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From: Taya F. <tay...@gl...> - 2017-01-31 12:43:22
|
Hello, I’m interested in running the program Kover for phenotype discovery: https://github.com/aldro61/kover In the methods of the BMC Genomics paper describing this program, it’s suggested that the Ray Surveyor tool can be used to split assembled genomes into k-mers. I am struggling to find the appropriate commands to run this from the Ray Surveyor documentation. Could someone please suggest how to go about doing this? Thanks for your help! Taya |
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From: Sébastien B. <se...@bo...> - 2016-12-05 07:59:20
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make HAVE_LIBZ=y ________________________________ From: Jason Tan <jas...@gm...> Sent: November 15, 2016 7:40 AM To: den...@li... Cc: Sébastien Boisvert Subject: Re: Request for guidance Hi Admin, I followed the INSTALL.txt guideline as attached to install Ray but i have no clue to go further. Could you please guide me how to enable .gz support? Thanks Jason On Tue, Nov 15, 2016 at 9:12 PM, Sébastien Boisvert <se...@bo...<mailto:se...@bo...>> wrote: Hi Jason, Please post your questions to the mailing list (in CC). Did you enable .gz support when you built the software Ray from source ? ________________________________ From: Jason Tan <jas...@gm...<mailto:jas...@gm...>> Sent: November 15, 2016 3:47 AM To: se...@bo...<mailto:se...@bo...> Subject: Request for guidance Dear Admin, Thank you for contributing this useful piece of software. 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 https://sourceforge.net/projects/denovoassembler/files/ Ray, a de novo assembler using MPI 2.2 - Browse Files at ...<https://sourceforge.net/projects/denovoassembler/files/> sourceforge.net<http://sourceforge.net> Ray -- Parallel genome assemblies for parallel DNA sequencing The command that i entered was mpiexec -n 2 ray-build/Ray -detect-sequence-files SRR1633365 -show memory-usage and the file SRR1633365.fastq.gz is in the folder SRR1633365 However, when i installed the Ray by using this command, it can be executed successfully. sudo apt-get install Ray mpiexec -n 2 Ray -detect-sequence-files SRR1633365 -show memory-usage Could you please guide me the solution to this problem? Thanks Jason |
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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>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">
<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>
</div>
<div>
<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>
<div id="m_-1493348473564484906LPBorder_GT_14792154405690.4930794339052682" style="margin-bottom:20px;overflow:auto;width:100%;text-indent:0px">
<table id="m_-1493348473564484906LPContainer_14792154405650.6102190903329934" style="width:90%;background-color:rgb(255,255,255);overflow:auto;padding-top:20px;padding-bottom:20px;margin-top:20px;border-top:1px
dotted rgb(200,200,200);border-bottom:1px
dotted rgb(200,200,200)" cellspacing="0">
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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
UI Light","Segoe WP
Light","Segoe
UI","Segoe
WP",Tahoma,Arial,sans-serif;line-height:21px">
<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>
<div id="m_-1493348473564484906LPMetadata_14792154405680.5752335230828212" style="margin:10px 0px
16px;color:rgb(102,102,102);font-weight:400;font-family:"wf_segoe-ui_normal","Segoe
UI","Segoe
WP",Tahoma,Arial,sans-serif;font-size:14px;line-height:14px">
<a moz-do-not-send="true" href="http://sourceforge.net" target="_blank">sourceforge.net</a></div>
<div id="m_-1493348473564484906LPDescription_14792154405680.6109963684092057" style="display:block;color:rgb(102,102,102);font-weight:400;font-family:"wf_segoe-ui_normal","Segoe
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Ray -- Parallel genome assemblies for parallel DNA sequencing</div>
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<span class="">
<div><br>
</div>
<div>The command that i entered was </div>
<div><br>
</div>
<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>
</span></div>
</div>
</div>
</div>
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From: Jason T. <jas...@gm...> - 2016-11-15 13:48:16
