Re: [Denovoassembler-users] Request for guidance
Ray -- Parallel genome assemblies for parallel DNA sequencing
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Re: [Denovoassembler-users] Request for guidance
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From: Pier-Luc P. <pie...@ul...> - 2016-11-15 16:59:12
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Hi Jason,<br>
you have to set<span class="pl-smi" style="box-sizing: border-box; color: rgb(51, 51, 51); font-family: Consolas, "Liberation Mono", Menlo, Courier, monospace; font-size: 12px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: pre; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);"></span><span style="color: rgb(51, 51, 51); font-family: Consolas, "Liberation Mono", Menlo, Courier, monospace; font-size: 12px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: pre; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); display: inline !important; float: none;">
</span><span class="pl-smi" style="box-sizing: border-box; color: rgb(51, 51, 51); font-family: Consolas, "Liberation Mono", Menlo, Courier, monospace; font-size: 12px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: pre; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);">HAVE_LIBZ </span><span style="color: rgb(51, 51, 51); font-family: Consolas, "Liberation Mono", Menlo, Courier, monospace; font-size: 12px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: pre; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); display: inline !important; float: none;"></span>in
the Makefile.<br>
<br>
Pier-Luc<br>
<br>
<div class="moz-cite-prefix">Le 2016-11-15 à 08:48, Jason Tan a écrit :<br>
</div>
<blockquote cite="mid:CAAED8wCpPWLJadDbt3AdvHBp4Lc+YGi...@ma..." type="cite">
<div dir="ltr"><span style="font-size:12.8px">Hi Admin,</span>
<div style="font-size:12.8px"><br>
</div>
<div style="font-size:12.8px">I followed the INSTALL.txt guideline as attached to install Ray but i have no clue to go further.</div>
<div style="font-size:12.8px">Could you please guide me how to enable .gz support?</div>
<div style="font-size:12.8px"><br>
</div>
<div style="font-size:12.8px">Thanks</div>
<div style="font-size:12.8px">Jason</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Tue, Nov 15, 2016 at 9:12 PM, Sébastien Boisvert <span dir="ltr">
<<a moz-do-not-send="true" href="mailto:se...@bo..." target="_blank">se...@bo...</a>></span> wrote:<br>
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<div id="m_-1493348473564484906divtagdefaultwrapper" style="font-size:12pt;color:#000000;font-family:Calibri,Arial,Helvetica,sans-serif" dir="ltr">
<p>Hi Jason,</p>
<p><br>
</p>
<p>Please post your questions to the mailing list (in CC).<br>
</p>
<br>
<p>Did you enable .gz support when you built the software Ray from source ?<br>
</p>
<br>
<div style="color:rgb(0,0,0)">
<hr style="display:inline-block;width:98%">
<div id="m_-1493348473564484906divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" face="Calibri, sans-serif" color="#000000"><b>From:</b> Jason Tan <<a moz-do-not-send="true" href="mailto:jas...@gm..." target="_blank">jas...@gm...</a>><br>
<b>Sent:</b> November 15, 2016 3:47 AM<br>
<b>To:</b> <a moz-do-not-send="true" href="mailto:se...@bo..." target="_blank">
se...@bo...</a><br>
<b>Subject:</b> Request for guidance</font>
<div> </div>
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<div dir="ltr"><span class="">
<div>Dear Admin,</div>
<div><br>
</div>
<div>Thank you for contributing this useful piece of software.</div>
<div><br>
</div>
<div>I am using Ubuntu as my working platform but i received an error "Rank 0 : no input files, aborting" when i executed Ray program of Ray-2.3.1.tar.bz2 which is downloaded from this website</div>
<div><br>
</div>
<div><a moz-do-not-send="true" href="https://sourceforge.net/projects/denovoassembler/files/" id="m_-1493348473564484906LPlnk473565" target="_blank">https://sourceforge.net/<wbr>projects/denovoassembler/<wbr>files/</a></div>
</span>
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<div id="m_-1493348473564484906LPTitle_14792154405670.2334252086263855" style="color:rgb(0,120,215);font-weight:400;font-size:21px;font-family:"wf_segoe-ui_light","Segoe
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<a moz-do-not-send="true" id="m_-1493348473564484906LPUrlAnchor_14792154405670.41932934014045864" style="text-decoration:none" href="https://sourceforge.net/projects/denovoassembler/files/" target="_blank">Ray, a de novo assembler using MPI 2.2 - Browse Files
at ...</a></div>
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<a moz-do-not-send="true" href="http://sourceforge.net" target="_blank">sourceforge.net</a></div>
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Ray -- Parallel genome assemblies for parallel DNA sequencing</div>
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<div>The command that i entered was </div>
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<div>mpiexec -n 2 ray-build/Ray -detect-sequence-files SRR1633365 -show memory-usage</div>
<div><br>
</div>
<div>and the file SRR1633365.fastq.gz is in the folder SRR1633365</div>
<div><br>
</div>
<div>However, when i installed the Ray by using this command, it can be executed successfully.</div>
<div><br>
</div>
<div>sudo apt-get install Ray</div>
<div>mpiexec -n 2 Ray -detect-sequence-files SRR1633365 -show memory-usage</div>
<div><br>
</div>
<div><br>
</div>
<div>Could you please guide me the solution to this problem?</div>
<div><br>
</div>
<div>Thanks</div>
<div>Jason</div>
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