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  • RE: Ray2.2.0

    More questions about the insert size:
    1) I checked the LibraryStatistics.txt, I found the number is quite different (303bp) from what my Lab tech provided (~1kb);
    2) Does this mean I have to run Ray first to get the insert size first then provide Ray with these parameters and run it again?
    I want to make sure each point, and Ray is really fast and it helps very much. Thanks a lot!
    YT
    Last edited by yifangt; 04-29-2013, 10:36 AM.

    Comment


    • I am having issues installing. When I run the make prefix=ray-build like the installation file says, I get the following error:

      Code:
      make prefix=ray-build
      make[1]: Entering directory `/home/eric.fritz/Ray-v2.2.0/RayPlatform'
        CXX RayPlatform/memory/ReusableMemoryStore.o
      make[1]: execvp: mpicxx: Not a directory
      make[1]: *** [memory/ReusableMemoryStore.o] Error 127
      make[1]: Leaving directory `/home/eric.fritz/Ray-v2.2.0/RayPlatform'
      make: *** [RayPlatform/libRayPlatform.a] Error 2
      I do have all the requirements on the system. Thanks.

      Comment


      • [QUOTE=seb567;103233]I fixed this build script.



        Thank you for fixing the buildscript. I have been able to make modifications to the makefile by altering the MAXKMERLENGTH and it is working alright. For some reason, every time I run Rayv2.2.0, the following error comes up (for any K-mer specification; I have tried values from 21-91; my reads are 101 bp in length):

        Rank 0: Assembler panic: no k-mers found in reads.
        Rank 0: Perhaps reads are shorter than the k-mer length (change -k).

        I am sure I am missing something very basic, but I am a newbie any comments would be greatly appreciated.

        Thanks,
        Akshaya

        Comment


        • problem with RAY assembly

          Hi,
          I've been using Ray very successfully on our cluster, but ran into a problem with my last data set. It's a relatively modest MySeq partial run of about 750k paired reads that originate from a pure bacterial strain. Originally, I ran the data and I got a decent assembly, but I discovered that there was some degree of read-through and that the adapters were not trimmed on the 3' end for all reads (not sure why illumina basespace does not check for that by default). I used Trimmomactic 0.3 to remove the adapters and tried re-assembling with Ray, but every time I do, it produces a crash. Basically, it goes into some sort of endless loop that ends up using 80 gig of swap at which point the cluster bounces my job. I sliced my data into three parts and assembled them separately or in combinations and the data assembles fine that way (so it's not corrupted data files). Only when I combine all three parts, do I get the crash. I added the stderr below. The stdout is >84gigs and I also added the end of the file.

          Any thoughts what the problem might be ?

          Thanks in advance !

          stderr:

          Ray:18680 terminated with signal 11 at PC=2aebbf8198d7 SP=7fff758b6340. Backtrace:
          /usr/mpi/intel/openmpi-1.4.3-qlc/lib64/libopen-pal.so.0(opal_memory_ptmalloc2_int_malloc+0xfd7)[0x2aebbf8198d7]
          /usr/mpi/intel/openmpi-1.4.3-qlc/lib64/libopen-pal.so.0(+0x49a05)[0x2aebbf817a05]
          /usr/lib64/libstdc++.so.6(_Znwm+0x1d)[0x2aebc014809d]
          /home/bstamps/Ray/Ray(_ZNSt6vectorI4KmerSaIS0_EE13_M_insert_auxEN9__gnu_cxx17__normal_iteratorIPS0_S2_EERKS0_+0x130)[0x473bc0]
          /home/bstamps/Ray/Ray(_ZN12SeedExtender28markCurrentVertexAsAssembledEP4KmerP13RingAllocatorPiP12StaticVectoriiP13ExtensionDataPbS9_S4_S9_PSt6vectorIS0_SaIS0_EEP7ChooserP10BubbleDataiP20OpenAssemblerChooseriPSA_I12AssemblySeedSaISK_EE+0x1371)[0x4e96e1]
          /home/bstamps/Ray/Ray(_ZN12SeedExtender29call_RAY_SLAVE_MODE_EXTENSIONEv+0x5f7)[0x4f16f7]
          /home/bstamps/Ray/Ray(_ZN11ComputeCore10runVanillaEv+0x9b)[0x534f7b]
          /home/bstamps/Ray/Ray(_ZN11ComputeCore3runEv+0x6e)[0x53638e]
          /home/bstamps/Ray/Ray(_ZN7Machine5startEv+0x1697)[0x4487a7]
          /home/bstamps/Ray/Ray(main+0x3a)[0x443bba]
          /lib64/libc.so.6(__libc_start_main+0xfd)[0x2aebc0a67cdd]
          /home/bstamps/Ray/Ray[0x443a89]


          end of stdout:

