Annovar db not downloading

[silviatgl]

Dear all,

I just installed tapes, and when I run the command:

python3 tapes.py db -s -A /path/to/annovar/

Throws an error (see photo)

Any help?

thanks!

[FedikZe]

Hi, I have same problem.. python3 tapes.py db -s -A /home/fil/annovar/

NOTICE: Web-based checking to see whether ANNOVAR new version is available ... Done NOTICE: Downloading annotation database http://www.openbioinformatics.org/annovar/download/hg19_avdblist.txt.gz ... Failed WARNING: Some files cannot be downloaded, including http://www.openbioinformatics.org/annovar/download/hg19_avdblist.txt.gz NOTICE: Web-based checking to see whether ANNOVAR new version is available ... Done NOTICE: Downloading annotation database http://www.openbioinformatics.org/annovar/download/hg38_avdblist.txt.gz ... Failed WARNING: Some files cannot be downloaded, including http://www.openbioinformatics.org/annovar/download/hg38_avdblist.txt.gz Traceback (most recent call last): File "tapes.py", line 421, in tf.check_online_annovar_dbs(annovar_path) File "/home/fil/tapes/src/t_func.py", line 888, in check_online_annovar_dbs with open(outfile_hg19, 'r') as file: FileNotFoundError: [Errno 2] No such file or directory: '/home/fil/annovar/hg19_avdblist.txt'

I think there is a problem with a link to db, because now is annovar.openbioinformatics....

[a-xavier]

Hi,

I had a look and I was able to replicate the error.

It looks like ANNOVAR itself does not produce the expected output hg19_avdblist.txt when using the command perl annotate_variation.pl -buildver hg19 -downdb -webfrom annovar avdblist ./.

The problem comes from ANNOVAR itself so we can expect it to be fixed pretty soon. Using any other argument (such as a real database such as clinvar_20190305 instead of avdblist) does work and downloads the proper database.

As a workaround, I attached 2 relatively recent avdblist files. hg19_avdblist.txt hg38_avdblist.txt They need to be placed in the ANNOVAR folder (where annotate_variation.pl is located)

When downloading the list of ANNOVAR database fails, it will use those instead.

I will investigate a better solution soon.

Kind regards, Alex

[silviatgl]

thank you so much!

On Mon, 9 Nov 2020 at 04:05, a-xavier notifications@github.com wrote:

Hi,

I had a look and I was able to replicate the error.

It looks like ANNOVAR itself does not produce the expected output hg19_avdblist.txt when using the command perl annotate_variation.pl -buildver hg19 -downdb -webfrom annovar avdblist ./.

The problem comes from ANNOVAR itself so we can expect it to be fixed pretty soon. Using any other argument (such as a real database such as clinvar_20190305 instead of avdblist) does work and downloads the proper database.

As a workaround, I attached 2 relatively recent avdblist files. hg19_avdblist.txt https://github.com/a-xavier/tapes/files/5507866/hg19_avdblist.txt hg38_avdblist.txt https://github.com/a-xavier/tapes/files/5507867/hg38_avdblist.txt They need to be placed in the ANNOVAR folder (where annotate_variation.pl is located)

When downloading the list of ANNOVAR database fails, it will use those instead.

I will investigate a better solution soon.

Kind regards, Alex

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[FedikZe]

Thank you, it works now with lists.