ANNOVAR not working

Question: ANNOVAR not working

2.9 years ago by

raitis • 20

Latvia

raitis • 20 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 • 1.2k views

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modified 5 months ago by ximenabonilla • 0 • written 2.9 years ago by raitis • 20

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 REPLY • link modified 2.9 years ago • written 2.9 years ago by Jennifer Hillman Jackson ♦ 25k

2.9 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 2.9 years ago by Jennifer Hillman Jackson ♦ 25k

2.9 years ago by

raitis • 20

Latvia

raitis • 20 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 COMMENT • link written 2.9 years ago by raitis • 20

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 REPLY • link written 16 months ago by Jennifer Hillman Jackson ♦ 25k

5 months ago by

ximenabonilla • 0

ximenabonilla • 0 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 COMMENT • link written 5 months ago by ximenabonilla • 0

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

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