Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • #31
    Ok, I've tracked down the problem. I believe this version should fix it for you. The fix will be included in the next release (4.0.4)

    Please let me know if you encounter any other problems.

    Edit: don't download this file - use the two posts below.
    Attached Files
    Last edited by apfejes; 08-06-2009, 10:29 AM. Reason: This file does not run to completion.
    The more you know, the more you know you don't know. —Aristotle

    Comment


    • #32
      Sorry...I'm still having problems, though it runs a bit further this time ...

      Exception in thread "main" java.lang.NoClassDefFoundError: src/lib/Error_handlin
      g/GenericProcessingException
      at src.lib.ioInterfaces.BowtieIterator.next...et cetera

      btw, thanks for being so responsive.

      Comment


      • #33
        Ok, caught that too - it was an inappropriately placed semicolon in the build file. Go figure. I've rebuilt and attached the new file.

        Sorry about all of the hassle - I've only used this function a few times before moving away from bowtie, so I hadn't done anything with the compiled version of the code (which was only recently added to the buildout process). Again, if you see anything fishy with the application, please let me know!

        Anthony
        Attached Files
        The more you know, the more you know you don't know. —Aristotle

        Comment


        • #34
          Thank you! It works well now. By the way, what program are you using now?

          Comment


          • #35
            Hi SeaJane,

            I'm glad it's finally working, and sorry that it was such a hassle to get it to that shape!

            Mostly I'm working with Maq, but I'll be putting BAM/SAM readers into the project shortly. BWA here we come....

            Anthony
            The more you know, the more you know you don't know. —Aristotle

            Comment


            • #36
              Hi apfejes,

              I got a problem with using the ConvertToBed.jar in a redhat system. I tried to convert from Bowtie to Bed (some mysterious reason also happens when I tried to use the sam2bed.py script on the site but it is a different problem...). when i ran ConvertToBed as:

              [root@my lab conversion_util]# java -jar ConvertToBed.jar -aligner bowtie -input /some input dir/input.txt -output ./output -name Name

              It reports:

              Exception in thread "main" java.lang.ClassFormatError: src.fileUtilities.ConvertToBed (unrecognized class file version)
              at java.lang.VMClassLoader.defineClass(libgcj.so.7rh)
              at java.lang.ClassLoader.defineClass(libgcj.so.7rh)
              at java.security.SecureClassLoader.defineClass(libgcj.so.7rh)
              at java.net.URLClassLoader.findClass(libgcj.so.7rh)
              at java.lang.ClassLoader.loadClass(libgcj.so.7rh)
              at java.lang.ClassLoader.loadClass(libgcj.so.7rh)
              at gnu.java.lang.MainThread.run(libgcj.so.7rh)

              Could you help on this? Thanks a lot.

              Comment


              • #37
                Hi heculase,

                The error you're showing is a java error, and not something to do with the jar file itself... The most recent versions were all compiled for Java 1.6 in order to support Picard (for SAM/BAM formats), and this is probably just be an indication that you need to upgrade to the latest java.

                Unfortunately, I'm currently away this week, but I can take a look when I get back if Java 1.6 doesn't solve your problem.

                Anthony
                The more you know, the more you know you don't know. —Aristotle

                Comment


                • #38
                  Thanks a lot Andy. It is indeed a java version problem. I updated to 1.6 and it worked great. Thank you very much!

                  heculase

                  Originally posted by apfejes View Post
                  Hi heculase,

                  The error you're showing is a java error, and not something to do with the jar file itself... The most recent versions were all compiled for Java 1.6 in order to support Picard (for SAM/BAM formats), and this is probably just be an indication that you need to upgrade to the latest java.

                  Unfortunately, I'm currently away this week, but I can take a look when I get back if Java 1.6 doesn't solve your problem.

                  Anthony

                  Comment


                  • #39
                    bowtie to .gff and .wig

                    Originally posted by graveley View Post
                    Dear Yogesh,

                    We do this by writing a perl script that reads in the alignment information and writes a new file in the appropriate format. I would send you what we use, but we do not use export.txt files. We are currently doing alignments with Bowtie and then converting the output to .gff and .wig files.

                    Brent
                    bowtie to .gff and .wig

                    Dear Brent,
                    As the users before me I would also appreciate the pearl script for the bowtie alignment files to .wig and .gff. Thanks a lot. My email is:
                    [email protected]

                    Comment


                    • #40
                      If it helps, there is a generic BAM to BED utility (bamToBed) available in BEDTools (bedtools.googlecode.com).

                      Aaron

                      Comment


                      • #41
                        @Apfejes
                        I attempted to use the ConverttoBed.jar utility on some Solexa data after bowtie alignment but I received this error:
                        "Couldn't write to analog file"

                        Can you please tell me why this occurred?

                        Cheers,

                        Comment


                        • #42
                          I've never seen that problem before. Could you provide the full output of the error for me, otherwise I don't know where to begin looking to solve this problem. Java normally gives more verbose errors than that, when throwing an error.
                          The more you know, the more you know you don't know. —Aristotle

                          Comment


                          • #43
                            @Apfejes,
                            I have the Vancouver Short Read package 4.0.1.2 and ran the ConverttoBed command because I have data from single paired end reads. I aligned them using Bowtie and the file had a .txt format. The ConverttoBed command follows:

                            java -jar conversion_util/ConvertToBed.jar -aligner -bowtie -input bowtie.txt -qualityfilter 10 -output output_dir/my_directory -noprepend

                            Cheers,

                            Comment


                            • #44
                              Hi Genbio,

                              Thanks for the information, however, what I'm actually looking for is the error you're observing. If it's caused by java, it should give information about where in the code the error occurred, or which module caused the error. Since I know nothing about the file you have or the operating system you're using, the best information that would help me solve your problem is the error thrown by java itself, which normally gives a clear indication of what was happening when the fault happened.

                              Cheers!
                              The more you know, the more you know you don't know. —Aristotle

                              Comment


                              • #45
                                It did not give a java specific code, only
                                "Error: coundn't creat log file:"

                                Comment

                                Latest Articles

                                Collapse

                                • seqadmin
                                  Strategies for Sequencing Challenging Samples
                                  by seqadmin


                                  Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
                                  03-22-2024, 06:39 AM
                                • seqadmin
                                  Techniques and Challenges in Conservation Genomics
                                  by seqadmin



                                  The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

                                  Avian Conservation
                                  Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
                                  03-08-2024, 10:41 AM

                                ad_right_rmr

                                Collapse

                                News

                                Collapse

                                Topics Statistics Last Post
                                Started by seqadmin, Yesterday, 06:37 PM
                                0 responses
                                10 views
                                0 likes
                                Last Post seqadmin  
                                Started by seqadmin, Yesterday, 06:07 PM
                                0 responses
                                10 views
                                0 likes
                                Last Post seqadmin  
                                Started by seqadmin, 03-22-2024, 10:03 AM
                                0 responses
                                51 views
                                0 likes
                                Last Post seqadmin  
                                Started by seqadmin, 03-21-2024, 07:32 AM
                                0 responses
                                67 views
                                0 likes
                                Last Post seqadmin  
                                Working...
                                X