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Hi Admin, I followed the INSTALL.txt guideline as attached to install Ray but i have no clue to go further. Could you please guide me how to enable .gz support? Thanks Jason On Tue, Nov 15, 2016 at 9:12 PM, Sébastien Boisvert <se...@bo...> wrote: > Hi Jason, > > > Please post your questions to the mailing list (in CC). > > Did you enable .gz support when you built the software Ray from source ? > > ------------------------------ > *From:* Jason Tan <jas...@gm...> > *Sent:* November 15, 2016 3:47 AM > *To:* se...@bo... > *Subject:* Request for guidance > > Dear Admin, > > Thank you for contributing this useful piece of software. > > 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 > > https://sourceforge.net/projects/denovoassembler/files/ > Ray, a de novo assembler using MPI 2.2 - Browse Files at ... > <https://sourceforge.net/projects/denovoassembler/files/> > sourceforge.net > Ray -- Parallel genome assemblies for parallel DNA sequencing > > The command that i entered was > > mpiexec -n 2 ray-build/Ray -detect-sequence-files SRR1633365 -show > memory-usage > > and the file SRR1633365.fastq.gz is in the folder SRR1633365 > > However, when i installed the Ray by using this command, it can be > executed successfully. > > sudo apt-get install Ray > mpiexec -n 2 Ray -detect-sequence-files SRR1633365 -show memory-usage > > > Could you please guide me the solution to this problem? > > Thanks > Jason > |
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From: Jason T. <jas...@gm...> - 2016-11-15 13:40:55
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You need: - A C++ compiler (C++ 1998 or later) - An MPI implementation - make == Quickstart on GNU/Linux == On GNU/Linux, you can use GNU C++ (g++) and Open-MPI. Then, type make PREFIX=ray-build make install ls ray-build mpiexec -n 1 ray-build/Ray -o test -p test_1.fastq test_2.fastq -k 31 == Options == You can provide compilation options to the Makefile. MPICXX The path to the C++ compiler wrapper (usually called mpicxx) PREFIX Where to install stuff MAXKMERLENGTH maximum k-mer length, default is MAXKMERLENGTH=32 FORCE_PACKING save memory by not aligning addresses, default is FORCE_PACKING=n ASSERT run assertions too, default is ASSERT=n For other options, read the Makefile header. == Working compilers == Anything that supports C++ 1998. see Documentation/COMPILERS.txt |
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From: Sébastien B. <se...@bo...> - 2016-11-15 13:24:55
|
Hi Jason, Please post your questions to the mailing list (in CC). Did you enable .gz support when you built the software Ray from source ? ________________________________ From: Jason Tan <jas...@gm...> Sent: November 15, 2016 3:47 AM To: se...@bo... Subject: Request for guidance Dear Admin, Thank you for contributing this useful piece of software. 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 https://sourceforge.net/projects/denovoassembler/files/ Ray, a de novo assembler using MPI 2.2 - Browse Files at ...<https://sourceforge.net/projects/denovoassembler/files/> sourceforge.net Ray -- Parallel genome assemblies for parallel DNA sequencing The command that i entered was mpiexec -n 2 ray-build/Ray -detect-sequence-files SRR1633365 -show memory-usage and the file SRR1633365.fastq.gz is in the folder SRR1633365 However, when i installed the Ray by using this command, it can be executed successfully. sudo apt-get install Ray mpiexec -n 2 Ray -detect-sequence-files SRR1633365 -show memory-usage Could you please guide me the solution to this problem? Thanks Jason |
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From: Jason T. <jas...@gm...> - 2016-11-15 09:42:18
|
Dear Ray Developers, Thank you for contributing this useful piece of software. 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 https://sourceforge.net/projects/denovoassembler/files/ The command that i entered was mpiexec -n 2 ray-build/Ray -detect-sequence-files SRR1633365 -show memory-usage and the file SRR1633365.fastq.gz is in the folder SRR1633365 However, when i installed the Ray by using this command, it can be executed successfully. sudo apt-get install Ray mpiexec -n 2 Ray -detect-sequence-files SRR1633365 -show memory-usage Could anyone please guide me the solution for this problem? Thanks Jason |
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From: Asker B. <ask...@gm...> - 2016-10-29 21:45:09
|
Dear Ray Developers, Thank you for contributing this useful piece of software. I have attempted to assign taxonomy as shown in the instructions, but running the script CreateRayInputStructures.sh fails because this url ftp://ftp.ncbi.nih.gov/genomes/Bacteria/all.fna.tar.gz does not exist at the ncbi FTP any more. Do you have a suggestion for what to replace it with? Thanks in advance, Asker Brejnrod |
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From: Sébastien B. <se...@bo...> - 2016-06-22 11:43:29
|
