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Syntax Error near unexpected token (

I try to convert tblout to gff

grep -v ^\# my.cmscan.tblout | awk ‘ { printf(“%s\tinfernal\t%s\t%s\t%s\t%s\t%s\t.\n”, $4, $2, $10, $11, $17, $12); }’ > my.cmscan.gff

syntax error near unexpected token »(«

infernal ncrna
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updated by GenoMax GenoMax • written by ana_maumau • ana_maumau

1 answer

You have to use single quotation ('') inside awk brackets:

grep -v ^# my.cmscan.tblout | awk {' printf(“%s\tinfernal\t%s\t%s\t%s\t%s\t%s\t.\n”, $4, $2, $10, $11, $17, $12); '} > my.cmscan.gff
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written by elcortegano elcortegano

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