[seb567]

I'm wondering if it's possible to re-run Ray on an identical cluster node and re-use the network test results. I.e. can I skip the network test for multiple runs in a row after the first run with a network test?

No, it is not possible to skip network testing. However, this steps usually only requires
a few seconds.

[snowbear24]

Running Ray multiple times with only one network test?

I'm wondering if it's possible to re-run Ray on an identical cluster node and re-use the network test results. I.e. can I skip the network test for multiple runs in a row after the first run with a network test?

[seb567]

It is fine.

But you should do

make clean
make PREFIX=Ray-Large-k-mers-64 MAXKMERLENGTH=64 
make install
mpiexec -n 1 Ray-Large-k-mers-64/Ray -version

and

make clean
make PREFIX=Ray-Large-k-mers-128 MAXKMERLENGTH=128 
make install
mpiexec -n 1 Ray-Large-k-mers-128/Ray -version

I have a question about multiple compilations of Ray. For instance, if I want to try multiple k-mer sizes by compiling with options such as:
PREFIX=Ray-Large-k-mers MAXKMERLENGTH=64
with values other than 64, can I keep multiple renamed Ray executables in the same directory and run them by calling a specific Ray_64 vs. Ray_127? I'm wondering if the underlying mechanisms (maybe TARGETS and PREFIX?) bind to a specific exe or can these different compilations co-exist peacefully in a single directory?

[snowbear24]

I have a question about multiple compilations of Ray. For instance, if I want to try multiple k-mer sizes by compiling with options such as:
PREFIX=Ray-Large-k-mers MAXKMERLENGTH=64
with values other than 64, can I keep multiple renamed Ray executables in the same directory and run them by calling a specific Ray_64 vs. Ray_127? I'm wondering if the underlying mechanisms (maybe TARGETS and PREFIX?) bind to a specific exe or can these different compilations co-exist peacefully in a single directory?

[seb567]

I'm impressed with Ray. However
what is a recommended method to find out the optimal k-mer size? just trial and error?
Typical datasets: --> 100bp paired end illumina (5-10mln pairs), bacterial genomes

For Illumina(R) HiSeq(R) data, I usually just set the k-mer length to 31.

Does anyone recommend a method to merge assemblies of different kmer size runs?

There is the Zorro assembler


and Minimus assembler based on the AMOS framework.

At that point, however, I think you may want to inspect your assembly with Hawkeye or Tablet and eventually finish it.

[VidJa]

I'm impressed with Ray. However
what is a recommended method to find out the optimal k-mer size? just trial and error?
Typical datasets: --> 100bp paired end illumina (5-10mln pairs), bacterial genomes
Does anyone recommend a method to merge assemblies of different kmer size runs?

[seb567]

Ray 2.0.0 released

Hello,

Ray 2.0.0 codenamed "Dark Astrocyte of Knowledge" is available for download.
This version ships with RayPlatform 1.0.3 codenamed "Gray Pylon of Wisdom".

Not much thing changed since v2.0.0-rc8.

Ray 2.0.0 can do de novo assembly of metagenomes and also taxonomic profiling
with k-mers.

To get Ray v2.0.0:

http://denovoassembler.sf.net

Also, there is a new section on the website for
frequently asked questions.



Changes in Ray between v2.0.0-rc8 and v2.0.0


commit 6adeef3d814dc2acbc32444ec3ed5a49a709e98c
Author: Sébastien Boisvert <[email protected]>
Date: Fri Jun 22 20:58:37 2012 -0400

This is Ray v2.0.0.

commit 2243df732615cb2419e81c57a233cb1ffd214583
Author: Sébastien Boisvert <[email protected]>
Date: Thu Jun 21 20:27:15 2012 -0400

Floating numbers must not be stored with the integer type 'int'.

commit 4b4815772354ea402b0ce5a9500d66eed37be8d7
Author: Sébastien Boisvert <[email protected]>
Date: Thu Jun 21 16:23:35 2012 -0400

This solves a division by 0.

commit d96047c2040bed3395ae36a13505608b617b3346
Author: Sébastien Boisvert <[email protected]>
Date: Thu Jun 21 15:21:24 2012 -0400

This change set improves the fidelity of Ray when computing peak
coverage for short seeds (let's say that a short seed has a length
lower than 512 vertices).

This closes an old ticket.

https://github.com/sebhtml/ray/issues/47

commit 22d4ec0f29d31a659fe5c4791039dd2497264039
Author: Sébastien Boisvert <[email protected]>
Date: Thu Jun 21 15:00:04 2012 -0400

The multiplicator used for spawning read helpers was changed from 2.0 to 1.5.
This should remove any assemblies and should not affect contiguity.

commit 048ba764c0424bb74f416276ef7f16cf463cc0fd
Author: Sébastien Boisvert <[email protected]>
Date: Thu Jun 21 14:12:24 2012 -0400

The peak finder should detects simulated data as well.

commit 7102b16f1f282a0003f9982b42a3a744d9bffe59
Author: Sébastien Boisvert <[email protected]>
Date: Wed Jun 20 14:48:20 2012 -0400

A compilation warning was removed for an integer comparison.

commit dcc738984c61a478d7da699f19dfae4e2d1ec1f2
Author: Sébastien Boisvert <[email protected]>
Date: Wed Jun 20 14:32:23 2012 -0400

Routing strategies were updated.

commit 91052b31051fb58561231c0cd2f3bab720184b56
Author: Sébastien Boisvert <[email protected]>
Date: Wed Jun 20 11:12:34 2012 -0400

Patch information was updated.

commit 8c950405d1695c2ca691537c1eba341155c9731a
Author: Sébastien Boisvert <[email protected]>
Date: Wed Jun 20 09:53:36 2012 -0400

The release procedure was updated.

commit 95f458950e9856c93b2af120845899975b74851e
Author: Sébastien Boisvert <[email protected]>
Date: Thu Jun 14 14:33:57 2012 -0400

A new option is available to disable read recycling.

commit 459f26f59076ffabe603f0d8b7163a69e2f51837
Author: Sébastien Boisvert <[email protected]>
Date: Thu Jun 14 14:10:11 2012 -0400

The options for using checkpointing features requires a
directory.





