Problem during references download using create_reference_dataset.pl

[jfspinella]

Hello,

When I'm running the create_reference_dataset.pl script, I obtain several warnings from bioperl (see below (1)) and a final error message (2).

deFuse version: 0.6.1
Perl version: v5.10.1, Operating system: linux

Thank you for your help.
Regards,

(1)
--------------------- WARNING ---------------------
MSG: Sequence is not dna or rna, but []. Attempting to revcom, but unsure if this is right

---

--------------------- WARNING ---------------------
MSG: Got a sequence with no letters in it cannot guess alphabet

---

(2)
Writing cds sequences
Use of uninitialized value in concatenation (.) or string at create_reference_dataset.pl line 365.

[Andrew]

Can you try deleting the bioperl fasta index? It may be corrupt. I believe the filename is:

Homo_sapiens.GRCh37.69.dna.chromosomes.fa.index

in your dataset directory.

Then rerun create_reference_dataset.pl

[jfspinella]

It works fine.
Thank you very much !