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  • #16
    I realise that, currently running some single end alignments, which take longer...

    But anyway, the software does not produce weird faults as above, all my reads get processed and by "fast"; I still mean several hours.

    Comment


    • #17
      It seems to me building the bwa indexes is error prone.
      I am just trying it again today and despite running what is supposed to be an
      identical script, I get different output (eg the first value in h_sapiens_37.5.amb is half
      the size of the value in the version bwt produced two weeks ago).

      Is anyone prepared to host a working version of the BWA index for the human genome?
      It would be about 4.5GB. I think it would take less than 2weeks to down load and I might
      have more confidence in it than either of the two version I have created using
      bwa index /tmp/INPUTS.fa -p h_sapiens_37.5 -a bwtsw

      Many thanks
      Bill

      Comment


      • #18
        Originally posted by wlangdon View Post
        Is anyone prepared to host a working version of the BWA index for the human genome?
        It would be about 4.5GB. I think it would take less than 2weeks to down load and I might
        have more confidence in it than either of the two version I have created using
        bwa index /tmp/INPUTS.fa -p h_sapiens_37.5 -a bwtsw

        Many thanks
        Bill
        Bill,

        Illumina built indexes are available at the iGenomes site.

        Last edited by GenoMax; 11-14-2012, 08:41 AM.

        Comment


        • #19
          I have only recently discovered this problem.
          Compiling using make runs ok, no errors.
          Indexing (human_g1k_v37 from the GATK website) on mac takes around an hour, as standard (I think).
          bwa aln runs with no errors, but as the OP mentions each step takes almost no time.
          bwa sampe also runs with no errors but fails to infer insert size at every step. The resulting sam file has no alignment coordinates in it, and flagstat shows 0% mapped reads.
          After transferring data to linux cluster, and rebuilding the index, everything seems ok and flagstat shows 89% of the reads have been mapped.

          I wonder is there some kind of library that a Standard Mac OSX lion is missing. Although is that was the case surely bwa would throw an error when it fails to import that library or package. I'm totally ignorant of C though so I'm guessing here.

          Comment


          • #20
            I realise I never got back on this thread: I have also not had any decent alignments using BWA 0.6.x. I since downgraded to 0.5.x and everything is running well.

            Comment


            • #21
              Originally posted by TabeaK View Post
              I realise I never got back on this thread: I have also not had any decent alignments using BWA 0.6.x. I since downgraded to 0.5.x and everything is running well.
              Yeah I might try using a 0.5.x version and compare the alignments to see if the upgrade is worth it.

              Comment


              • #22
                I do not know the command to run fasta file in bwa
                Anyone can help me?
                Thanks very much

                Comment


                • #23
                  Originally posted by maivantan View Post
                  I do not know the command to run fasta file in bwa
                  Anyone can help me?
                  Thanks very much
                  Maivantan: You have probably looked at the bwa manual already. http://bio-bwa.sourceforge.net/bwa.shtml Main commands are in the synopsis.

                  bwa will accept fasta files in place of fastq (*.fq) files on those commands.

                  Comment


                  • #24
                    Thank you GenoMax,
                    but when i type bra index ref.fa
                    error is command not found.
                    Do you have any suggestion?

                    Comment


                    • #25
                      How familiar are you with unix? Did you download/compile bwa from sourceforge?

                      Comment


                      • #26
                        Dear GenoMax,
                        I am using matchbook pro v10.7.5, ram 4gb, core i7.
                        i did down load from the web site and make it in terminal.
                        Do you have any suggestion?

                        Comment


                        • #27
                          Are you able to see the executable file (should be called bwa)? You can verify that it is executable by trying to run it like this (assuming that you are in the bwa directory):

                          Code:
                          $ ./bwa
                          If that does not work then you may need to make the file executable

                          Code:
                          $ chmod u+x bwa
                          $ ./bwa
                          The second command should produce bwa "help" output. Then you should be ready to run.

                          Comment


                          • #28
                            Dear GenoMax,
                            I am sorry to disturb you, but I got the problem here:
                            when try to index the reference as the following, its fail. Would you please help me
                            Thank you very much

                            USER-no-MacBook-Pro-4:bwa-0.7-1.5a user$ ./bwa index ref.fa
                            [bwa_index] fail to open file 'ref.fa' : No such file or directory
                            USER-no-MacBook-Pro-4:bwa-0.7-1.5a user$ ./bwa mem ref.fa reads.fq > aln-se.sam
                            [E::bwa_idx_load] fail to locate the index files
                            USER-no-MacBook-Pro-4:bwa-0.7-1.5a user$

                            Comment


                            • #29
                              Originally posted by maivantan View Post
                              USER-no-MacBook-Pro-4:bwa-0.7-1.5a user$ ./bwa index ref.fa
                              [bwa_index] fail to open file 'ref.fa' : No such file or directory
                              It would be useful to invest a day in learning UNIX essentials. A very useful resource for biologists to learn UNIX (I assume you are one) can be found at this link: http://korflab.ucdavis.edu/Unix_and_...1.1.html#part1

                              As for your specific problem. Your ref.fa (fasta reference file) does not appear to be in the same directory as the bwa program. I have highlighted the error in red above.

                              Best option is to change to the directory where the ref.fa file is present. Then run the bwa command providing full path to the bwa executable.
                              Code:
                              $ cd to_directory_with_ref.fa
                              $ /provide_full_path_to_directory/bwa index ref.fa

                              Comment


                              • #30
                                Thank yu GenoMax very much.
                                I am going to learn it

                                Comment

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