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lh3 / bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
GNU General Public License v3.0
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run-gen-ref hs38 link broken #115

Closed d-cameron closed 7 years ago

d-cameron commented 7 years ago

run-gen-ref cannot be used to download hs38/hs38DH as the dowload link is broken:

 $ ./run-gen-ref hs38DH
--2017-03-16 10:58:37--  ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_full_analysis_set.fna.gz
           => â-â
Resolving ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)... 130.14.250.12, 2607:f220:41e:250::12
Connecting to ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)|130.14.250.12|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done.    ==> PWD ... done.
==> TYPE I ... done.  ==> CWD (1) /genomes/all/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids ...
No such directory âgenomes/all/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_idsâ.

gzip: stdin: unexpected end of file

Please run 'bwa index hs38DH.fa'...
d-cameron commented 7 years ago

Same underlying issue as #110

lh3 commented 7 years ago

Via #123.