Question: ANNOVAR not working
2
gravatar for raitis
2.4 years ago by
raitis20
Latvia
raitis20 wrote:

Hello,

 

Tried using ANNOVAR Annotate VCF and got following message in return (tested with several files that worked before and different settings):

 

582 ANNOVAR Annotate VCF on data 379

empty

formatvcf

databasehg19

Log: tool progress Log: tool progress Unknown option: vcfinput

Usage: table_annovar.pl [arguments] <query-file> <database-location>

Optional arguments: -h, --help print help message -m, --man

 

Does others have the same problem? Is ANNOVAR down? Any workarround?

 

Thanks!

 

It was caused by output file type set as VCF. When output is switched to tabular everything works fine.

software error • 909 views
ADD COMMENTlink modified 12 days ago by ximenabonilla0 • written 2.4 years ago by raitis20

Hi - Are you working at http://usegalaxy.org? If the dataset is in an error state (red), please send in a bug report. If it is green (indicating success but with no useful output), please create a shared history link and mail that galaxy-bugs@lists.galaxyproject.org. Include a link to this post with either. We'd like to investigate using your exact inputs and option selection. Thanks! Jen, Galaxy team

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by Jennifer Hillman Jackson25k
0
gravatar for Jennifer Hillman Jackson
2.4 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello Raitis,

This is a true bug, thanks for sharing the history so we could confirm. It appears that the VCF option was added but may not be implemented correctly. Our development team will investigate the root cause.

You can track the resolution of the problem by following this github issue: https://github.com/galaxyproject/tools-devteam/issues/323

For now, the workaround is to use tabular output.

Thank you! Jen, Galaxy team

ADD COMMENTlink written 2.4 years ago by Jennifer Hillman Jackson25k
0
gravatar for raitis
2.4 years ago by
raitis20
Latvia
raitis20 wrote:

Hello,

Now it seems that ANNOVAR tool is totally down. Got empty file and following (green) message:

 

605 ANNOVAR Annotate VCF on data 604

1 line

format:tabular

database:hg19

Log: tool progress Log: tool progress Can't use an undefined value as a symbol reference at /galaxy/main/deps/annovar/20140211/bin/convert2annovar.pl line 1844, <VAR> line 1. ----------------------------------------------------------------- NOTICE: Proce

ADD COMMENTlink written 2.4 years ago by raitis20

For you and others finding this post. This is a known issue and the development team will be reviewing. Use the prior version of the tool for now. Follow the ticket linked above plus the one associated with it in Github for progress and details.

ADD REPLYlink written 11 months ago by Jennifer Hillman Jackson25k
0
gravatar for ximenabonilla
12 days ago by
ximenabonilla0 wrote:

Hello! Has this problem been looked into? I am still having this problem years later and I am not sure if I'm doing something wrong or if it has not been solved. thanks!

ADD COMMENTlink written 12 days ago by ximenabonilla0
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