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Old 11-04-2012, 01:28 PM   #201
cwzkevin
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Hi Sebastien,
I am going to try Ray. Make and install is successful when I don't turn on LIBZ or LIBBZ2.

However, make error if I turn on "HAVE_LIBZ = y" and/or "HAVE_LIBBZ2 = y".

The system here has both library installed:
Code:
$ ll /usr/lib64/libz*
-rwxr-xr-x 1 root root 108628 Mar 16  2011 /usr/lib64/libz.a*
lrwxrwxrwx 1 root root     19 Sep 16  2011 /usr/lib64/libz.so -> ../../lib64/libz.so*
lrwxrwxrwx 1 root root     21 Sep 16  2011 /usr/lib64/libz.so.1 -> ../../lib64/libz.so.1*
lrwxrwxrwx 1 root root     25 Sep 16  2011 /usr/lib64/libz.so.1.2.3 -> ../../lib64/libz.so.1.2.3*
ll /usr/lib64/libbz2*
-rwxr-xr-x 1 root root 77606 Sep 20  2010 /usr/lib64/libbz2.a*
lrwxrwxrwx 1 root root    11 Dec 10  2010 /usr/lib64/libbz2.so -> libbz2.so.1*
lrwxrwxrwx 1 root root    15 Dec 10  2010 /usr/lib64/libbz2.so.1 -> libbz2.so.1.0.3*
-rwxr-xr-x 1 root root 67792 Sep 20  2010 /usr/lib64/libbz2.so.1.0.3*
I am not sure, but I think the problem might be that the /usr/lib64 is not in my search path. I have bellow line in my ~/.bashrc
Code:
export LD_RUN_PATH=$MYSOFT/openmpi-1.6.3/lib:/usr/lib64
So, the question is that if the problem comes from the library search path, how to edit the Makefile to get it work? If the problem is not from the library search path, then how? Thank you.
Here is the error messages:
Code:
mpicxx  -lz -lbz2  code/TheRayGenomeAssembler.a RayPlatform/libRayPlatform.a -o Ray
code/TheRayGenomeAssembler.a(Loader.o): In function `Loader::load(std::basic_string<char, std::char_traits<char>, std::allocator<char> >, bool)':
Loader.cpp:(.text+0x8a3): undefined reference to `FastqBz2Loader::open(std::basic_string<char, std::char_traits<char>, std::allocator<char> >, int)'
Loader.cpp:(.text+0x8c3): undefined reference to `FastqBz2Loader::getSize()'
Loader.cpp:(.text+0xb3b): undefined reference to `FastqGzLoader::open(std::basic_string<char, std::char_traits<char>, std::allocator<char> >, int)'
Loader.cpp:(.text+0xb5b): undefined reference to `FastqGzLoader::getSize()'
Loader.cpp:(.text+0xc5e): undefined reference to `FastqGzLoader::open(std::basic_string<char, std::char_traits<char>, std::allocator<char> >, int)'
Loader.cpp:(.text+0xd0c): undefined reference to `FastqBz2Loader::open(std::basic_string<char, std::char_traits<char>, std::allocator<char> >, int)'
code/TheRayGenomeAssembler.a(Loader.o): In function `Loader::loadSequences()':
Loader.cpp:(.text+0x1ac): undefined reference to `FastqGzLoader::load(int, ArrayOfReads*, MyAllocator*, int)'
Loader.cpp:(.text+0x20c): undefined reference to `FastqBz2Loader::load(int, ArrayOfReads*, MyAllocator*, int)'
collect2: ld returned 1 exit status
make: *** [Ray] Error 1
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Old 11-04-2012, 02:41 PM   #202
seb567
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You don't need to edit the Makefile.

Are you compiling with this:
make HAVE_LIBZ=y HAVE_LIBBZ2=y
?

This should work as is if you have openmpi, zlib, and bzip2 (and associated
-devel packages depending of your system).

It seems that in your case that FastqBz2Loader.o and FastqGzLoader.o are not compiled
and therefore not linked. FastqBz2Loader.o is compiled and linked only with HAVE_LIBBZ2=y and FastqGzLoader.o is only compiled and linked with HAVE_LIBZ=y.

I suspect that you edited the Makefile.

Can you provide your make command with all its output in pastebin [1] ?

