR new version is available ... Done

NOTICE: Downloading annotation database http://www.openbioinformatics.org/annovar/download/hg19_ALL.sites.2015_08.txt.gz ... Failed

NOTICE: Downloading annotation database http://www.openbioinformatics.org/annovar/download/hg19_ALL.sites.2015_08.txt.idx.gz ... Failed

WARNING: Some files cannot be downloaded, including http://www.openbioinformatics.org/annovar/download/hg19_ALL.sites.2015_08.txt.idx.gz, http://www.openbioinformatics.org/annovar/download/hg19_ALL.sites.2015_08.txt.gz

perl ../annovar/table_annovar.pl example/ex1.avinput ../annovar/humandbm -buildver hg19 -remove -out example/myanno -protocol refGene,esp6500siv2_all,1000g2015aug_all,avsnp144,dbnsfp30a,clinvar_20160302,exac03,dbscsnv11,dbnsfp31a_interpro,rmsk,ensGene,knownGene -operation g,f,f,f,f,f,f,f,f,r,g,g -nastring .

Error: the required database file ../annovar/humandbm/hg19_ALL.sites.2015_08.txt does not exist.

Error: can't read the OMIM morbidmap disorder file intervardb/morbidmap

Error: Please download it from http://www.omim.org/downloads

Best wishes,

Nicky

From: Kai Wang <notifications@github.com mailto:notifications@github.com%3cmailto:notifications@github.com mailto:notifications@github.com> Reply-To: WGLab/InterVar <reply@reply.github.com mailto:reply@reply.github.com%3cmailto:reply@reply.github.com mailto:reply@reply.github.com> Date: Thursday, 9 February 2017 15:47 To: WGLab/InterVar <InterVar@noreply.github.com mailto:InterVar@noreply.github.com%3cmailto:InterVar@noreply.github.com mailto:InterVar@noreply.github.com> Cc: "Whiffin, Nicola" <n.whiffin@lms.mrc.ac.uk mailto:n.whiffin@lms.mrc.ac.uk%3cmailto:n.whiffin@lms.mrc.ac.uk mailto:n.whiffin@lms.mrc.ac.uk>, Author <author@noreply.github.com mailto:author@noreply.github.com%3cmailto:author@noreply.github.com mailto:author@noreply.github.com> Subject: Re: [WGLab/InterVar] Error downloading from Annovar (#2) Resent-From: <n.whiffin@lms.mrc.ac.uk mailto:n.whiffin@lms.mrc.ac.uk%3cmailto:n.whiffin@lms.mrc.ac.uk mailto:n.whiffin@lms.mrc.ac.uk> Resent-Date: Thursday, 9 February 2017 15:48

Nicky, You are not supposed to download this file hg19_ALL.sites.2015_08.txt.gz, which is why I asked you to provide your command. This file never existed. -Kai

On Thu, Feb 9, 2017 at 10:44 AM, Nicky Whiffin <notifications@github.com mailto:notifications@github.com%3cmailto:notifications@github.com mailto:notifications@github.com> wrote:

Hi Quan Li,

Thank you very much for this. When I run the command the tool still tries to download 'hg19_ALL.sites.2015_08.txt.gz' - the name of the file you sent is different. How do I tell the tool to download this alternative file?

Many thanks, Nicky

From: Quan LI <notifications@github.com mailto:notifications@github.com%3cmailto:notifications@github.com mailto:notifications@github.commailto:notifications@github.com> Reply-To: WGLab/InterVar <reply@reply.github.com mailto:reply@reply.github.com%3cmailto:reply@reply.github.com mailto:reply@reply.github.com<mailto: <mailto:%0b> reply@reply.github.com mailto:reply@reply.github.com%3cmailto:reply@reply.github.com mailto:reply@reply.github.com>> Date: Thursday, 9 February 2017 15:09 To: WGLab/InterVar <InterVar@noreply.github.com mailto:InterVar@noreply.github.com%3cmailto:InterVar@noreply.github.com mailto:InterVar@noreply.github.com<mailto:InterVar@noreply. mailto:InterVar@noreply.%0b github.com>> Cc: "Whiffin, Nicola" <n.whiffin@lms.mrc.ac.uk mailto:n.whiffin@lms.mrc.ac.uk%3cmailto:n.whiffin@lms.mrc.ac.uk mailto:n.whiffin@lms.mrc.ac.uk<mailto: <mailto:%0b> n.whiffin@lms.mrc.ac.uk mailto:n.whiffin@lms.mrc.ac.uk%3cmailto:n.whiffin@lms.mrc.ac.uk mailto:n.whiffin@lms.mrc.ac.uk>>, Author <author@noreply.github.com mailto:author@noreply.github.com%3cmailto:author@noreply.github.com mailto:author@noreply.github.com<mailto: <mailto:%0b> author@noreply.github.com mailto:author@noreply.github.com%3cmailto:author@noreply.github.com mailto:author@noreply.github.com>> Subject: Re: [WGLab/InterVar] Error downloading from Annovar (#2) Resent-From: <n.whiffin@lms.mrc.ac.uk mailto:n.whiffin@lms.mrc.ac.uk%3cmailto:n.whiffin@lms.mrc.ac.uk mailto:n.whiffin@lms.mrc.ac.ukmailto:n.whiffin@lms.mrc.ac.uk> Resent-Date: Thursday, 9 February 2017 15:09

The web server of http://www.openbioinformatics.org/annovar was in manitenance.

Now it is ok, you can download now.

NOTICE: Downloading annotation database http://www.openbioinformatics. org/annovar/download/hg19_1000g2015aug.zip ... OK

NOTICE: Uncompressing downloaded files

Also you can try http://wintervar.wglab.org for searching when there are some downloading problems

Best,

Quan LI

leequan@gmail.com mailto:leequan@gmail.com%3cmailto:leequan@gmail.com%3e%3cmailto:leequan@gmail.com mailto:leequan@gmail.commailto:leequan@gmail.com

From: Kai Wang [mailto:notifications@github.com] Sent: Thursday, February 09, 2017 10:43 AM To: WGLab/InterVar <InterVar@noreply.github.com mailto:InterVar@noreply.github.com%3cmailto:InterVar@noreply.github.com mailto:InterVar@noreply.github.com<mailto:InterVar@noreply. mailto:InterVar@noreply.%0b github.com>> Cc: Subscribed <subscribed@noreply.github.com mailto:subscribed@noreply.github.com%3cmailto:subscribed@noreply.github.com mailto:subscribed@noreply.github.com<mailto:subscribed@noreply. mailto:subscribed@noreply.%0b github.com>> Subject: Re: [WGLab/InterVar] Error downloading from Annovar (#2)

please read FAQ #1.

On Thu, Feb 9, 2017 at 9:10 AM, Nicky Whiffin <notifications@github.com mailto:notifications@github.com%3cmailto:notifications@github.com mailto:notifications@github.com< mailto:notifications@github.com> mailto:notifications@github.com > wrote:

I am getting the following notices when trying to run the tool:

NOTICE: Downloading annotation database http://www.openbioinformatics. org/annovar/download/hg19_ALL.sites.2015_08.txt.gz ... Failed NOTICE: Downloading annotation database http://www.openbioinformatics. org/annovar/download/hg19_ALL.sites.2015_08.txt.idx.gz ... Failed

These then result in an error:

Error: the required database file ../annovar/humandbm/hg19_ALL. sites.2015_08.txt does not exist.

When I go to the above addresses I get a URL not found error.

Please can you advise how to fix this?

Many thanks, Nicky

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