Changes in RayPlatform between v1.0.2 and v1.0.3:


commit 09517b6862d04743f64abc181de21b7d8c8b5dbd
Author: Sébastien Boisvert <[email protected]>
Date: Fri Jun 22 20:59:58 2012 -0400

This is the release of RayPlatform v1.0.3 codenamed
"Gray Pylon of Wisdom".

commit 86ddad8ee7b9cdbb6142561f38fd75e05e4622f2
Author: Sébastien Boisvert <[email protected]>
Date: Tue Jun 5 13:51:08 2012 -0400

Ray crashed sometimes when the number of processor cores was less or equal to 3.
This change fixes this. Ray can run of 1 processor core up to 4096 processor cores
at the moment with routing. Without routing, the maximum number of cores is larger.

Reported-by: krobinson#seqanswers.com
Reported-by: severin#seqanswers.com


Sébastien Boisvert
Granularity specialist/PhD student
Université Laval

[seb567]

This was fixed on 2012-04-27.

https://github.com/sebhtml/ray/commit/53495ad591bf0c9ac665595d5a1feef979767411

v2.0.0-rc8 is quite stable too.

Hi everyone,

I encountered a problem when trying to build the latest stable version of Ray (1.7) with the latest version of GCC (v4.7.0).

The problem occured at the make step.

With GCC v4.7.0, I got the following errors:

code/communication/MessageProcessor.cpp: In member function 'void MessageProcessor::call_RAY_MPI_TAG_ASK_VERTEX_PATH(Message*)':
code/communication/MessageProcessor.cpp:1685:7: error: redeclaration of 'int i'
code/communication/MessageProcessor.cpp:1675:10: error: 'int i' previously declared here
make: *** [code/communication/MessageProcessor.o] Error

However, when I used GCC v4.1.2 (which was also installed on this machine) instead, the installation finished correctly.

[seb567]

Hi there,

Do you have any news on the colourspace issue? We ran RAY today for the first time and was very impressed, except that we mostly deal with SOLiD data and would need the contigs in base space eventually :-)

Thanks!

Anelda

We have not worked on color space recently.

Ray can assemble color space reads, but will generate a double-encoded color space assembly.

[seb567]

So this could be achieved by typing something like:

mpiexec -n <#> Ray -o <$$$$> -read-checkpoints
(after you did a run with -write-checkpoints)

Is it possible to change the k-mer size for instance?

Thanks,

Santiago

No, you can not change the k-mer size if you use the same checkpointing files.

There is the option -read-write-checkpoints that read and write these checkpoints too.

[gringer]

That's because the more recent versions of GCC do more code checking. Redeclaring variables introduces some scoping issues, and usually means that the coder hasn't realised there's an ambiguity. Luckily, these redeclaration errors are usually easily fixed, for example by changing the name of the inner loop variable to j instead of i.

[steph]

Problem at compilation with latest GCC version

Hi everyone,

I encountered a problem when trying to build the latest stable version of Ray (1.7) with the latest version of GCC (v4.7.0).

The problem occured at the make step.

With GCC v4.7.0, I got the following errors:

code/communication/MessageProcessor.cpp: In member function 'void MessageProcessor::call_RAY_MPI_TAG_ASK_VERTEX_PATH(Message*)':
code/communication/MessageProcessor.cpp:1685:7: error: redeclaration of 'int i'
code/communication/MessageProcessor.cpp:1675:10: error: 'int i' previously declared here
make: *** [code/communication/MessageProcessor.o] Error

However, when I used GCC v4.1.2 (which was also installed on this machine) instead, the installation finished correctly.

[Anelda]

RAY on colourspace

Hi there,

Do you have any news on the colourspace issue? We ran RAY today for the first time and was very impressed, except that we mostly deal with SOLiD data and would need the contigs in base space eventually :-)

Thanks!

Anelda

[santiagosnchez]

So this could be achieved by typing something like:

mpiexec -n <#> Ray -o <$$$$> -read-checkpoints
(after you did a run with -write-checkpoints)

Is it possible to change the k-mer size for instance?

Thanks,

Santiago

[seb567]

Greetings !

Sébastien,

Is there a way to reuse some of Ray's output files in order to avoid some of the initial computations on the same data?

Cheers,
Santiago

Yes, they are called checkpoints.

You just have to add -read-write-checkpoints

However, note that checkpointing files (they are binary and have the .ray extension) are only valid with the same command using the same data with the same number of MPI rank.

This mechanism is a checkpointing facility.

mpiexec -n 1 Ray -help | less

  Checkpointing

       -write-checkpoints
              Write checkpoint files

       -read-checkpoints
              Read checkpoint files

       -read-write-checkpoints
              Read and write checkpoint files