Hopefully, Ray will soon be available as precompiled packages for Debian [2], Fedora [3], and ArchLinux [4]. Packages will probably be distributed in Ubuntu (via Debian) and Red Hat Enterprise Linux (via Fedora).

Just out of curiosity, what operating system are you running Ray on ?

---

[1] http://pastebin.com/
[2] http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=692238
[3] https://bugzilla.redhat.com/show_bug.cgi?id=872783
[4] https://github.com/sebhtml/Ray-on-ArchLinux
Quote:
Originally Posted by cwzkevin View Post
Hi Sebastien,
I am going to try Ray. Make and install is successful when I don't turn on LIBZ or LIBBZ2.

However, make error if I turn on "HAVE_LIBZ = y" and/or "HAVE_LIBBZ2 = y".

The system here has both library installed:
Code:
$ ll /usr/lib64/libz*
-rwxr-xr-x 1 root root 108628 Mar 16  2011 /usr/lib64/libz.a*
lrwxrwxrwx 1 root root     19 Sep 16  2011 /usr/lib64/libz.so -> ../../lib64/libz.so*
lrwxrwxrwx 1 root root     21 Sep 16  2011 /usr/lib64/libz.so.1 -> ../../lib64/libz.so.1*
lrwxrwxrwx 1 root root     25 Sep 16  2011 /usr/lib64/libz.so.1.2.3 -> ../../lib64/libz.so.1.2.3*
ll /usr/lib64/libbz2*
-rwxr-xr-x 1 root root 77606 Sep 20  2010 /usr/lib64/libbz2.a*
lrwxrwxrwx 1 root root    11 Dec 10  2010 /usr/lib64/libbz2.so -> libbz2.so.1*
lrwxrwxrwx 1 root root    15 Dec 10  2010 /usr/lib64/libbz2.so.1 -> libbz2.so.1.0.3*
-rwxr-xr-x 1 root root 67792 Sep 20  2010 /usr/lib64/libbz2.so.1.0.3*
I am not sure, but I think the problem might be that the /usr/lib64 is not in my search path. I have bellow line in my ~/.bashrc
Code:
export LD_RUN_PATH=$MYSOFT/openmpi-1.6.3/lib:/usr/lib64
So, the question is that if the problem comes from the library search path, how to edit the Makefile to get it work? If the problem is not from the library search path, then how? Thank you.
Here is the error messages:
Code:
mpicxx  -lz -lbz2  code/TheRayGenomeAssembler.a RayPlatform/libRayPlatform.a -o Ray
code/TheRayGenomeAssembler.a(Loader.o): In function `Loader::load(std::basic_string<char, std::char_traits<char>, std::allocator<char> >, bool)':
Loader.cpp:(.text+0x8a3): undefined reference to `FastqBz2Loader::open(std::basic_string<char, std::char_traits<char>, std::allocator<char> >, int)'
Loader.cpp:(.text+0x8c3): undefined reference to `FastqBz2Loader::getSize()'
Loader.cpp:(.text+0xb3b): undefined reference to `FastqGzLoader::open(std::basic_string<char, std::char_traits<char>, std::allocator<char> >, int)'
Loader.cpp:(.text+0xb5b): undefined reference to `FastqGzLoader::getSize()'
Loader.cpp:(.text+0xc5e): undefined reference to `FastqGzLoader::open(std::basic_string<char, std::char_traits<char>, std::allocator<char> >, int)'
Loader.cpp:(.text+0xd0c): undefined reference to `FastqBz2Loader::open(std::basic_string<char, std::char_traits<char>, std::allocator<char> >, int)'
code/TheRayGenomeAssembler.a(Loader.o): In function `Loader::loadSequences()':
Loader.cpp:(.text+0x1ac): undefined reference to `FastqGzLoader::load(int, ArrayOfReads*, MyAllocator*, int)'
Loader.cpp:(.text+0x20c): undefined reference to `FastqBz2Loader::load(int, ArrayOfReads*, MyAllocator*, int)'
collect2: ld returned 1 exit status
make: *** [Ray] Error 1
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Old 11-04-2012, 03:33 PM   #203
cwzkevin
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Yes, I edited the Makefile. Changed was made as below:
Code:
MAXKMERLENGTH = 96
HAVE_LIBZ = y
HAVE_LIBBZ2 = y
My make command is just simple as
Code:
$ make PREFIX=bin
My system is
Code:
$ uname -mrs
Linux 2.6.18-308.8.2.el5 x86_64
$ lsb_release -a
LSB Version:    :core-4.0-amd64:core-4.0-ia32:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-ia32:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-ia32:printing-4.0-noarch
Distributor ID: RedHatEnterpriseServer
Description:    Red Hat Enterprise Linux Server release 5.8 (Tikanga)
Release:        5.8
Codename:       Tikanga
Here is the link for full output http://pastebin.com/Kf35v5SK

Thank you for your help.

