problem with installation of NCBI database for Ribopicker standalone

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hha...@gmail.com

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Oct 23, 2014, 9:38:28 PM10/23/14

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Hello,

I have encountered issues with the Green Genes database formatting for Ribopicker (see separated post).

Now I am having issues with the NCBI archaeal/bacterial complete genomes rRNA database. It seems like the perl script for formatting this database is broken as I get the following errors when I try to run it:

[hh09@dev3 helen]$ perl formatNcbiData.pl gbk_files.txt ncbibact20120117 > missing.txt
syntax error at formatNcbiData.pl line 192, near "$t qw(16S 23S 5S)"
Global symbol "$t" requires explicit package name at formatNcbiData.pl line 194.
Global symbol "$t" requires explicit package name at formatNcbiData.pl line 194.
Global symbol "$t" requires explicit package name at formatNcbiData.pl line 194.
Global symbol "$t" requires explicit package name at formatNcbiData.pl line 197.
Global symbol "$t" requires explicit package name at formatNcbiData.pl line 198.
Global symbol "$t" requires explicit package name at formatNcbiData.pl line 199.
Global symbol "$t" requires explicit package name at formatNcbiData.pl line 202.
Global symbol "$t" requires explicit package name at formatNcbiData.pl line 202.
Global symbol "$t" requires explicit package name at formatNcbiData.pl line 203.
Global symbol "$t" requires explicit package name at formatNcbiData.pl line 206.
Global symbol "$t" requires explicit package name at formatNcbiData.pl line 206.
Global symbol "$t" requires explicit package name at formatNcbiData.pl line 206.
Global symbol "$t" requires explicit package name at formatNcbiData.pl line 206.
syntax error at formatNcbiData.pl line 211, near "}"
formatNcbiData.pl has too many errors.

I have all the genomes ready to go so can someone please help me by fixing the script? TIA.