download data- no genome

[fifdick]

I followed the instructions on the README.
I executed downloadData.sh, which threw no error. All subsequent steps were also successful until I wanted to start alignment. The index file for the genome was missing. I failed to index it with samtools. After checking the file (the genome), I saw it was empty.
I checked the script downloadData.sh for the genome download link and found this:

url38="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"

Trying to execute:
wget --progress=bar -O test.gz 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
Gave me error:

No such directory ‘genomes/all/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids’.

After checking the ftp page I found this to be the correct link, with which the download of the genome worked and subsequently also the indexing with samtools and the rest of the following steps.

ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/

[GodloveD]

I also ran into this error. It would be nice to see the download script updated.

[martenj]

Hi,
sorry for this (huge) delay. The download scripts should be fixed now in release 0.3.

Best.