I have some WGS data from mouse models and I am trying to use annovar for gene annotation. However I am getting stuck at the step where I download the mouse database for my analysis. I get this error when I attempt to download the mouse database from web.

NOTICE: the FASTA file for the genome is not available to download but can be generated by the ANNOVAR software.

PLEASE RUN THE FOLLOWING TWO COMMANDS CONSECUTIVELY TO GENERATE THE FASTA FILES (you may need to change -seqdir to -seqfile for some genomes):

annotate_variation.pl --buildver mm10 --downdb seq mousedb/mm10_seq

retrieve_seq_from_fasta.pl mousedb/mm10_refGene.txt -seqdir mousedb/mm10_seq -format refGene -outfile mousedb/mm10_refGeneMrna.fa

After running the two commands I am getting this error:

NOTICE: Downloading annotation database http://hgdownload.cse.ucsc.edu/goldenPath/mm10/bigZips/chromFa.zip ... Failed

NOTICE: Downloading annotation database http://hgdownload.cse.ucsc.edu/goldenPath/mm10/bigZips/chromFa.tar.gz ...

[ Done

NOTICE: Downloading annotation database http://hgdownload.cse.ucsc.edu/goldenPath/mm10/bigZips/mm10.chromFa.tar.gz ... Failed

NOTICE: Downloading annotation database http://hgdownload.cse.ucsc.edu/goldenPath/mm10/bigZips/mm10.fa.gz ...

Done

NOTICE: Uncompressing downloaded files

chr2.fa: truncated gzip input

tar: Error exit delayed from previous errors.

gunzip: mm10.fa.gz: unexpected end of file

gunzip: mm10.fa.gz: uncompress failed

NOTICE: Finished downloading annotation files for mm10 build version, with files saved at the 'mousedb/mm10_seq' directory

I am not sure how to fix this error. Any help would be highly appreciated.

Thank you

Vrushali