Thanks Sebastian! I tried fixing that as well! Now both my libraries have
good quality equal number of sequences: Here is the content of
NumberOfSequences file:
Files: 2
FileNumber: 0
FilePath: /scratch/sucheta/out1.fastq
NumberOfSequences: 69393976
FirstSequence: 0
Does this segfault happen right after section of optimal reads?
Matt
_
Matthew MacManes, Ph.D.
University of New Hampshire I Assistant Professor
Department of Molecular, Cellular, & Biomedical Sciences
Durham, NH 03824
Phone: 603-862-4052 I Twitter:
@Pero
I have only one 454 dataset here, but when I put that together with my Illumina
data, I got worse assemblies with it. I assumed, like Sebastian mentioned, that
this could be due to the homopolymer errors.
From: raw...@gmail.com [raw...@gmail.com]
Sent: Fri
Hello,
It would be important to know one way or another.
Does it?
Cheers
Rick
--
Richard Allen White III M.S.
PhD Candidate - Suttle Lab
Department of Microbiology & Immunology
The University of British Columbia
Vancouver, BC, Canada
cell. 604-440-5150
http://www.ocgy.ubc.ca/~suttle/
Hello,
Yes, I tried both. When I put Ion torrent reads with illumina or do just Ion
torrent reads I get terrible assemblies. I am more of a fan of illumina but I
have the Ion Torrent data and would like to get something out of it.
Also, any thoughts for 454 and Illumina Hybrid assembly? I get o
On 22/11/13 03:18 AM, Hornung, Bastian wrote:
> Okay, email header sounds probably more scaring than it is ^^.
> I just checked with what options my assembly is running (...SOP...), and
> noticed that all my recent runs were with "-wirte-kmers", instead of
> "-write-kmers" (yeah, stupid typo).
>
On 26/11/13 02:22 PM, Rick White wrote:
> I have some 200bp Ion Torrent Mate Pair data, Paired 250x2 MiSeq reads and
> have merged the overlapping reads from the Illumina data.
>
> When I try to run standard parameters in Ray the assemblies are worse with
> the addition of the Ion Data.
>
> Do yo
On 02/12/13 07:32 PM, Jeff Tan wrote:
> Hi all,
>
> We're seeing this seg fault occur in Vertex.cpp, it seems, using Ray 2.3.0 on
> x86 launched via Slurm:
Do you have a tail of stdout. Maybe it is related to what Matthew MacManes is
seeing too.
>
> [jtan@barcoo-m barcoo]$ grep 27960 slurm-3497
This is Ray version 2.3.1-devel. I pulled from github a couple of days ago.
Mat
_
Matthew MacManes, Ph.D.
University of New Hampshire I Assistant Professor
Department of Molecular, Cellular, & Biomedical Sciences
Durham, NH 03824
Phone: 603-862-4052 I Twit
On 05/12/13 05:19 PM, MacManes, Matthew wrote:
> Hi All,
>
> Having problems with segfault on a Cray XE6m-200 using 480 ranks: Looks like
> 'Selection of optimal read markers’ had just finished.
Which Ray version are you using ?
>
> error code:
>> _pmiu_daemon(SIGCHLD): [NID 00285] [c1-0c2s1n3]
On 01/12/13 04:12 AM, Sucheta Tripathy wrote:
>
> I am trying to run Ray for a while now on our Illumina data. It is run in
> parallel mode and memory is not a constraint now because we have a cluster
> with 16 X 16 GB memory in each node.
>
The problem is this: tmp1 and tmp2 don't contain the s
On 02/12/13 07:43 PM, Jeff Tan wrote:
>> In the tests I did on this platform, I found that in general
>> Ray needed between 400 MiB and 1 GiB of RAM per MPI rank.
>
> We must be doing something wrong then, because we were crashing out with
> debug messages indicating over 2 GB in some ranks at leas
On 02/12/13 12:00 PM, MacManes, Matthew wrote:
> Hello,
>
> Does anybody have experience using Ray on a Cray XE system?
>
> make MAXKMERLENGTH=96
>CXX code/application_core/ray_main.o
> make: mpicxx: Command not found
>
For example, mpicxx invokes "g++ -I/usr/include/openmpi-x86_64 -pthread -m
On 26/11/13 04:18 AM, Francesco Strozzi wrote:
> Hi all,
> I would like to raise a question to this point of the Biological Abundances
> estimation.
> How can we calculate the proportion of information that is not classified by
> Ray Meta i.e. that part of the assembled information which is not c
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