<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif; "><div>Hello Jasmin,</div><div><br></div><div>I haven't used MAKER in parralel on the cloud before (just tutorial images); however, I believe there is an iPlant atmosphere image available through iPlant with MAKER version 2.27. You can get maximum 16 cpus per instance there.</div><div>--> <a href="http://www.iplantcollaborative.org/discover/atmosphere">http://www.iplantcollaborative.org/discover/atmosphere</a></div><div><br></div><div>Alternatively if you have any US based collaborators you can apply for a startup allocation on the Lonestar cluster via XSEDE (allocation can be requested by any US based researcher and only takes a few days to approve) --> <a href="https://www.xsede.org/">https://www.xsede.org/</a></div><div>That cluster was used recently to process the largest genome ever annotated (the pine genome). Total run time will be less than a day on that cluster, because you can request thousands of CPUs for your job with very short queue wait times.</div><div><br></div><div>There is also a work in progress to give access to MAKER on the same cluster via the iPlant discovery environment. I've CC'd Joshua Stein who can correct me if I'm wrong, but I believe that resource would be available to non-US based researchers as well, and will be available in the very very near future (potentially within the next month or less).</div><div><br></div><div>Perhaps someone else on the mailing list may want to share their experience using MAKER on the cloud?</div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> Jasmin Zohren <<a href="mailto:j.zohren@qmul.ac.uk">j.zohren@qmul.ac.uk</a>><br><span style="font-weight:bold">Date: </span> Thursday, September 5, 2013 11:58 AM<br><span style="font-weight:bold">To: </span> <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] Maker in the cloud<br></div><div><br></div><div xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"><meta name="Generator" content="Microsoft Word 14 (filtered medium)"><style><!--
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</o:shapelayout></xml><![endif]--><div 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-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-family: '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-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-family: '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-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-family: '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-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-family: '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-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-family: '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></div></div>_______________________________________________
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