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problem with auto_annovar seqsyd Bioinformatics 5 06-27-2012 01:29 AM
quation on using kjaja Bioinformatics 0 01-03-2012 06:57 AM

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Old 07-27-2011, 01:38 AM   #1
Location: den haag

Join Date: Jul 2011
Posts: 10
Default auto_annovar

can anyone tell me what's wrong

[abakelaar@iPipeline annovar]$ perl -model recessive 0004_61WDG_s_5 humandb/hg18/ --buildver hg18 NOTICE: the --ver1000g argument is set as '1000g' by default

NOTICE: Running step 1 with system command < -geneanno -buildver hg18 -dbtype refgene -outfile 0004_61WDG_s_5.step1 0004_61WDG_s_5 humandb/hg18/>
Can't exec "": No such file or directory at line 131.
Error running system command: < -geneanno -buildver hg18 -dbtype refgene -outfile 0004_61WDG_s_5.step1 0004_61WDG_s_5 humandb/hg18/>
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Old 07-27-2011, 03:56 AM   #2
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Location: Netherlands

Join Date: Mar 2011
Posts: 2

Annovar requires that the script is somewhere in your global execution path.

What I've done is make a symbolic link in /usr/local/bin that points to the script.

Use ln -s to do so (
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Old 08-26-2012, 06:49 AM   #3
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Location: China

Join Date: Oct 2011
Posts: 3

Hey guy,
When I finished making the "symbolic link" as you indicated , the "Error running system command" message was still there ,with the message "Can't exec "" missed. And now I was so confused.
[ps] I use Cygwin.
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