To understand the differences, go read the paragram "From Ray to Ray Meta" http://genomebiology.biomedcentral.com/articles/10.1186/gb-2012-13-12-r122#Sec11 ________________________________ From: Vishal N Koparde <vnk...@vc...> Sent: June 22, 2016 5:28 AM To: Sébastien Boisvert Subject: Re: Question about Ray Meta? So it auto detects if the input reads are coming from one genome versus a metagenome?? Vishal Koparde, PhD Bioinformatics Scientist Virginia Commonwealth University Richmond VA USA On Wed, Jun 22, 2016 at 7:27 AM -0400, "Sébastien Boisvert" <se...@bo...<mailto:se...@bo...>> wrote: There are no difference. There is a section in the Genome Biology 2012 explaning the changes made to the software. ________________________________ From: Vishal N Koparde <vnk...@vc...> Sent: June 22, 2016 5:21 AM To: Sébastien Boisvert Subject: Re: Question about Ray Meta? I understand that part. Could you please point out the difference in commands if I am assembly a single genome versus a metagenomic assembly?? Vishal Koparde, PhD Bioinformatics Scientist Virginia Commonwealth University Richmond VA USA On Wed, Jun 22, 2016 at 7:19 AM -0400, "Sébastien Boisvert" <se...@bo...<mailto:se...@bo...>> wrote: Ray Meta is the collective name for the set of option to perform profiling in Ray. ________________________________ From: Vishal N Koparde <vnk...@vc...> Sent: June 14, 2016 8:13 PM To: Sébastien Boisvert Subject: Re: Question about Ray Meta? I have submitted the question on github too. But, since i didn't get any response, I thought I would email you directly. Vishal Koparde, PhD Bioinformatics Scientist Virginia Commonwealth University Richmond VA USA On Tue, Jun 14, 2016 at 10:12 PM -0400, "Sébastien Boisvert" <se...@bo...<mailto:se...@bo...>> wrote: Please send your questions to the mailing list. I will answer to the mailing list. ________________________________ From: Vishal N Koparde <vnk...@vc...> Sent: June 3, 2016 8:26 AM To: se...@bo... Subject: Question about Ray Meta? Hello Seb, I have successfully compiled and run Ray, but have no clue how to run Ray Meta? What is the difference in the command line to run Ray Meta vs. Ray vanilla? I have a metagenomic sample with 3 closely related species as a test case. Thanks, -Vishal Vishal N Koparde, Ph. D. NGS Bioinformatics Scientist, Nucleic Acid Research Facilities/ Center for Study of Biological Complexity, 1101 East Marshall Street, #5-050, P.O. Box 980678 Virginia Commonwealth University Richmond VA 23298-0678 Email: vnk...@vc...<mailto:vnk...@vc...> Phone: +1-804-628-3060 |
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From: marina e. <me...@um...> - 2016-04-07 09:51:39
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El 05.04.2016 15:58, Animesh Sharma escribió: > Marina I am using Ray with paired end reads, but wondering if the > defaults work for you? Something like: > > mpiexec -np 64 ./Ray -k 25 -s Cleanup_454/sequences_.fastq -s > Cleanup_ill/output_files/sequences_.fastq -o testK25def > > Regards, > > Ani > > --------------------------"The Answer Lies In The > Genome"-------------------------- > > On Tue, Apr 5, 2016 at 3:36 PM, marina espigares <me...@um...> > wrote: > >> El 05.04.2016 14:07, Animesh Sharma escribió: >> >> Hi Marina, >> >> Which Ray version and how are you invoking it? If you simply >> assemble >> with -k and -input files, they won't call these other routines. >> >> Regards, >> >> Ani >> >> --------------------------"The Answer Lies In The >> Genome"-------------------------- >> >> On Tue, Apr 5, 2016 at 12:49 PM, marina espigares <me...@um...> >> wrote: >> >> Hello, >> >> I am using RAY to assembly the transcriptome of the chestnut tree. >> It >> can generate the contigs pretty fast but the program keep working on >> the >> BiologicalAbundances for a long time. What are those files for? It >> that >> affects the assembly results?, it is possible to deactivate? >> >> Thank you >> >> -- >> Marina Espigares >> >> > ------------------------------------------------------------------------------ >> >> _______________________________________________ >> Denovoassembler-users mailing list >> Den...@li... >> https://lists.sourceforge.net/lists/listinfo/denovoassembler-users >> [1] >> [1] >> >> Links: >> ------ >> [1] >> https://lists.sourceforge.net/lists/listinfo/denovoassembler-users >> [1] > > Hello Ani, > > I'm using ray/2.3.1, and I call it this way: > > -mpiexec -np 64 Ray -k 25 -s Cleanup_454/sequences_.fastq -s > Cleanup_ill/output_files/sequences_.fastq -route-messages > -connection-type debruijn -routing-graph-degree 4 > > Any suggestion? > > Regards > > Marina > > > > Links: > ------ > [1] https://lists.sourceforge.net/lists/listinfo/denovoassembler-users Ani, thank you for your advise. It works much faster now. I guess all those options were slow down the execution. Best regards Marina -- Marina Espigares |
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From: Animesh S. <sha...@gm...> - 2016-04-05 13:58:39
