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  • seb567
    replied
    Originally posted by bossanova352 View Post
    I'm trying to use Ray on some environmental metagenomes, but every time I set up a run, the output contig and scaffold files are empty. I haven't seen any indication during the assembly run, and all sequences are recognized by Ray. One possibility that comes to mind is from some errors that came up while compiling. Specifically, when trying to use the make install command, an error pops up saying there is no README file in ray-build/RayPlatform. If I place the README file in RayPlatform and try again, I get an error saying there is already a file named RayPlatform.

    Edit: After reinstalling Ray with the developer package, there are no installation errors. As of now, I'm stumped why there are no assembled sequences in either of the output Contigs.fasta or Scaffolds.fasta files.
    What is the content of RayOutput/NumberOfSequences.txt ?

    Do you have any error in your standard output file ? ("grep Error log.stdout")

    Leave a comment:


  • VidJa
    replied
    I'm trying to use Ray with a mix of Illumina SE and 454 data using the -amos
    mpiexec -n 10 Ray -s illumina.fasta -s 454.fasta -k 31 -amos -o mix
    454 reads have an avg length of 396bp and the illumina reads are 60bp

    The resulting amos file AMOS.afg can be browsed using Tablet, but I noticed that the original read names are converted to just a number and thus making it impossible to easily trace which reads end up in a particular contig. Is it possible to save the original readnames in the AMOS output?

    Leave a comment:


  • bossanova352
    replied
    I'm trying to use Ray on some environmental metagenomes, but every time I set up a run, the output contig and scaffold files are empty. I haven't seen any indication during the assembly run, and all sequences are recognized by Ray. One possibility that comes to mind is from some errors that came up while compiling. Specifically, when trying to use the make install command, an error pops up saying there is no README file in ray-build/RayPlatform. If I place the README file in RayPlatform and try again, I get an error saying there is already a file named RayPlatform.

    Edit: After reinstalling Ray with the developer package, there are no installation errors. As of now, I'm stumped why there are no assembled sequences in either of the output Contigs.fasta or Scaffolds.fasta files.
    Last edited by bossanova352; 01-12-2014, 12:25 AM.

    Leave a comment:


  • seb567
    replied
    Originally posted by Brian E View Post
    So, to add to an already massive thread, it's looking like Ray is going to be the assembler we're going to be using for our Metagenome work,

    There is a thread for Ray Meta (Ray for Metagenomics):

    Discussion of any scientific study related to high content or next generation genomics. Whole genome association, metagenomics, digital gene expression, etc.


    Paper: http://genomebiology.com/2012/13/12/R122

    Originally posted by Brian E View Post

    and I was wondering if it is possible to obtain the location that each read ends up in the assembly.
    There is the -amos option, but on the mailing list, I see more people relying on post-assembly read mapping onto the contigs.

    Originally posted by Brian E View Post

    We're using multiple biological replicates, sequenced separately (multiplexed) and we know that there is some variation in the abundance of the organisms that are present in the community. What I would like is the contribution of each individual sample to the local coverage of the whole assembly. I think this could help with pulling out individual genomes.
    If you are sequencing barcoded samples, then demultiplexing should be done before feeding the data to Ray.

    Originally posted by Brian E View Post

    I know could get at this by mapping with e.g. Bowtie, but if it is possible to keep track of where these reads are ending up, it would save a significant amount of time on our computer cluster allocation. Is this possible?
    As stated above, Ray can generate an AMOS file, which contains read usage.

    Séb

    Leave a comment:


  • Brian E
    replied
    So, to add to an already massive thread, it's looking like Ray is going to be the assembler we're going to be using for our Metagenome work, and I was wondering if it is possible to obtain the location that each read ends up in the assembly. We're using multiple biological replicates, sequenced separately (multiplexed) and we know that there is some variation in the abundance of the organisms that are present in the community. What I would like is the contribution of each individual sample to the local coverage of the whole assembly. I think this could help with pulling out individual genomes.
    I know could get at this by mapping with e.g. Bowtie, but if it is possible to keep track of where these reads are ending up, it would save a significant amount of time on our computer cluster allocation. Is this possible?

    Leave a comment:


  • seb567
    replied
    Originally posted by OTU View Post
    Em....

    And after this, what should I do? Does this mean the end of installation of Ray-v2.2.0?
    I am sorry, I am just confused with all this stuff...
    No. The command above is to build Ray with gz support but no bz2 support.


    Did you try:

    make clean
    make HAVE_LIBZ=y HAVE_LIBBZ2=n

    Leave a comment:


  • OTU
    replied
    Em....

    And after this, what should I do? Does this mean the end of installation of Ray-v2.2.0?
    I am sorry, I am just confused with all this stuff...

    Leave a comment:


  • seb567
    replied
    Originally posted by OTU View Post
    Through yum - got success! Thank you!
    And with libz2:
    [root@localhost Ray-v2.2.0]# file -L /usr/lib64/libbz2.so
    /usr/lib64/libbz2.so: ELF 64-bit LSB shared object, x86-64, version 1 (SYSV), dynamically linked, BuildID[sha1]=0x7705fc6fbd1d6aa0ffde9b4f54189a5b637e3ee0, stripped

    Is this ok?
    The package you installed with yum is 2.1.0-6.fc19 (not 2.2.0).