Quote:
Originally Posted by seb567 View Post
You don't need to edit the Makefile.

Are you compiling with this:
make HAVE_LIBZ=y HAVE_LIBBZ2=y
?

This should work as is if you have openmpi, zlib, and bzip2 (and associated
-devel packages depending of your system).

It seems that in your case that FastqBz2Loader.o and FastqGzLoader.o are not compiled
and therefore not linked. FastqBz2Loader.o is compiled and linked only with HAVE_LIBBZ2=y and FastqGzLoader.o is only compiled and linked with HAVE_LIBZ=y.

I suspect that you edited the Makefile.

Can you provide your make command with all its output in pastebin [1] ?

Hopefully, Ray will soon be available as precompiled packages for Debian [2], Fedora [3], and ArchLinux [4]. Packages will probably be distributed in Ubuntu (via Debian) and Red Hat Enterprise Linux (via Fedora).

Just out of curiosity, what operating system are you running Ray on ?

---

[1] http://pastebin.com/
[2] http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=692238
[3] https://bugzilla.redhat.com/show_bug.cgi?id=872783
[4] https://github.com/sebhtml/Ray-on-ArchLinux
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Old 11-04-2012, 03:50 PM   #204
cwzkevin
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Oh, I see. With below, it is good now.
Code:
$ make PREFIX=bin HAVE_LIBZ=y HAVE_LIBBZ2=y
Seems my below question is more related to common sense of linux/compiler instead of Ray:
Q: What is the difference between Method 1 and Method 2, shouldn't they be the same?
Method 1: I edited the Makefile, changed to "HAVE_LIBZ = y", "HAVE_LIBBZ2 = y", then $ make PREFIX=bin
Method 2: $ make PREFIX=bin HAVE_LIBZ=y HAVE_LIBBZ2=y
Thanks.

Last edited by cwzkevin; 11-04-2012 at 03:59 PM.
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Old 11-04-2012, 04:19 PM   #205
seb567
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Hi !

Thanks for the logs, that really helps understanding what's going
on.

You can build Ray with these options without any Makefile modification:

$ make clean
$ make MAXKMERLENGTH=96 HAVE_LIBZ=y HAVE_LIBBZ2=y PREFIX=bin
$ make install

$ mpiexec -n 1 bin/Ray -version
Ray version 2.1.0
License for Ray: GNU General Public License version 3
RayPlatform version: 1.1.0
License for RayPlatform: GNU Lesser General Public License version 3

MAXKMERLENGTH: 96 <=========== Here you go !
KMER_U64_ARRAY_SIZE: 3
Maximum coverage depth stored by CoverageDepth: 4294967295
MAXIMUM_MESSAGE_SIZE_IN_BYTES: 4000 bytes
FORCE_PACKING = n
ASSERT = n
HAVE_LIBZ = y <=========== Here you go !
HAVE_LIBBZ2 = y <=========== Here you go !
CONFIG_PROFILER_COLLECT = n
CONFIG_CLOCK_GETTIME = n
__linux__ = y
_MSC_VER = n
__GNUC__ = y
RAY_32_BITS = n
RAY_64_BITS = y
MPI standard version: MPI 2.1
MPI library: Open-MPI 1.5.4
Compiler: GNU gcc/g++ 4.7.2 20120921 (Red Hat 4.7.2-2)

Quote:
Originally Posted by cwzkevin View Post
Oh, I see. With below, it is good now.
Code:
$ make PREFIX=bin HAVE_LIBZ=y HAVE_LIBBZ2=y
Seems my below question is more related to common sense of linux/compiler instead of Ray:
Q: What is the difference between Method 1 and Method 2, shouldn't they be the same?
Method 1: I edited the Makefile, changed to "HAVE_LIBZ = y", "HAVE_LIBBZ2 = y", then $ make PREFIX=bin
Method 2: $ make PREFIX=bin HAVE_LIBZ=y HAVE_LIBBZ2=y
Thanks.

