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Old 09-19-2012, 11:41 PM   #1
Sini
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Default Annovar: summarize_annovar.pl error

Hi!
I have been using Annovar for a little while now and so far I have only used the annotate annotate_variation.pl. Now I would like to use the summarize_annovar.pl for my exome data. I have been using this command:

summarize_annovar.pl -buildver hg19 inputsnp.human humandb/ -outfile summarizeoutput

and have been getting this error message:

NOTICE: Running step 1 with system command <annotate_variation.pl -geneanno -buildver hg19 -dbtype refgene -outfile summarizeoutput -exonsort inputsnp.human humandb/>
Can't exec "annotate_variation.pl": No such file or directory at summarize_annovar.pl line 110.
Error running system command: <annotate_variation.pl -geneanno -buildver hg19 -dbtype refgene -outfile summarizeoutput -exonsort inputsnp.human humandb/>


Have someone had similar problem and how can this be fixed?

sincerely,

Sini
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Old 09-20-2012, 01:53 AM   #2
oyvindbusk
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Hi Sini,

Have you remembered to put Annovar in your PATH? Unless you have, I think you will get that error message.

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Old 09-20-2012, 03:51 AM   #3
Sini
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Hi,

unfortunately I have very little experience about working with command lines.. so i don't actually know what this PATH is.. Could you tell me how I could put Annovar in my PATH, please?

Sini
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Old 09-20-2012, 04:45 AM   #4
oyvindbusk
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Hi,

If the path to your executables are e.g. "/illumina/runs/pipeline/annovar_2012/annovar", I would type:

"export PATH=$PATH:/illumina/runs/pipeline/annovar_2012/annovar"

Then you can type "echo $PATH" to see whether it has been added.

Not sure if this will solve it for you, but its worth a try.

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Old 09-21-2012, 12:22 AM   #5
Sini
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Hi,
I'll give it a try thank you!

Sini
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Old 09-21-2012, 06:54 AM   #6
AJERYC
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Quote:
Originally Posted by Sini View Post
Hi,
I'll give it a try thank you!

Sini
for me it had worked if you put "perl" at the start of the sentence if you have perl in the path. e.g.
perl summarize_annovar.pl -buildver hg19 inputsnp.human humandb/ -outfile summarizeoutput
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Old 09-21-2012, 06:55 AM   #7
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Quote:
Originally Posted by Sini View Post
Hi,
I'll give it a try thank you!

Sini
for me it had worked if you put "perl" at the start of the sentence provided that you have perl in the path. e.g.
perl summarize_annovar.pl -buildver hg19 inputsnp.human humandb/ -outfile summarizeoutput
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Old 09-26-2012, 03:02 AM   #8
Sini
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Hi!
I tried what oyvindbusk suggested, but unfortunately I get the same error message still. I have also used "perl" infront. Unfortunately my problems remains.

Sini
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Old 09-26-2012, 10:57 PM   #9
oyvindbusk
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Hm,

Does your Annovar-folder contain the annotate_variation.pl-file?

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Old 09-27-2012, 02:00 AM   #10
Sini
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Yes it does. I even downloaded the Annovar again and switched to more powerful computer, but it didn't help.

Sini
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Old 10-10-2012, 01:16 PM   #11
msl
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I'm experiencing the same problem. Sini, did you ever figure this out?
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Old 10-10-2012, 01:57 PM   #12
swbarnes2
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It sounds like you don't have perl installed, or your path to perl isn't working.

I'm surprised that you ever got the perl scripts to run without putting "perl" in front of them.
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Old 10-10-2012, 02:14 PM   #13
msl
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I have been starting each line with "perl" and annotate_variation.pl has worked for me, at least for downloading databases and such. Still getting that error.
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Old 10-10-2012, 04:11 PM   #14
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Ah nevermind. I followed oyvindbusk's tip and it seems to be running now. I had previously just misspelled something in my path. Thanks!
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