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Marina I am using Ray with paired end reads, but wondering if the defaults work for you? Something like: mpiexec -np 64 ./Ray -k 25 -s Cleanup_454/sequences_.fastq -s Cleanup_ill/output_files/sequences_.fastq -o testK25def Regards, Ani --------------------------"The Answer Lies In The Genome"-------------------------- On Tue, Apr 5, 2016 at 3:36 PM, marina espigares <me...@um...> wrote: > El 05.04.2016 14:07, Animesh Sharma escribió: > >> Hi Marina, >> >> Which Ray version and how are you invoking it? If you simply assemble >> with -k and -input files, they won't call these other routines. >> >> Regards, >> >> Ani >> >> --------------------------"The Answer Lies In The >> Genome"-------------------------- >> >> On Tue, Apr 5, 2016 at 12:49 PM, marina espigares <me...@um...> >> wrote: >> >> Hello, >>> >>> I am using RAY to assembly the transcriptome of the chestnut tree. >>> It >>> can generate the contigs pretty fast but the program keep working on >>> the >>> BiologicalAbundances for a long time. What are those files for? It >>> that >>> affects the assembly results?, it is possible to deactivate? >>> >>> Thank you >>> >>> -- >>> Marina Espigares >>> >>> >>> >> ------------------------------------------------------------------------------ >> >>> _______________________________________________ >>> Denovoassembler-users mailing list >>> Den...@li... >>> https://lists.sourceforge.net/lists/listinfo/denovoassembler-users >>> [1] >>> >> >> >> >> Links: >> ------ >> [1] https://lists.sourceforge.net/lists/listinfo/denovoassembler-users >> > > Hello Ani, > > I'm using ray/2.3.1, and I call it this way: > > -mpiexec -np 64 Ray -k 25 -s Cleanup_454/sequences_.fastq -s > Cleanup_ill/output_files/sequences_.fastq -route-messages -connection-type > debruijn -routing-graph-degree 4 > > > Any suggestion? > > Regards > > Marina > |
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From: marina e. <me...@um...> - 2016-04-05 13:36:54
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El 05.04.2016 14:07, Animesh Sharma escribió: > Hi Marina, > > Which Ray version and how are you invoking it? If you simply assemble > with -k and -input files, they won't call these other routines. > > Regards, > > Ani > > --------------------------"The Answer Lies In The > Genome"-------------------------- > > On Tue, Apr 5, 2016 at 12:49 PM, marina espigares <me...@um...> > wrote: > >> Hello, >> >> I am using RAY to assembly the transcriptome of the chestnut tree. >> It >> can generate the contigs pretty fast but the program keep working on >> the >> BiologicalAbundances for a long time. What are those files for? It >> that >> affects the assembly results?, it is possible to deactivate? >> >> Thank you >> >> -- >> Marina Espigares >> >> > ------------------------------------------------------------------------------ >> _______________________________________________ >> Denovoassembler-users mailing list >> Den...@li... >> https://lists.sourceforge.net/lists/listinfo/denovoassembler-users >> [1] > > > > Links: > ------ > [1] https://lists.sourceforge.net/lists/listinfo/denovoassembler-users Hello Ani, I'm using ray/2.3.1, and I call it this way: -mpiexec -np 64 Ray -k 25 -s Cleanup_454/sequences_.fastq -s Cleanup_ill/output_files/sequences_.fastq -route-messages -connection-type debruijn -routing-graph-degree 4 Any suggestion? Regards Marina |
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From: Animesh S. <sha...@gm...> - 2016-04-05 12:07:33
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Hi Marina, Which Ray version and how are you invoking it? If you simply assemble with -k and -input files, they won't call these other routines. Regards, Ani --------------------------"The Answer Lies In The Genome"-------------------------- On Tue, Apr 5, 2016 at 12:49 PM, marina espigares <me...@um...> wrote: > Hello, > > I am using RAY to assembly the transcriptome of the chestnut tree. It > can generate the contigs pretty fast but the program keep working on the > BiologicalAbundances for a long time. What are those files for? It that > affects the assembly results?, it is possible to deactivate? > > Thank you > > -- > Marina Espigares > > > ------------------------------------------------------------------------------ > _______________________________________________ > Denovoassembler-users mailing list > Den...@li... > https://lists.sourceforge.net/lists/listinfo/denovoassembler-users > |
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From: marina e. <me...@um...> - 2016-04-05 10:50:09
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Hello, I am using RAY to assembly the transcriptome of the chestnut tree. It can generate the contigs pretty fast but the program keep working on the BiologicalAbundances for a long time. What are those files for? It that affects the assembly results?, it is possible to deactivate? Thank you -- Marina Espigares |
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From: patrick s. <pa...@si...> - 2016-04-04 15:24:33