Now, if why editing the Makefile fails ?

There are many Makefile files actually (distributed Makefiles)

Ray-v2.1.0/Makefile
Ray-v2.1.0/code/Makefile
Ray-v2.1.0/code/*/Makefile (23)

When you provide the variables in the make command line, they will
be given to child processes because they are exported. However,
variables within a Makefile are not exported.

It fails because of this:

Ray-v2.1.0/code/plugin_SequencesLoader/Makefile:

SequencesLoader-$(HAVE_LIBBZ2) += plugin_SequencesLoader/BzReader.o
SequencesLoader-$(HAVE_LIBBZ2) += plugin_SequencesLoader/FastqBz2Loader.o
SequencesLoader-$(HAVE_LIBZ) += plugin_SequencesLoader/FastqGzLoader.o

These configuration options are used by the Makefiles, but also by the
C++ code. For example, HAVE_LIBZ is valued to y in all the Makefiles,
and the -D HAVE_LIBZ passed to gcc defines HAVE_LIBZ in all C++ files
too.

If you really want to edit the Makefile, you have to do it like this:

--- Ray-v2.1.0/Makefile 2012-10-30 18:29:34.000000000 -0400
+++ Ray-v2.1.0-copy/Makefile 2012-11-04 20:05:54.099217300 -0500
@@ -33,13 +33,13 @@
# needs libz
# set to no if you don't have libz
# y/n
-HAVE_LIBZ = n
+export HAVE_LIBZ = y

# support for .bz2 files
# needs libbz2
# set to no if you don't have libbz2
# y/n
-HAVE_LIBBZ2 = n
+export HAVE_LIBBZ2 = y

# use Intel's compiler
# the name of the Intel MPI C++ compiler is mpiicpc

If you know programming, you can send me a patch that fixes this bug
in the Makefile that would add 'export ' in front of build options.

If you have other questions regarding the Ray build system,
let me know.


Otherwise, I'll put this in my patchwork queue !

***
Cheers, Sébastien


Quote:
Originally Posted by cwzkevin View Post
Yes, I edited the Makefile. Changed was made as below:
Code:
MAXKMERLENGTH = 96
HAVE_LIBZ = y
HAVE_LIBBZ2 = y
My make command is just simple as
Code:
$ make PREFIX=bin
My system is
Code:
$ uname -mrs
Linux 2.6.18-308.8.2.el5 x86_64
$ lsb_release -a
LSB Version:    :core-4.0-amd64:core-4.0-ia32:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-ia32:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-ia32:printing-4.0-noarch
Distributor ID: RedHatEnterpriseServer
Description:    Red Hat Enterprise Linux Server release 5.8 (Tikanga)
Release:        5.8
Codename:       Tikanga
Here is the link for full output http://pastebin.com/Kf35v5SK

Thank you for your help.

Last edited by seb567; 11-04-2012 at 04:22 PM.
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Old 11-04-2012, 06:38 PM   #206
cwzkevin
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Thank you very much for the detail, I understand now. Great appreciate it!

Sorry, I am not a programmer. (I think a programmer should already know there could be distributed Makefiles instead of the one that I edited. ^_^)

Now, it is time to try it out.
Thanks!
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Old 11-07-2012, 03:17 PM   #207
kmkocot
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Hi all,

Quick question: I have a paired-end data from a MiSeq that I would like to assemble in Ray. The library was made with a Nextera kit and sequenced using the new 2 X 250 reagent kits. The average size distribution of my library was around 500 bp but some smaller fragments were present. For those fragments, the read pairs will at least partially overalp. Does Ray have a problem when the two members of a pair of reads overlap? Should I treat the data as non paired end?

Thanks!
Kevin
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Old 11-08-2012, 12:21 PM   #208
cwzkevin
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Hi, I have a question here.
Does Ray expect the sequence order in two pair-end files the same?
I ask because the sequence order in my two pair-end fastq files happened to be different the last time. They are indeed pair files, just the sequences are in different order. And I ran these pair-end files with Ray, got output1. After I realized the sequence order are not the same, I sort the fastq files to make them same order. I then re-ran Ray, got output2. It seems the two run results are different.
Thank you.
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Old 02-04-2013, 07:24 PM   #209
seb567
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Quote:
Originally Posted by kmkocot View Post
Hi all,

Quick question: I have a paired-end data from a MiSeq that I would like to assemble in Ray. The library was made with a Nextera kit and sequenced using the new 2 X 250 reagent kits. The average size distribution of my library was around 500 bp but some smaller fragments were present. For those fragments, the read pairs will at least partially overalp. Does Ray have a problem when the two members of a pair of reads overlap? Should I treat the data as non paired end?

