Dear Jen. Yes, that was my problem, I skipped some steps by relying too much on the screencast and ignoring the text. Now I am reluctant to launch the AMI as I having trouble estimating my usage and costs on AWS - as a new user I have little idea what to set many of the parameters in the usage calculator. Are there any examples of typical parameters and costs for running Galaxy on the cloud? My first task is to map about 80 gbp of total paired end reads from genomic DNA from two accessions to a 900 mbp reference genome and then find SNPs and INDELs. A ball-park figure would be reassuring! regards Andrew ________________________________ From: Jennifer Jackson [jen@bx.psu.edu] Sent: 09 April 2013 15:11 To: Thompson, Andrew Cc: 'galaxy-user@lists.bx.psu.edu' Subject: Re: [galaxy-user] merging fastq files Hi Andrew, My first guess is that perhaps the region is not set correctly? http://wiki.galaxyproject.org/CloudMan/AWS/GettingStarted See " Step 1: One Time Amazon Setup", subsection 2, where region is " set your AWS Region to US East (Virginia)". The image in the wiki for step 1.2 is slightly outdated, instead it will look like this: [cid:part2.09010203.02020409@bx.psu.edu] Please give this a try and let us know if you continue to have issues. Thanks! Jen Galaxy team On 4/8/13 3:56 PM, Thompson, Andrew wrote: Dear Jen Thanks. I have merged the files and end up with 4 x 47 G fastq files for read mapping to the reference. It seems this is too much data to analyse on the public main instance if the size limit is 250 G? So I tried to set up the cloud option following the screencast (http://screencast.g2.bx.psu.edu/cloud/), but when I search for the current AMI name (861460482541/galaxy-cloudman-2011-03-22) it is not found in the list of community AMIs under Amazon's EC2 Management Console. Any ideas why this is not working? regards Andrew -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org