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Hi, I'm having 5 metagenomics soil sample from different areas. It is sequenced by using Illumina pair-end, 2 X 101 nt, 1GB file size for each sample, insert size is 300 - 400 nt. The objective of this research is to determine and compare the spectrum of microbiodata of the soil sources in different areas. I have done the standard pre-processing step (trim adaptor, remove duplicate read, remove low quality read, etc). I got 5 sets of clean read (proper pair-end but variable length due to trim process) metagenomics soil sample now. Below is the command I try: *mpiexec -n 60 Ray -k 31 -p s1_1.fastq s1_2.fastq -p s2_1.fastq s2_2.fastq -p s3_1.fastq s3_2.fastq -p s4_1.fastq s4_2.fastq -p s5_1.fastq s5_2.fastq -o Soil_Metagenomics* Can I know that is the above command correct if I wanna to run Ray meta? I'm not too sure how to specific the command to run Ray meta. How to optimize my metagenomics assembly result? Is it I need to run at different mer etc? Once I get the Thanks a lot and again for your advice. |
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From: Tan, Y. <Yif...@nr...> - 2015-10-21 19:52:42
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Hello group and Sebastien: I use Ray as default assembler for the project (chromosome broken into individual BAC clones) as it gives better result with default settings based on: 1) The total assembly length is always close to the physical fingerprinting result; 2) Less scaffolds number as the aim is to get "single" scaffold of each data set; 3) Longer maximum scaffold when more than 1 scaffolds created; 4) Longer N50 if many scaffolds exist, although this metrics does not make much sense to my case as normally not very many scaffolds (<30) I got single scaffold assembly for 25% of the (cases), but I am hoping to get single scaffold for most of the clones as the sequence depth is quite big (>100x generally). Now I am trying to change some of the settings firstly with: -merge seeds or -ignore seeds -minimum-contig-length (a) I am not sure how the seeds will impact the final assembly as I do not understand what "seeds" really means in Ray algorithm; (b) Will setting minimum-contig-length lose informative contigs when some of the contigs are short, especially in high repetitive genome which is my case? Any experience with these would be appreciated. Bastien, can you elaborate these settings, please? Thank you very much! Yifang -use-minimum-seed-coverage -minimum-contig-length -merge-seeds Yifang ________________________________________________________________________ Bioinformatics Support Specialist | Spécialiste de soutien en bioinformatiques National Research Council of Canada | Conseil national de recherches Canada Government of Canada | Gouvernement du Canada 110 Gymnasium Place|110, place Gymnasium Saskatoon, Saskatchewan S7N 0W9 Tel / Tél : 306-975-5279 Fax | Télécopieur : 306-975-4839 ________________________________________ From: Sébastien Boisvert [seb...@ul...] Sent: Friday, February 06, 2015 8:43 AM To: Marco van het Hoog Cc: den...@li... Subject: [Denovoassembler-users] RE : Ray assembly of Hamster genome. > ________________________________________ > De : Marco van het Hoog [ma...@va...] > Date d'envoi : 20 janvier 2015 19:50 > À : Sébastien Boisvert > Objet : Ray assembly of Hamster genome. > Hello Sébastien ... Hi, > I am working for the National Research Council, Biotechnology Research > Institute in Montreal, and therefore (like you) I have access to all the > Calcul Quebec servers, including Colosse and Guillimin. I don't have to these resources now because I am currently working in the U.S. > We just received 3 HiSeq lanes of reads to construct a genome assembly > of a Hamster CHO cell line. > The estimated genome size of Hamster is about 2.8 GB, for Human (if I > remember well) it's about 3.3 GB, so it's a similar size. > The 3 lane coverage should be around 30X. > Could you tell me, if you were to start such a project with Ray, what > kind of settings you would use? Take a look at the Ray job scripts that were used for the Assemblathon 2: https://github.com/sebhtml/assemblathon-2-ray > Would you use Colosse and Guillimin with 30 cores each, or would you use > Mammouth Parallèle with 256 or 512 GB in memory? You would want to use many machines with something like 24 GB RAM each. > The memory requirements of Ray are a bit confusing to me :) > Thanks in advance for any suggestion. > - Marco. > ------------------------------------------------------------------------------ Dive into the World of Parallel Programming. The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ _______________________________________________ Denovoassembler-users mailing list Den...@li... https://lists.sourceforge.net/lists/listinfo/denovoassembler-users |
