kaichop
commented
1 week ago You need to use perl annovar/annotate_variation.pl -build hg38 -downdb ensGene -webfrom annovar . to download the database first
There are two problems with your command: (1) you did not add "-webfrom annovar" (2) You cannot use "/file_gencode_v38" in your command because this is a directory under the root, and in most cases you do not have write permission to a root directory. I hope this helps.
On Tue, Nov 19, 2024 at 4:26 PM iegab @.***> wrote:
Hello everyone,
I am currently trying to run the following ANNOVAR command: perl annovar/annotate_variation.pl -build hg38 -out /file_gencode_v38 -dbtype ensGene
However, I'm encountering an issue that isn't providing any clear direction on how to proceed. I've also tried running the suggested commands provided in the error message, but unfortunately, I haven't had any success. Here is a summary of the issue: Error: The gene annotation database /file/hg38_ensGene.txt does not exist. Please use 'annotate_variation.pl --downdb ensGene /file -build hg38' to download the database. Then, NOTICE: Web-based checking to see whether ANNOVAR new version is available ... Done NOTICE: Downloading annotation database http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/ensGene.txt.gz ... Failed WARNING: Some files cannot be downloaded, including http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/ensGene.txt.gz ---------------------------ADDITIONAL PROCEDURE---------------------------
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 hg38 --downdb seq /file/hg38_seqretrieve_seq_from_fasta.pl /file/hg38_ensGene.txt -seqdir /file/hg38_seq -format ensGene -outfile /file/hg38_ensGeneMrna.fa
The last error after running these two codes are : 1- NOTICE: Web-based checking to see whether ANNOVAR new version is available ... Done NOTICE: Downloading annotation database http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/chromFa.zip ... Failed NOTICE: Downloading annotation database http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/chromFa.tar.gz ... Failed NOTICE: Downloading annotation database http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.chromFa.tar.gz ... OK NOTICE: Downloading annotation database http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz ... OK NOTICE: Uncompressing downloaded files NOTICE: Finished downloading annotation files for hg38 build version, with files saved at the '/file' directory. 2- Error: cannot read from regionfile /file/hg38_ensGene.txt: No such file or directory
Despite trying these steps, I'm still unable to successfully proceed. Could anyone please provide guidance on how to resolve this issue or any insights into what might be going wrong? Your help would be highly appreciated!
Thank you so much! Best
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iegab
Hello everyone,
I am currently trying to run the following ANNOVAR command: perl annovar/annotate_variation.pl -build hg38 -out /file_gencode_v38 -dbtype ensGene
However, I'm encountering an issue that isn't providing any clear direction on how to proceed. I've also tried running the suggested commands provided in the error message, but unfortunately, I haven't had any success. Here is a summary of the issue:
Error: The gene annotation database /file/hg38_ensGene.txt does not exist. Please use 'annotate_variation.pl --downdb ensGene /file -build hg38' to download the database. Then, NOTICE: Web-based checking to see whether ANNOVAR new version is available ... Done NOTICE: Downloading annotation database http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/ensGene.txt.gz ... Failed WARNING: Some files cannot be downloaded, including http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/ensGene.txt.gz ---------------------------ADDITIONAL PROCEDURE---------------------------
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):
The last error after running these two codes are : 1- NOTICE: Web-based checking to see whether ANNOVAR new version is available ... Done NOTICE: Downloading annotation database http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/chromFa.zip ... Failed NOTICE: Downloading annotation database http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/chromFa.tar.gz ... Failed NOTICE: Downloading annotation database http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.chromFa.tar.gz ... OK NOTICE: Downloading annotation database http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz ... OK NOTICE: Uncompressing downloaded files NOTICE: Finished downloading annotation files for hg38 build version, with files saved at the '/file' directory. 2- Error: cannot read from regionfile /file/hg38_ensGene.txt: No such file or directory
Despite trying these steps, I'm still unable to successfully proceed. Could anyone please provide guidance on how to resolve this issue or any insights into what might be going wrong? Your help would be highly appreciated!
Thank you so much! Best