    So if you also want 2.2.0, can you try this (with gz support but without bz2 support):


    make clean
    make HAVE_LIBZ=y HAVE_LIBBZ2=n

    Leave a comment:


  • OTU
    replied
    Through yum - got success! Thank you!
    And with libz2:
    [root@localhost Ray-v2.2.0]# file -L /usr/lib64/libbz2.so
    /usr/lib64/libbz2.so: ELF 64-bit LSB shared object, x86-64, version 1 (SYSV), dynamically linked, BuildID[sha1]=0x7705fc6fbd1d6aa0ffde9b4f54189a5b637e3ee0, stripped

    Is this ok?

    Leave a comment:


  • seb567
    replied
    Originally posted by OTU View Post
    Yes, I was trying to use make command..
    I am installing Ray-v2.2.0

    I tried to install what you told:
    [root@localhost Ray-v2.2.0]# rpm -Uvh '/home/annet/Downloads/epel-release-6-8.noarch.rpm'
    warning: /home/annet/Downloads/epel-release-6-8.noarch.rpm: Header V3 RSA/SHA256 Signature, key ID 0608b895: NOKEY
    error: Failed dependencies:
    fedora-release conflicts with epel-release-6-8.noarch
    You can simply type this to install in Fedora 19:

    sudo yum install Ray-openmpi




    For your buddy libbz2.so, can you type this command:

    file -L /usr/lib64/libbz2.so


    I suppose this is an issue with the architecture of the library.

    Leave a comment:


  • OTU
    replied
    Yes, I was trying to use make command..
    I am installing Ray-v2.2.0

    I tried to install what you told:
    [root@localhost Ray-v2.2.0]# rpm -Uvh '/home/annet/Downloads/epel-release-6-8.noarch.rpm'
    warning: /home/annet/Downloads/epel-release-6-8.noarch.rpm: Header V3 RSA/SHA256 Signature, key ID 0608b895: NOKEY
    error: Failed dependencies:
    fedora-release conflicts with epel-release-6-8.noarch

    Leave a comment:


  • seb567
    replied
    Originally posted by OTU View Post
    Ok,

    I got:
    # file /usr/lib64/libbz2.so
    /usr/lib64/libbz2.so: symbolic link to `libbz2.so.1'

    I am using MPI, as stated to be done in instructions...
    Operating system - Fedora19
    Did you try to build Ray using the Makefile using the
    "make" command ?


    Which version of Ray are you building ?


    In Fedora 19, there is the precompiled package Ray-openmpi.x86_64
    that provides Ray.

    I am using Fedora 18 myself ( x86_64) and I never saw this cryptic error message
    from the linker ld.

    Leave a comment:


  • OTU
    replied
    Ok,

    I got:
    # file /usr/lib64/libbz2.so
    /usr/lib64/libbz2.so: symbolic link to `libbz2.so.1'

    I am using MPI, as stated to be done in instructions...
    Operating system - Fedora19

    Leave a comment:


  • seb567
    replied
    Originally posted by OTU View Post
    Hi everyone!

    I am having troubles with installing Ray.
    So, after trying to run this line:
    ./scripts/Build-Link-Time-Optimization.sh

    I am having an error message:
    /bin/ld: skipping incompatible /usr/lib64/libbz2.so when searching for -lbz2
    /bin/ld: cannot find -lbz2
    collect2: error: ld returned 1 exit status
    strip: 'Ray': No such file

    What can be an issue with -lbz2?

    Please, need help!
    Hello,

    The message "skipping incompatible /usr/lib64/libbz2.so when searching for -lbz2"
    means something I guess. I never saw this message before.
    It is likely related to your tool chain, not Ray.

    Can you do:

    file /usr/lib64/libbz2.so

    Also:


    Which compiler are you using ?

    What is your operating system ?

    Leave a comment:


  • OTU
    replied
    Hi everyone!

    I am having troubles with installing Ray.
    So, after trying to run this line:
    ./scripts/Build-Link-Time-Optimization.sh

    I am having an error message:
    /bin/ld: skipping incompatible /usr/lib64/libbz2.so when searching for -lbz2
    /bin/ld: cannot find -lbz2
    collect2: error: ld returned 1 exit status
    strip: 'Ray': No such file

    What can be an issue with -lbz2?

    When I am looking for this library, I got:
    # locate libbz2
    /opt/google/chrome/libbz2.so.1.0
    /usr/lib/libbz2.so.1
    /usr/lib/libbz2.so.1.0.6
    /usr/lib64/libbz2.so
    /usr/lib64/libbz2.so.1
    /usr/lib64/libbz2.so.1.0.6

    Please, need help!
    Last edited by OTU; 08-11-2013, 09:35 AM.

    Leave a comment:

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