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From: Yifan L. <yi...@en...> - 2015-10-19 19:42:36
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Hi smart guys, I want to assemble paired end sequences from three samples. And due to certain reason, I want to assemble them into a pan-assembly file. But there is no such option in Ray, do you have any suggestion? Any help will be appreciated :) Yifan |
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From: Xabier V. C. <xva...@gm...> - 2015-10-06 06:06:39
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Hi, I have been dealing with Ray for few days and I got it running in our cluster as follows: mpiexec -n 64 Ray \ > -read-write-checkpoints \ > -o assembly \ > -p \ /srv/scratch/z3382651/metagenomes/VZQ515A1-27724777/028-LFA_S1_L001_R1_001_val_1.fq > \ > /srv/scratch/z3382651/metagenomes/VZQ515A1-27724777/028-LFA_S1_L001_R2_001_val_2.fq > \ > ... > but it crashes without leaving an error message in the log (see ray_1strun.log). The only thing I could find as error was RAY_MPI_TAG_NOTIFY_ERROR but I have no idea what it is. I tried to resume it few times, often ending in the same way, others showing dirty buffer messages in the middle of the log and in another situation, what I believe it was, a problem of the nodes communicating and/or the MPI: [kc07b05][[3753,1],51][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv] > [kc06b05][[3753,1],8][btl_tcp_endpoint.c:657:mca_btl_tcp_endpoint_complete_connect] > connect() to 10.3.2.15 failed: Connection refused (111) > [kc06b15][[3753,1],31][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv] > [kc06b13][[3753,1],17][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv] > mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) > [kc07b04][[3753,1],42][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv] > mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) > mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) > mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) > [kc07b05][[3753,1],53][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv] > mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) > [kc06b15][[3753,1],28][btl_tcp_endpoint.c:657:mca_btl_tcp_endpoint_complete_connect] > connect() to 10.3.2.15 failed: Connection refused (111) > [kc07b05][[3753,1],49][btl_tcp_endpoint.c:657:mca_btl_tcp_endpoint_complete_connect] > connect() to 10.3.2.15 failed: Connection refused (111) > [kc07b05][[3753,1],48][btl_tcp_endpoint.c:657:mca_btl_tcp_endpoint_complete_connect] > connect() to 10.3.2.15 failed: Connection refused (111) > [kc07b04][[3753,1],46][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv] > mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) > [kc07b05][[3753,1],50][btl_tcp_endpoint.c:657:mca_btl_tcp_endpoint_complete_connect] > [kc07b01][[3753,1],38][btl_tcp_endpoint.c:657:mca_btl_tcp_endpoint_complete_connect] > connect() to 10.3.2.15 failed: Connection refused (111) > [kc06b15][[3753,1],30][btl_tcp_endpoint.c:657:mca_btl_tcp_endpoint_complete_connect] > connect() to 10.3.2.15 failed: Connection refused (111) > [kc06b13][[3753,1],16][btl_tcp_endpoint.c:657:mca_btl_tcp_endpoint_complete_connect] > connect() to 10.3.2.15 failed: Connection refused (111) > [kc06b15][[3753,1],24][btl_tcp_endpoint.c:657:mca_btl_tcp_endpoint_complete_connect] > connect() to 10.3.2.15 failed: Connection refused (111) > [kc07b04][[3753,1],45][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv] > mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) > connect() to 10.3.2.15 failed: Connection refused (111) > [kc07b01][[3753,1],36][btl_tcp_endpoint.c:657:mca_btl_tcp_endpoint_complete_connect] > connect() to 10.3.2.15 failed: Connection refused (111) > [kc07b04][[3753,1],40][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv] > mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) > [kc07b05][[3753,1],52][btl_tcp_endpoint.c:657:mca_btl_tcp_endpoint_complete_connect] > connect() to 10.3.2.15 failed: Connection refused (111) > [kc07b01][[3753,1],34][btl_tcp_endpoint.c:657:mca_btl_tcp_endpoint_complete_connect] > connect() to 10.3.2.15 failed: Connection refused (111) > [kc06b15][[3753,1],25][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv] > [kc07b01][[3753,1],37][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv] > mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) > mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) > [kc07b01][[3753,1],39][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv] > [kc07b01][[3753,1],35][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv] > mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) > [kc07b01][[3753,1],33][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv] > mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) > mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104) > I