http://permalink.gmane.org/gmane.science.biology.ray-genome-assembler hourly 1 1901-01-01T00:00+00:00 http://gmane.org/img/gmane-25t.png http://gmane.org http://permalink.gmane.org/gmane.science.biology.ray-genome-assembler/527 <pre>Well, the error tells you what the problem is:) you really need mpi, and mpd running. So install MPICH2.After installing it, just type "mpd &amp;" and try again running ray. On Fri, May 24, 2013 at 11:39 AM, Rick White &lt;raw937-Re5JQEeQqe8AvxtiuMwx3w&lt; at &gt;public.gmane.org &lt;mailto:raw937-Re5JQEeQqe8AvxtiuMwx3w&lt; at &gt;public.gmane.org&gt;&gt; wrote: It appeared the install went well but then I got this error on my ubuntu server. cannot connect to local mpd (/tmp/mpd2.console_labop); possible causes: 1. no mpd is running on this host 2. an mpd is running but was started without a "console" (-n option) In case 1, you can start an mpd on this host with: mpd &amp; and you will be able to run jobs just on this host. For more details on starting mpds on a set of hosts, see the MPICH2 Installation Guide. Does any one have a quick fix? Or patch to fix it? Want to start running Ray! Cheers Rick -- Richard Allen White III M.S. PhD Candidate - Suttle Lab </pre> Adrian Pelin 2013-05-24T19:48:47 http://permalink.gmane.org/gmane.science.biology.ray-genome-assembler/526 <pre> </pre> Rick White 2013-05-24T19:43:50 http://permalink.gmane.org/gmane.science.biology.ray-genome-assembler/525 <pre> Let's say you installed Ray in /the/path/to/Ray. Your PATH need to contain this information. Usually, this is done with: PATH=/the/path/to/Ray:$PATH Ray Meta is the collective name for the changes made to the de novo assembly algorithms. See "From Ray to Ray Meta" in http://genomebiology.com/2012/13/12/R122#sec3 ------------------------------------------------------------------------------ Try New Relic Now &amp; We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, &amp; servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_may </pre> Sébastien Boisvert 2013-05-24T14:49:59 http://permalink.gmane.org/gmane.science.biology.ray-genome-assembler/524 <pre> The executable has to be in your path on every node. ------------------------------------------------------------------------------ Try New Relic Now &amp; We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, &amp; servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_may </pre> Sébastien Boisvert 2013-05-24T14:45:59 http://permalink.gmane.org/gmane.science.biology.ray-genome-assembler/523 <pre>Hi, I have used Ray-meta for assembling some bacterial fastq sample. I am very eager to learn to analyze the results obtained from Ray-meta. Is there any tool to analyze Ray-meta results?. I am looking forward to hear from you. Regards Rajadurai ------------------------------------------------------------------------------ Try New Relic Now &amp; We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, &amp; servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_may</pre> Raja durai 2013-05-22T07:22:53 http://permalink.gmane.org/gmane.science.biology.ray-genome-assembler/522 <pre> So the problem is reproducible ? Is the datat public ? ------------------------------------------------------------------------------ Try New Relic Now &amp; We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, &amp; servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_may </pre> Sébastien Boisvert 2013-05-21T17:36:47 http://permalink.gmane.org/gmane.science.biology.ray-genome-assembler/521 <pre>[CC'ed to the list] Hello, On 14/05/13 01:18 PM, David Hernandez wrote: OK. I remember your name from the Edena paper which showed that overlap-layout-consensus works on short reads too [1]. Which MPI library are you using ? So is the part missing consistentely in every assembly ? Can you try the following script on your CoverageDistribution.txt file ? https://github.com/sebhtml/NGS-Pipelines/blob/master/Calculate-Genome-Size.py (You can get a copy of this tool with "git clone git://github.com/sebhtml/NGS-Pipelines.git"). This will estimate the genome size using kmer frequencies. It is quite accurate. Otherwise, this is a typical use case for Ray Cloud Browser to help understand what is going on. See: http://browser.cloud.raytrek.com/client/?map=3&amp;section=0&amp;region=9&amp;location=0&amp;depth=10&amp;zoom=1.2255452109421872 --- [1] http://genome.cshlp.org/content/18/5/802.long ------------------------------------------------------------------------------ AlienVault Unified Security Management (US</pre> Sébastien Boisvert 2013-05-15T14:12:13 http://permalink.gmane.org/gmane.science.biology.ray-genome-assembler/520 <pre> Does it work if you omit the -amos option ? So the problem occurs when receiving a message during the computation. Which version of Ray are you using ? How many reads do you have ? ------------------------------------------------------------------------------ Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. This 200-page book is written by three acclaimed leaders in the field. The early access version is available now. Download your free book today! http://p.sf.net/sfu/neotech_d2d_may </pre> Sébastien Boisvert 2013-05-10T21:25:50 http://permalink.gmane.org/gmane.science.biology.ray-genome-assembler/519 <pre> Yes, this is done at compilation. You need to recompile the software. ------------------------------------------------------------------------------ Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. This 200-page book is written by three acclaimed leaders in the field. The early access version is available now. Download your free book today! http://p.sf.net/sfu/neotech_d2d_may </pre> Sébastien Boisvert 2013-05-10T21:19:22 http://permalink.gmane.org/gmane.science.biology.ray-genome-assembler/518 <pre> In our paper, we aligned all the assembled contigs to the set of sequences using MUMmer. We did not clasify contigs before alignment because MUMmer reports maximum unique matches. See Section "Validation of assemblies" in our paper [1]. --- [1] http://genomebiology.com/2012/13/12/R122 ------------------------------------------------------------------------------ Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. This 200-page book is written by three acclaimed leaders in the field. The early access version is available now. Download your free book today! http://p.sf.net/sfu/neotech_d2d_may </pre> Sébastien Boisvert 2013-05-10T15:38:31 http://permalink.gmane.org/gmane.science.biology.ray-genome-assembler/517 <pre> We actually verified the assembly quality in our paper [1] for the 100-genome metagenome and for the 1000-genome metagenome (in the Results section). --- [1] http://genomebiology.com/2012/13/12/R122 ------------------------------------------------------------------------------ Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. This 200-page book is written by three acclaimed leaders in the field. The early access version is available now. Download your free book today! http://p.sf.net/sfu/neotech_d2d_may </pre> Sébastien Boisvert 2013-05-10T14:49:33 http://permalink.gmane.org/gmane.science.biology.ray-genome-assembler/516 <pre>Hello, I recently started using Ray in an attempt to assemble a metatranscriptome. I have tried multiple assemblies and repeatedly get a segmentation fault. The fault happens after contigs are written and the AMOS file is generated, however I don't think Ray gets to the scaffolding stage or any downstream plugins (gene ontology, etc...). Below is my RayCommand.txt file and the last few lines of stdout showing the segfault. RayCommand.txt ################################### mpiexec -n 25 Ray \ # This was also run with "--mca btl ^sm" and the same segfault -p \ TAH-19.1_rejected_reads.fastq \ TAH-19.2_rejected_reads.fastq \ -p \ TAH-20.1_rejected_reads.fastq \ TAH-20.2_rejected_reads.fastq \ -p \ TAH-21.1_rejected_reads.fastq \ TAH-21.2_rejected_reads.fastq \ -p \ TAH-22.1_rejected_reads.fastq \ TAH-22.2_rejected_reads.fastq \ -p \ TAH-23.1_rejected_reads.fastq \ TAH-23.2_rejected_reads.fastq \ -p \ TAH-24.1_rejected_reads.fastq \ TAH-24.2_rejected_reads.fastq \ -o \ ray</pre> Cedar Hesse 2013-05-09T21:58:04 http://permalink.gmane.org/gmane.science.biology.ray-genome-assembler/515 <pre> I think you should use paired reads for your tutorial (you have Illumina data). Ray is much better with paired reads. ------------------------------------------------------------------------------ Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. This 200-page book is written by three acclaimed leaders in the field. The early access version is available now. Download your free book today! http://p.sf.net/sfu/neotech_d2d_may </pre> Sébastien Boisvert 2013-05-08T18:04:41 http://permalink.gmane.org/gmane.science.biology.ray-genome-assembler/514 <pre> Yes. The Ray executable is generalized to work on multi-cell single-genome samples and on multi-cell multiple-genome samples. ------------------------------------------------------------------------------ Get 100% visibility into Java/.NET code with AppDynamics Lite It's a free troubleshooting tool designed for production Get down to code-level detail for bottlenecks, with &lt;2% overhead. Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap2 </pre> Sébastien Boisvert 2013-05-03T15:31:44 http://permalink.gmane.org/gmane.science.biology.ray-genome-assembler/513 <pre> IN your case, I think you should contact the helpdesk of your supercomputer center as the problem really seems to be in the job submission process, not in Ray. ------------------------------------------------------------------------------ Try New Relic Now &amp; We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, &amp; servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr </pre> Sébastien Boisvert 2013-04-29T18:09:05 http://permalink.gmane.org/gmane.science.biology.ray-genome-assembler/512 <pre>Hi I am using Intel i-Dataplex 88 nœuds de calcul IBM dx360 M3 intégrés dans 42 châssis IBM 2U Flex. Chaque nœud de calcul proposé est configuré comme suit : • 2 processeurs SIX CORE INTEL (WESTMERE) cadencés à 2.66GHz • 24 Go de mémoire vive DDR3 1066 Mhz • 1 carte Infiniband 40 Gb/s (passage de message + système de fichier) Marcelino = = = = ======================================================================== oOOOOo Marcelino Suzuki, Assoc. Professor, Intl. Chair, Platform Responsible oOOO Univ Pierre Marie Curie (Paris 6) - Observatoire Océanologique de Banyuls oOOOOOo. UMR 7621 - Laboratoire d'Océanographie Microbienne (LOMIC) .oOOOOOOOo. Marine Biodiversity and Biotechnology (bio2mar) Platform .oOOOOOOOOOoo. suzuki-1udt5kSnSqfnUm+lbSL22w&lt; at &gt;public.gmane.org http://bit.ly/fq3nbE bio2mar.obs-banyuls.fr .oOOOOOOOOOOOooooo. Ave du Fontaulé,</pre> Marcelino Suzuki 2013-04-29T17:39:02 http://permalink.gmane.org/gmane.science.biology.ray-genome-assembler/511 <pre>[Please CC the mailing list] On 24/04/13 12:33 PM, Alison Cloutier wrote: With such a huge amount of data, you should not be collapsing all the files in 3 huge files. Ray will perform better if you provide it with your overlapping paired reads because its heuristics for paired reads are much better than its heuristics for single-end reads. Do you have 5 independant unrelated samples or you have 5 HiSeq runs for the same sample ? Oh I see. You did these small assemblies to weed out contaminations, right ? That's not a lot considering that you had 5 HiSeq runs (on HiSeq 2000 run is 6 000 000 000 sequences), unless you are talking about partial HiSeq runs. Again, Ray will perform better with the non-merged version of these pairs. You should update to Ray v2.2.0 as it has an adaptive Bloom filter that will take lower the memory usage of sequencing errors. It depends if you get a bad latency. What are the first few lines of NetworkTest.txt ? Where exactly is Ray stalling on your dataset ? (Yo</pre> Sébastien Boisvert 2013-04-29T17:24:59 http://permalink.gmane.org/gmane.science.biology.ray-genome-assembler/510 <pre> Optimal read markers are read markers as described by Daniel Zerbino in his PhD thesis. =&gt; http://www.ebi.ac.uk/sites/ebi.ac.uk/files/shared/documents/phdtheses/daniel_zerbino.pdf =&gt; http://www.homolog.us/blogs/2013/01/05/optimal-assembly-for-high-throughput-shotgun-sequencing/ No­. You should get acquainted first with de novo genome assembly. A seminal work in the field include: * http://www.pnas.org/content/98/17/9748.full A nice and accessible review: * http://www.nature.com/nmeth/journal/v6/n11s/abs/nmeth.1376.html Then, you can read the Ray-related papers: * http://genomebiology.com/2012/13/12/R122 * http://online.liebertpub.com/doi/abs/10.1089/cmb.2009.0238 -Sébastien ------------------------------------------------------------------------------ Try New Relic Now &amp; We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, &amp; servers with just a fe</pre> Sébastien Boisvert 2013-04-29T16:17:51 http://permalink.gmane.org/gmane.science.biology.ray-genome-assembler/509 <pre>[Please use the mailing list] On 26/04/13 08:30 AM, Marcelino Suzuki wrote: No. it is distributed across the allocated ranks. The -amos option will do a lot of input/output operations­. Which version of Ray are you using ? What type of cluster are you using ? ------------------------------------------------------------------------------ Try New Relic Now &amp; We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, &amp; servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr </pre> Sébastien Boisvert 2013-04-29T16:10:35 http://permalink.gmane.org/gmane.science.biology.ray-genome-assembler/508 <pre> Can you provide your command line for your 2-node job for which you are experiencing problems ? Also, which version are you using ? v2.2.0 has a lot of bug fixes under the hood. ------------------------------------------------------------------------------ Try New Relic Now &amp; We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, &amp; servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr </pre> Sébastien Boisvert 2013-04-29T15:50:38 http://permalink.gmane.org/gmane.science.biology.ray-genome-assembler/507 <pre>Well, seeing this post, I am a bit worried about my jobs, since using loadleveler in an idataplex cluster, I don't see the outputs from different rank numbers, but they all are labeled Rank 0. In fact with two tasks only two of the -output-filenames are written to and both gave labels Rank 0. Is this only a difference of the clusters or am I missing something? #!/bin/sh # &lt; at &gt; job_name = crambe_ray # &lt; at &gt; output = $(job_name).out # &lt; at &gt; error = $(job_name).err # &lt; at &gt; job_type = mpich # &lt; at &gt; node = 2 # &lt; at &gt; total_tasks = 16 # &lt; at &gt; restart = yes # &lt; at &gt; wall_clock_limit = 60:00:00,59:55:00 # &lt; at &gt; queue mpirun -np $LOADL_TOTAL_TASKS -output-filename cr -machinefile $LOADL_HOSTFILE /work/OOBMECO/bin/ray/Ray -read-write-checkpoints checkpoints -k 31 -amos -o crambe.3 -s /scratch/suzukim/mira/ CCB1a.fastq -search /scratch/suzukim/NCBI-taxonomy/NCBI-Eukaryote- Genomes -search /scratch/suzukim/NCBI-taxonomy/NCBI-Finished-Virus- Genomes -search /scratch/suzukim/NCBI-taxonomy/NCBI-Draft-Bacteria- Genomes -search /scratc</pre> Marcelino Suzuki 2013-04-23T21:38:15 Search the mailing list at Gmane query http://search.gmane.org/?group=$group=gmane.science.biology.ray-genome-assembler