I was wondering if anyone could give me advice about how to get the watson snps from biomart. I have already emailed the biomart user group.
I presume the problem I am having is due to the size of the data. I tried downloading all of the watson snps. A file download started but downloaded at a rate of 1kb per second and timed out after 12 hours. I then tried requesting the data by email but still hadn't received an email within 2 days. I tried the same thing by requesting just a single chromosome and faced the same problems: nothing received by an email request and a very slow download of about 1kb per second which i gave up on after 12 hours as it seemed stuck at 10mb and obviously wasn't going to get me the data.
What am i doing wrong? I appreciate it is a large data set and a slow query with complicated joins in the table but that doesn't seem to be the problem as the data starts to download.
I am also trying to get the watson snps via the ensembl perl api but there are 3mil and my code has only got 3k so far and I'm scared I'll have my ip blocked if i keep it running
retry or check your connection , it works fine here:
timecurl"ftp://jimwatsonsequence.cshl.edu/jimwatsonsequence/watson_snp.gff.gz"> /dev/null
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 27.2M 100 27.2M 0 0 114k 0 0:04:03 0:04:03 --:--:-- 123k
real 4m3.558s
user 0m0.336s
sys 0m0.568s
Just had a reply from them. They are checking the issue. I will let you know what they say