          Rank 43: assembler memory usage: 24483328 KiB
          Rank 43 reached 536865000 vertices from seed 0, flow 2
          Speed RAY_SLAVE_MODE_EXTENSION 9921 units/second
          Rank 43: assembler memory usage: 24483328 KiB
          Rank 43 reached 536866000 vertices from seed 0, flow 2
          Speed RAY_SLAVE_MODE_EXTENSION 12596 units/second
          Rank 43: assembler memory usage: 24483328 KiB
          Rank 43 reached 536867000 vertices from seed 0, flow 2
          Speed RAY_SLAVE_MODE_EXTENSION 12235 units/second
          Rank 43: assembler memory usage: 24483328 KiB
          Rank 43 reached 536868000 vertices from seed 0, flow 2
          Speed RAY_SLAVE_MODE_EXTENSION 13596 units/second
          Rank 43: assembler memory usage: 24483328 KiB
          Rank 43 reached 536869000 vertices from seed 0, flow 2
          Speed RAY_SLAVE_MODE_EXTENSION 10610 units/second
          Rank 43: assembler memory usage: 24483328 KiB
          Rank 43 reached 536870000 vertices from seed 0, flow 2
          Speed RAY_SLAVE_MODE_EXTENSION 12145 units/second
          Rank 43: assembler memory usage: 24483328 KiB
          Job /lsf/7.0/linux2.6-glibc2.3-x86_64/bin/openmpi_wrapper /home/bstamps/Ray/Ray -k 31 -p /scratch/bwawrik/Colin/output_forward_paired2.fastq /scratch/bwawrik/Colin/output_reverse_paired2.fastq -o /scratch/bwawrik/Colin/ray_adapt_rem -minimum-contig-length 1000

          Comment


          • Originally posted by yifangt View Post
            More questions about the insert size:
            1) I checked the LibraryStatistics.txt, I found the number is quite different (303bp) from what my Lab tech provided (~1kb);
            2) Does this mean I have to run Ray first to get the insert size first then provide Ray with these parameters and run it again?
            I want to make sure each point, and Ray is really fast and it helps very much. Thanks a lot!
            YT
            Hi !

            You can use the data in the LibraryData.xml to check the actual distribution of your libraries and then maybe show this information to your laboratory technician. The 303 bp reported by Ray is an average for the detected peak in the data.

            For mates, sometimes you will have a low-frequency peak on the right (in your case at 1 kb).

            Thanks for the good words about Ray. It is appreciated !

            Comment


            • Originally posted by ercfrtz View Post
              I am having issues installing. When I run the make prefix=ray-build like the installation file says, I get the following error:

              Code:
              make prefix=ray-build
              make[1]: Entering directory `/home/eric.fritz/Ray-v2.2.0/RayPlatform'
                CXX RayPlatform/memory/ReusableMemoryStore.o
              make[1]: execvp: mpicxx: Not a directory
              make[1]: *** [memory/ReusableMemoryStore.o] Error 127
              make[1]: Leaving directory `/home/eric.fritz/Ray-v2.2.0/RayPlatform'
              make: *** [RayPlatform/libRayPlatform.a] Error 2
              I do have all the requirements on the system. Thanks.
              Can you provide the output of this command:

              type mpicxx

              Comment


              • [QUOTE=akshaya.ramesh;105505]
                Originally posted by seb567 View Post
                I fixed this build script.



                Thank you for fixing the buildscript. I have been able to make modifications to the makefile by altering the MAXKMERLENGTH and it is working alright. For some reason, every time I run Rayv2.2.0, the following error comes up (for any K-mer specification; I have tried values from 21-91; my reads are 101 bp in length):

                Rank 0: Assembler panic: no k-mers found in reads.
                Rank 0: Perhaps reads are shorter than the k-mer length (change -k).

                I am sure I am missing something very basic, but I am a newbie any comments would be greatly appreciated.

                Thanks,
                Akshaya
                How many reads do you have ? This information is available in the file

                RayOutput/NumberOfSequences.txt


                This is usually due to using k-mers that are longer than reads or to assembling 0 reads.

                Comment


                • Originally posted by bwawrik View Post
                  Hi,
                  I've been using Ray very successfully on our cluster, but ran into a problem with my last data set. It's a relatively modest MySeq partial run of about 750k paired reads that originate from a pure bacterial strain. Originally, I ran the data and I got a decent assembly, but I discovered that there was some degree of read-through and that the adapters were not trimmed on the 3' end for all reads (not sure why illumina basespace does not check for that by default). I used Trimmomactic 0.3 to remove the adapters and tried re-assembling with Ray, but every time I do, it produces a crash. Basically, it goes into some sort of endless loop that ends up using 80 gig of swap at which point the cluster bounces my job. I sliced my data into three parts and assembled them separately or in combinations and the data assembles fine that way (so it's not corrupted data files). Only when I combine all three parts, do I get the crash. I added the stderr below. The stdout is >84gigs and I also added the end of the file.

                  Any thoughts what the problem might be ?

