[ensembl-dev] Error in dump_transcripts.pl from the blog post Human BodyMap 2.0 data from Illumina

th3 th3 at sanger.ac.uk
Fri Aug 24 15:15:34 BST 2012


Hi Jerry,
You need bioperl in your PERL5LIB.
We are using bioperl-1.2.3 so I would recommend you to use this one. 
(But the newest bioperl should work too)

Hope this help

Thibaut

==============================================================

I ran the script dump_transcripts.pl listed above and got a whole bunch 
of errors such as those listed below. Does the new release of Ensembl 68 
have something to do with it where modules were changed? I re-installed 
Emsembl API but it still doesn’t work. Perhaps the name of the modules 
changed thus they need to be changed in the script as well? Please 
advice. Thank you!

Error Output:
——————– WARNING ———————-
MSG: ‘Bio::EnsEMBL::DBSQL::GeneAdaptor’ cannot be found.
Exception Can’t locate Bio/PrimarySeqI.pm in @INC (

BEGIN failed–compilation aborted at 
/home/jli/src/ensembl/modules/Bio/EnsEMBL/Slice.pm line 62.
Compilation failed in require at 
/home/jli/src/ensembl/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm line 99.
BEGIN failed–compilation aborted at 
/home/jli/src/ensembl/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm line 99.
Compilation failed in require at 
/home/jli/src/ensembl/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm line 67.
BEGIN failed–compilation aborted at 
/home/jli/src/ensembl/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm line 67.
Compilation failed in require at (eval 8) line 3.

FILE: Bio/EnsEMBL/Registry.pm LINE: 1015
CALLED BY: dump_transcripts.pl LINE: 88
Date (localtime) = Thu Aug 23 16:54:56 2012
Ensembl API version = 68

Jerry





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