don't know what can be wrong. By the way, I'm using 8 nodes with 8 processes per node and a total vmem of 196GB. Our cluster has more than 100 blades with a minimum of 12 cores/blade and most of them with 96GB each. I leave the details in case the config of my job submitted to the cluster can be one of the problems or even if it can be improved. By the way, the job includes several libraries as fastq, which together (uncompressed) add up almost 150GB Thank you in advance, Xabier -- Xabier Vázquez-Campos, *PhD* *Research Associate* Water Research Centre School of Civil and Environmental Engineering The University of New South Wales Sydney NSW 2052 AUSTRALIA |
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From: Boisvert, S. <boi...@an...> - 2015-07-10 20:27:27
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I am not aware of any updated build script to generate the desired files from the new input files. ________________________________________ From: Marc P. Hoeppner [m.h...@ik...] Sent: Monday, June 29, 2015 9:05 AM To: den...@li... Subject: [Denovoassembler-users] Question about "build script" for the annotation files - repositing, since the first one didn't go through - Hi, I've been trying to get all the various files Ray can use to annotate/profile metagenomic assemblies. For that, I used the scripts that are included with the git repo for the 2012 publication. Unfortunately, these scripts no longer work (mostly due to changed file locations on remote servers, but I think also because some of the input files are no longer maintained or have changed format). This makes it a bit unclear how get all of this set up so that Ray could use it. Is there perhaps an updated build script or some more detailed explanation of what is needed, exactly? Kind regards, Marc -- Marc P. Hoeppner, PhD Institute of Clinical Molecular Biology Christian-Albrechts-University of Kiel University Hospital Schleswig Holstein · Campus Kiel Schittenhelmstr. 12 · 24105 Kiel, Germany +49 (0) 431 / 597 - 38 82 m.h...@ik... ------------------------------------------------------------------------------ Monitor 25 network devices or servers for free with OpManager! OpManager is web-based network management software that monitors network devices and physical & virtual servers, alerts via email & sms for fault. Monitor 25 devices for free with no restriction. Download now http://ad.doubleclick.net/ddm/clk/292181274;119417398;o _______________________________________________ Denovoassembler-users mailing list Den...@li... https://lists.sourceforge.net/lists/listinfo/denovoassembler-users |
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From: Hornung, B. <bas...@wu...> - 2015-06-29 18:07:18
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I have not really any specific idea, but "Killed (signal 9)" can mean (I think) that the Kernel could have killed your process (at least it sounds like it to me). Reasons can be that you ran out of RAM + swap on your machine. ________________________________ From: Alma Parada <alm...@gm...> Sent: Monday, June 29, 2015 18:07 To: Boisvert, Sebastien Cc: den...@li... Subject: Re: [Denovoassembler-users] (no subject) Hello, What other information would be useful in figuring out the reason I received this signal? I'd be glad to get you more info. thanks, alma On Jun 29, 2015, at 7:32 AM, Boisvert, Sebastien <boi...@an...<mailto:boi...@an...>> wrote: The signal 9 is SIGKILL. It is hard to tell the exact reason why your process received this signal with the information you provided. ________________________________ From: Alma Parada [alm...@gm...<mailto:alm...@gm...>] Sent: Saturday, June 27, 2015 9:50 AM To: den...@li...<mailto:den...@li...> Subject: [Denovoassembler-users] (no subject) Hello, I was running an assembly of 12 metagenomes and got the message below, what does it mean? Thanks, alma =================================================================================== = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = EXIT CODE: 9 = CLEANING UP REMAINING PROCESSES = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES =================================================================================== YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Killed (signal 9) This typically refers to a problem with your application. Please see the FAQ page for debugging suggestions |
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From: Alma P. <alm...@gm...> - 2015-06-29 16:07:53