Thanks!
Kevin
Hi,

Ray will be fine with those.

I suggest you run something like this:

mpiexec -n 16 Ray -k 71 -p file_R1.fastq.gz file_R2.fastq.gz -o MiSeq+Ray


Also, you can use Ray Cloud Browser too to visualize your assembly in your web browser.

Demo: http://genome.ulaval.ca/corbeillab/Ray-Cloud-Browser


p.s.: you'll need to compile with this:

make MAXKMERLENGTH=96 HAVE_LIBZ=y

---
-Sébastien

Last edited by seb567; 02-04-2013 at 07:26 PM. Reason: added http://; added -k 71
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Old 02-04-2013, 07:28 PM   #210
seb567
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Quote:
Originally Posted by cwzkevin View Post
Hi, I have a question here.
Does Ray expect the sequence order in two pair-end files the same?
yes

Quote:
Originally Posted by cwzkevin View Post
I ask because the sequence order in my two pair-end fastq files happened to be different the last time. They are indeed pair files, just the sequences are in different order. And I ran these pair-end files with Ray, got output1. After I realized the sequence order are not the same, I sort the fastq files to make them same order. I then re-ran Ray, got output2. It seems the two run results are different.
Thank you.
Ray need both files to list sequences in the same order.

By default, most sequencing technologies do that by default, and the dominant sequencing technology is just like that too.

Thanks for the feedback !

-Sébastien
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Old 02-04-2013, 07:28 PM   #211
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Quote:
Originally Posted by kmkocot View Post
The library was made with a Nextera kit and sequenced using the new 2 X 250 reagent kits. The average size distribution of my library was around 500 bp but some smaller fragments were present. For those fragments, the read pairs will at least partially overalp. Does Ray have a problem when the two members of a pair of reads overlap? Should I treat the data as non paired end?
Quote:
Originally Posted by seb567 View Post
Ray will be fine with those.
... as long as your computer cluster is up to the challenge (which depends more on the target genome size than the number of input reads). While Ray is quite memory efficient, you may have a bit of difficulty assembling a human genome using Ray on a small cluster or desktop.

Last edited by gringer; 02-04-2013 at 07:31 PM.
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Old 02-04-2013, 07:33 PM   #212
seb567
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Quote:
Originally Posted by gringer View Post
... as long as your computer cluster is up to the challenge. While Ray is quite memory efficient, you may have a bit of difficulty assembling a human genome using Ray on a small cluster or desktop.
Sure.

And it depends what is implied by "assembling a human genome".

Assemblathon 2 results indicate that Ray is really good with gene content, but its scaffolder is way too conservative.

Our group is mostly into bacterial genomes and human microbiomes.

See our recent paper: http://genomebiology.com/2012/13/12/R122/abstract


Thanks for the feedback !

-Sébastien
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Old 02-04-2013, 07:41 PM   #213
gringer
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Quote:
Originally Posted by seb567 View Post
Assemblathon 2 results indicate that Ray is really good with gene content, but its scaffolder is way too conservative.
FWIW, I've been able to improve on Ray assemblies a little by running the scaffolds through AMOS' minimus2 (in the default all-vs-all mode). That was able to pick up a few more SNPs and merge contigs that were almost identical.
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Old 02-25-2013, 01:54 PM   #214
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Thanks guys! Sorry for the great delay in my reply. I have been at sea.

We are working with invertebrate genomes of unknown size but we're after the mitochondrial genomes for this project and they've been shaking out OK on our 80 CPU cluster.

Best,
Kevin
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Old 02-25-2013, 01:55 PM   #215
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Me again. seb567, the link to the visualization tool you posted (http://genome.ulaval.ca/corbeillab/Ray-Cloud-Browser) is broken.
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Old 02-26-2013, 05:05 PM   #216
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Quote:
Originally Posted by kmkocot View Post
Thanks guys! Sorry for the great delay in my reply. I have been at sea.

We are working with invertebrate genomes of unknown size but we're after the mitochondrial genomes for this project and they've been shaking out OK on our 80 CPU cluster.

