I'm trying to install GRCh38 and it fails each time with an unexpected end of file (run-gen-ref for hs38a and hs38DH fail exactly the same way). It seems to be unable to locate all of the chromosomes, unplaced and unlocalized contigs and EBV files.

Any help would be greatly appreciated.

Thank you very much.

-bash-4.1$ bwa.kit/run-gen-ref hs38
--2016-05-27 15:52:54-- ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh38/seqs_for_alignment_pipelines/GCA_000001405.15_GRCh38_full_analysis_set.fna.gz
=> “-”
Resolving ftp.ncbi.nlm.nih.gov... 130.14.250.10, 2607:f220:41e:250::12
Connecting to ftp.ncbi.nlm.nih.gov|130.14.250.10|:21… connected.

Logging in as anonymous ... Logged in!
==> SYST ... done. ==> PWD … done.
==> TYPE I ... done. ==> CWD (1) /genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh38/seqs_for_alignment_pipelines …
No such directory “genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh38/seqs_for_alignment_pipelines”.

gzip: stdin: unexpected end of file