Changed back the overlap and chunk_size to 1000 and 100000. The chunk_size was too big at 1000000.  Added quotes round dbname to allow for white spaces in species name. Added :s when using the run directory in the compile_BLAT_results routine.
Changed back the overlap and chunk_size to 1000 and 100000. The chunk_size was too big at 1000000.  Added quotes round dbname to allow for white spaces in species name. Added :s when using the run directory in the compile_BLAT_results routine.

danstaines/ensembl-compara,Ensembl/ensembl-compara,kumarsaurabh20/ensembl-compara,etapanari/ensembl-compara,Ensembl/ensembl-compara,ckongEbi/ensembl-compara,Ensembl/ensembl-compara,ckongEbi/ensembl-compara,ckongEbi/ensembl-compara,danstaines/ensembl-compara,etapanari/ensembl-compara,Ensembl/ensembl-compara,kumarsaurabh20/ensembl-compara,etapanari/ensembl-compara,kumarsaurabh20/ensembl-compara,danstaines/ensembl-compara,dbolser-ebi/ensembl-compara,danstaines/ensembl-compara,Ensembl/ensembl-compara,Ensembl/ensembl-compara,danstaines/ensembl-compara,etapanari/ensembl-compara,kumarsaurabh20/ensembl-compara,Ensembl/ensembl-compara,dbolser-ebi/ensembl-compara,dbolser-ebi/ensembl-compara,Ensembl/ensembl-compara