Best,
Kevin
Cool !


Quote:
Originally Posted by kmkocot View Post
Me again. seb567, the link to the visualization tool you posted (http://genome.ulaval.ca/corbeillab/Ray-Cloud-Browser) is broken.
It's the IT at my institution that failed I guess. Anyway, I have set up DNS canonical names (CNAME), which are more robust.

All my Ray Cloud Browser deployments are in the cloud.

4 demos (these are canonical names to cloud instances):

E. coli on a t1.micro spot instance in Amazon EC2

Some microbiomes of a colleague on 1 t1.micro spot instance in Amazon EC2

E. coli on a small Linux Virtual Machine in Windows Azure

A vertebrate genome (American eel) on a Silver instance in IBM SmartCloud


In all these links, raytrek.com can be replaced by boisvert.info (example: browser.cloud.raytrek.com and browser.cloud.boisvert.info are the same instance).
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Old 03-09-2013, 12:49 PM   #217
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Default A bit confused about parameters - help...

Hi,
What is the meaning of averageOuterDistance and standardDeviation for paired end files? Is it just average read length in the dataset?
If so, then why it is not required for single read file?
If not, is it an average fragment length in the library? Such as surmised from BioAnalyzer trace, for example?
If so, then default autocalc may give very wrong estimate, could it? For example, one of my paired read runs was done with a library of 600 bp +/- 15%, but during assembly autocalc estimate was something 150 bp - how this can be so much off?
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Old 03-09-2013, 06:10 PM   #218
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Default More help needed....

Hi,

I tried to run Ray (maxkmer 32) on 2 x quad core RHEl58 with hyper-threading enabled:

mpiexec -n 16 Ray <Ray.conf> and got the error:
Code:
........
Loader::load] File: /media/FantomHD/Data/MiSeq/SC/AdQ30/SC-MILLib1-Herc2s10cFr1Fr2run2R1AdQ30.fastq (please wait...)
[Loader::load] File: /media/FantomHD/Data/MiSeq/SC/AdQ30/SC-MILLib1-Herc2s10cFr1Fr2run2R1AdQ30.fastq (please wait...)
[Loader::load] File: /media/FantomHD/Data/MiSeq/SC/AdQ30/SCPfx3s25cFr3-150-200run1R1AdQ30.fastq (please wait...)
[Loader::load] File: /media/FantomHD/Data/MiSeq/SC/AdQ30/SCPfx3s25cFr3-150-200run1R1AdQ30.fastq (please wait...)
[Loader::load] File: /media/FantomHD/Data/MiSeq/SC/AdQ30/SCPfx3s25cFr3-150-200run2R1AdQ30.fastq (please wait...)
[Loader::load] File: /media/FantomHD/Data/MiSeq/SC/AdQ30/SCPfx3s25cFr3-150-200run2R1AdQ30.fastq (please wait...)
[Loader::load] File: /media/FantomHD/AssRefMap/SC/SCold/SColdAll.fasta (please wait...)
[Loader::load] File: /media/FantomHD/AssRefMap/SC/SCold/SColdAll.fasta (please wait...)
[Loader::load] File: /media/FantomHD/AssRefMap/SC/SCold/SCallSanger.fasta (please wait...)
[Loader::load] File: /media/FantomHD/AssRefMap/SC/SCold/SCallSanger.fasta (please wait...)
[Loader::load] File: /home/yaximik/AssRefMap/SC/minia/SCMiSeqAllFGMGPGIGclean_k27.contigs.fasta (please wait...)
[G5NNJN1:07040] *** Process received signal ***
[G5NNJN1:07040] Signal: Segmentation fault (11)
[G5NNJN1:07040] Signal code:  (128)
[G5NNJN1:07040] Failing at address: (nil)
--------------------------------------------------------------------------
mpiexec noticed that process rank 0 with PID 7040 on node G5NNJN1 exited on signal 11 (Segmentation fault).
The last file loaded was a file with fasta contigs from another assembler (minia). Does this mean contigs from other assemblers cannot be used in Ray?
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Old 03-09-2013, 06:12 PM   #219
yaximik
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Oops The machine has 96 GB memory
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Old 03-09-2013, 09:01 PM   #220
KirillK
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Hi guys!

Is there a way to provide a reference genome for Ray?

cheers,
KK
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