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WGLab / icages

iCAGES (integrated CAncer GEnome Score) is an effective tool for prioritizing cancer driver genes for a patient
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Problem of db.tar.gz #7

Open Tinalxt opened 7 years ago

Tinalxt commented 7 years ago

hi~ I had got a problem. It feels like there are something wrong with the database. I had downloaded the database twice. tar -xzvf /Workspace/Software/icages-1.0.2/db.tar.gz ./db/ ./db/cgc.gene ./db/drug.score ./db/hg19_example_db_generic.txt ./db/hg19_example_db_gff3.txt ./db/hg19_funseq2.txt

gzip: stdin: invalid compressed data--format violated tar: Unexpected EOF in archive tar: Unexpected EOF in archive tar: Error is not recoverable: exiting now How can I fit it? Thanks~

kaichop commented 7 years ago

Download again, file is corrupted.

Sent from my iPhone

On Apr 20, 2017, at 5:51 AM, Tinalxt notifications@github.com wrote:

hi~ I had got a problem. It feels like there are something wrong with the database. I had downloaded the database twice. tar -xzvf /Workspace/Software/icages-1.0.2/db.tar.gz ./db/ ./db/cgc.gene ./db/drug.score ./db/hg19_example_db_generic.txt ./db/hg19_example_db_gff3.txt ./db/hg19_funseq2.txt

gzip: stdin: invalid compressed data--format violated tar: Unexpected EOF in archive tar: Unexpected EOF in archive tar: Error is not recoverable: exiting now How can I fit it? Thanks~

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baopinjie commented 5 years ago

i face to same problem. how can I download database file? thanks.

kaichop commented 5 years ago

You can get the file from http://www.openbioinformatics.org/annovar/download/icages/hg18_db.tar.gz and http://www.openbioinformatics.org/annovar/download/icages/hg38_db.tar.gz .

On Thu, Feb 7, 2019 at 12:21 AM baopinjie notifications@github.com wrote:

i face to same problem. how can I download database file? thanks.

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coco90417 commented 5 years ago

Thanks Dr. Wang,

I’ve already replied him privately days ago, but will remember to keep you posted next time.

Sincerely,

Coco

On Feb 9, 2019, at 1:35 PM, Kai Wang notifications@github.com wrote:

You can get the file from http://www.openbioinformatics.org/annovar/download/icages/hg18_db.tar.gz and http://www.openbioinformatics.org/annovar/download/icages/hg38_db.tar.gz .

On Thu, Feb 7, 2019 at 12:21 AM baopinjie notifications@github.com wrote:

i face to same problem. how can I download database file? thanks.

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gongsj commented 5 years ago

hi, I have a problem with the db.tar.gz. I cannot download the db.tar.gz database from URL http://icages.wglab.org/download/icages/db.tar.gz, given by the official website. how can I download the db.tar.gz? Thanks!

kaichop commented 5 years ago

you can read the comments above and download from those URL

gongsj commented 5 years ago

Thanks for reply so timely! But I guess the URL you gave in the above comment is about the reference genome. When I run the ICAGES like this: mypath-to-the-icages/icages.pl ./input.txt ...... NOTICE: start loading databases NOTICE: start extracting suppressor genes cannot open /thinker/globe/udata/big/gongshj/software/icages/db/suppressor.gene ERROR: cannot call icagesMutation module

maybe I didn't download the db.tar.gz database which contains the information ICAGES needed. where can I download it?Thanks!

kaichop commented 5 years ago

You can get the file from http://www.openbioinformatics.org/annovar/download/icages/hg18_db.tar.gz and http://www.openbioinformatics.org/annovar/download/icages/hg38_db.tar.gz or hg19.

On Tue, Mar 5, 2019 at 12:24 AM gongsj notifications@github.com wrote:

Thanks for reply so timely! But I guess the URL you gave in the above comment is about the reference genome. When I run the ICAGES like this: mypath-to-the-icages/icages.pl ./input.txt ...... NOTICE: start loading databases NOTICE: start extracting suppressor genes cannot open /thinker/globe/udata/big/gongshj/software/icages/db/suppressor.gene ERROR: cannot call icagesMutation module

maybe I didn't download the db.tar.gz database which contains the information ICAGES needed. where can I download it?Thanks!

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/WGLab/icages/issues/7#issuecomment-469542852, or mute the thread https://github.com/notifications/unsubscribe-auth/AFptuOyfBthy1tpFp7C_dhDmBxJ5ehoQks5vTf-WgaJpZM4NCy_p .

coco90417 commented 5 years ago

Dr. Wang,

Is there a copy of the directory that I previously used, I can take a look over the next weekend and update the corresponding url? It seems that he is missing several db files, not just exome wide annotation.

Sincerely,

Coco

On Mar 5, 2019, at 12:37 AM, Kai Wang notifications@github.com wrote:

You can get the file from http://www.openbioinformatics.org/annovar/download/icages/hg18_db.tar.gz and http://www.openbioinformatics.org/annovar/download/icages/hg38_db.tar.gz or hg19.

On Tue, Mar 5, 2019 at 12:24 AM gongsj notifications@github.com wrote:

Thanks for reply so timely! But I guess the URL you gave in the above comment is about the reference genome. When I run the ICAGES like this: mypath-to-the-icages/icages.pl ./input.txt ...... NOTICE: start loading databases NOTICE: start extracting suppressor genes cannot open /thinker/globe/udata/big/gongshj/software/icages/db/suppressor.gene ERROR: cannot call icagesMutation module

maybe I didn't download the db.tar.gz database which contains the information ICAGES needed. where can I download it?Thanks!

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/WGLab/icages/issues/7#issuecomment-469542852, or mute the thread https://github.com/notifications/unsubscribe-auth/AFptuOyfBthy1tpFp7C_dhDmBxJ5ehoQks5vTf-WgaJpZM4NCy_p .

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npavlovikj commented 3 years ago

Dear,

I am trying to download the data files for icages, but both provided links http://www.openbioinformatics.org/annovar/download/icages/hg18_db.tar.gz and http://icages.wglab.org/download/icages/db.tar.gz do not work. Can you please provide me links I can use instead?

Thank you, Natasha