                  Thanks in advance !

                  stderr:

                  Ray:18680 terminated with signal 11 at PC=2aebbf8198d7 SP=7fff758b6340. Backtrace:
                  /usr/mpi/intel/openmpi-1.4.3-qlc/lib64/libopen-pal.so.0(opal_memory_ptmalloc2_int_malloc+0xfd7)[0x2aebbf8198d7]
                  /usr/mpi/intel/openmpi-1.4.3-qlc/lib64/libopen-pal.so.0(+0x49a05)[0x2aebbf817a05]
                  /usr/lib64/libstdc++.so.6(_Znwm+0x1d)[0x2aebc014809d]
                  /home/bstamps/Ray/Ray(_ZNSt6vectorI4KmerSaIS0_EE13_M_insert_auxEN9__gnu_cxx17__normal_iteratorIPS0_S2_EERKS0_+0x130)[0x473bc0]
                  /home/bstamps/Ray/Ray(_ZN12SeedExtender28markCurrentVertexAsAssembledEP4KmerP13RingAllocatorPiP12StaticVectoriiP13ExtensionDataPbS9_S4_S9_PSt6vectorIS0_SaIS0_EEP7ChooserP10BubbleDataiP20OpenAssemblerChooseriPSA_I12AssemblySeedSaISK_EE+0x1371)[0x4e96e1]
                  /home/bstamps/Ray/Ray(_ZN12SeedExtender29call_RAY_SLAVE_MODE_EXTENSIONEv+0x5f7)[0x4f16f7]
                  /home/bstamps/Ray/Ray(_ZN11ComputeCore10runVanillaEv+0x9b)[0x534f7b]
                  /home/bstamps/Ray/Ray(_ZN11ComputeCore3runEv+0x6e)[0x53638e]
                  /home/bstamps/Ray/Ray(_ZN7Machine5startEv+0x1697)[0x4487a7]
                  /home/bstamps/Ray/Ray(main+0x3a)[0x443bba]
                  /lib64/libc.so.6(__libc_start_main+0xfd)[0x2aebc0a67cdd]
                  /home/bstamps/Ray/Ray[0x443a89]


                  end of stdout:

                  Rank 43: assembler memory usage: 24483328 KiB
                  Rank 43 reached 536865000 vertices from seed 0, flow 2
                  Speed RAY_SLAVE_MODE_EXTENSION 9921 units/second
                  Rank 43: assembler memory usage: 24483328 KiB
                  Rank 43 reached 536866000 vertices from seed 0, flow 2
                  Speed RAY_SLAVE_MODE_EXTENSION 12596 units/second
                  Rank 43: assembler memory usage: 24483328 KiB
                  Rank 43 reached 536867000 vertices from seed 0, flow 2
                  Speed RAY_SLAVE_MODE_EXTENSION 12235 units/second
                  Rank 43: assembler memory usage: 24483328 KiB
                  Rank 43 reached 536868000 vertices from seed 0, flow 2
                  Speed RAY_SLAVE_MODE_EXTENSION 13596 units/second
                  Rank 43: assembler memory usage: 24483328 KiB
                  Rank 43 reached 536869000 vertices from seed 0, flow 2
                  Speed RAY_SLAVE_MODE_EXTENSION 10610 units/second
                  Rank 43: assembler memory usage: 24483328 KiB
                  Rank 43 reached 536870000 vertices from seed 0, flow 2
                  Speed RAY_SLAVE_MODE_EXTENSION 12145 units/second
                  Rank 43: assembler memory usage: 24483328 KiB
                  Job /lsf/7.0/linux2.6-glibc2.3-x86_64/bin/openmpi_wrapper /home/bstamps/Ray/Ray -k 31 -p /scratch/bwawrik/Colin/output_forward_paired2.fastq /scratch/bwawrik/Colin/output_reverse_paired2.fastq -o /scratch/bwawrik/Colin/ray_adapt_rem -minimum-contig-length 1000
                  It says "Rank 43 reached 536870000 vertices from seed 0, flow 2"

                  That is a lot of vertices !

                  Which version of Ray are you using ?

                  I believe that this issue was fixed in Ray 2.2.0. The ticket was https://github.com/sebhtml/ray/issues/161


                  You can obtain the version of Ray with this command:


                  mpiexec -n 1 Ray -version

                  Comment


                  • Originally posted by seb567 View Post
                    It says "Rank 43 reached 536870000 vertices from seed 0, flow 2"

                    That is a lot of vertices !

                    Which version of Ray are you using ?

                    I believe that this issue was fixed in Ray 2.2.0. The ticket was https://github.com/sebhtml/ray/issues/161
                    You can obtain the version of Ray with this command:
                    mpiexec -n 1 Ray -version
                    We were running v2.1.0. After installing 2.3.0, the data ran great, thank you. I also think you link was right on. Somehow it created an endless loop and we think that it ended up reaching the swap limit on one of our nodes, bouncing the job.

                    Regardless, it works great now ! Thanks for the help !

                    B

                    Comment


                    • 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.

                      Comment


                      • 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 ?

                        Comment


                        • 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

                          Comment


                          • 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.

                            Comment


                            • 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

                              Comment


                              • 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.

                                Comment

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