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</o:shapelayout></xml><![endif]--></head><body lang=EN-GB link=blue vlink=purple><div class=WordSection1><p class=MsoNormal>Dear Maker developers,<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>I’ve already contacted you a while ago about my annotation of the birch genome (Betula nana). As I am constantly running into problems using our cluster facilities at QMUL I thought of moving into the cloud. As I am rather inexperienced in cloud computing I have several questions:<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoListParagraph style='text-indent:-18.0pt;mso-list:l1 level1 lfo2'><![if !supportLists]><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'> </span></span><![endif]>To me it seems that there are two different Maker images on EC2 – ami-ea661f83 and <span class=value>ami-b10abed8 – which one is “the right one”?</span><o:p></o:p></p><p class=MsoListParagraph style='text-indent:-18.0pt;mso-list:l1 level1 lfo2'><![if !supportLists]><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'> </span></span><![endif]>Can I use this Maker AMI for the annotation of a whole genome or is it only suitable for the tutorial tasks?<o:p></o:p></p><p class=MsoListParagraph style='text-indent:-18.0pt;mso-list:l1 level1 lfo2'><![if !supportLists]><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'> </span></span><![endif]>Also, when I followed the steps outlined in the tutorial, there seemed to be a problem with RepeatMasker. Although Maker would run and produce output files, the log file stated that the contig had failed after the second attempt. I launched the image on a T1.micro instance, maybe that wasn’t enough computing power? Or do you have another explanation for this?<o:p></o:p></p><p class=MsoListParagraph style='text-indent:-18.0pt;mso-list:l1 level1 lfo2'><![if !supportLists]><span style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'> </span></span><![endif]>Would it be possible to run the annotation in parallel (e.g. using MPICH2) in the cloud? I’ve also recently heard about a parallelisation module for use in the cloud developed by Era7, called “nispero”. But I am not sure whether it is publicly available yet.<o:p></o:p></p><p class=MsoListParagraph style='text-indent:-18.0pt;mso-list:l1 level1 lfo2'><![if !supportLists]><span style='mso-list:Ignore'>5.<span style='font:7.0pt "Times New Roman"'> </span></span><![endif]>Do you have any experience of how long an annotation task in the cloud would take and also what the expected costs would be? The birch genome is only 500 MB in size and currently I am simply annotating it with a SNAP trained HMM. However, in the future I will feed it with RNAseq data as well.<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Many thanks in advance and kind regards,<o:p></o:p></p><p class=MsoNormal>Jasmin<o:p></o:p></p><p class=MsoNormal> <o:p></o:p></p><p class=MsoNormal><span style='mso-fareast-language:EN-GB'>-----------------------------<o:p></o:p></span></p><p class=MsoNormal><i><span style='mso-fareast-language:EN-GB'>Jasmin Zohren<o:p></o:p></span></i></p><p class=MsoNormal><i><span style='mso-fareast-language:EN-GB'>PhD student in the INTERCROSSING ITN<o:p></o:p></span></i></p><p class=MsoNormal><i><span style='mso-fareast-language:EN-GB'>Queen Mary University of London<o:p></o:p></span></i></p><p class=MsoNormal><i><span style='mso-fareast-language:EN-GB'><o:p> </o:p></span></i></p><p class=MsoNormal><i><span style='mso-fareast-language:EN-GB'><a href="http://intercrossing.wikispaces.com/">intercrossing.wikispaces.com</a><o:p></o:p></span></i></p><p class=MsoNormal><i><span style='mso-fareast-language:EN-GB'><a href="http://evolve.sbcs.qmul.ac.uk/buggs/jasmin-zohren/">evolve.sbcs.qmul.ac.uk</a><o:p></o:p></span></i></p><p class=MsoNormal><o:p> </o:p></p></div></body></html>