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Hello, What other information would be useful in figuring out the reason I received this signal? I'd be glad to get you more info. thanks, alma > On Jun 29, 2015, at 7:32 AM, Boisvert, Sebastien <boi...@an...> wrote: > > The signal 9 is SIGKILL. > > It is hard to tell the exact reason why your process received this signal > with the information you provided. > > From: Alma Parada [alm...@gm...] > Sent: Saturday, June 27, 2015 9:50 AM > To: den...@li... > Subject: [Denovoassembler-users] (no subject) > > Hello, > I was running an assembly of 12 metagenomes and got the message below, what does it mean? > Thanks, > alma > > > =================================================================================== > = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES > = EXIT CODE: 9 > = CLEANING UP REMAINING PROCESSES > = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES > =================================================================================== > YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Killed (signal 9) > This typically refers to a problem with your application. > Please see the FAQ page for debugging suggestions > |
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From: Boisvert, S. <boi...@an...> - 2015-06-29 14:32:52
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The signal 9 is SIGKILL. It is hard to tell the exact reason why your process received this signal with the information you provided. ________________________________ From: Alma Parada [alm...@gm...] Sent: Saturday, June 27, 2015 9:50 AM To: den...@li... Subject: [Denovoassembler-users] (no subject) Hello, I was running an assembly of 12 metagenomes and got the message below, what does it mean? Thanks, alma =================================================================================== = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = EXIT CODE: 9 = CLEANING UP REMAINING PROCESSES = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES =================================================================================== YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Killed (signal 9) This typically refers to a problem with your application. Please see the FAQ page for debugging suggestions |
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From: Marc P. H. <m.h...@ik...> - 2015-06-29 14:05:31
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- repositing, since the first one didn't go through - Hi, I've been trying to get all the various files Ray can use to annotate/profile metagenomic assemblies. For that, I used the scripts that are included with the git repo for the 2012 publication. Unfortunately, these scripts no longer work (mostly due to changed file locations on remote servers, but I think also because some of the input files are no longer maintained or have changed format). This makes it a bit unclear how get all of this set up so that Ray could use it. Is there perhaps an updated build script or some more detailed explanation of what is needed, exactly? Kind regards, Marc -- Marc P. Hoeppner, PhD Institute of Clinical Molecular Biology Christian-Albrechts-University of Kiel University Hospital Schleswig Holstein · Campus Kiel Schittenhelmstr. 12 · 24105 Kiel, Germany +49 (0) 431 / 597 - 38 82 m.h...@ik... |
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From: Alma P. <alm...@gm...> - 2015-06-27 14:50:59
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Hello, I was running an assembly of 12 metagenomes and got the message below, what does it mean? Thanks, alma =================================================================================== = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = EXIT CODE: 9 = CLEANING UP REMAINING PROCESSES = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES =================================================================================== YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Killed (signal 9) This typically refers to a problem with your application. Please see the FAQ page for debugging suggestions |
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From: Boisvert, S. <boi...@an...> - 2015-06-10 14:21:27
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The reads are numbered using their ordering when concatenating the input files. ________________________________ From: Namrata Patel [nam...@gm...] Sent: Tuesday, June 09, 2015 11:48 PM To: Boisvert, Sebastien Subject: About Read Names in Ray Meta Hello Sir, I am Trying to run Ray Meta for my Metagenomic data, and i want to know which reads were used to form a particular Contig. I tried to run Ray Meta with -amos option and it is giving me AMOS.afg file. When i am parsing this .afg file to get reads used in contigs, it gives me numbers instead of read names. Please tell me what this numbers are or how can i get reads used in each contig. Awaiting for Your Kind Response, Thanking You, Namrata Patel |
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