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  • Warning: Exhausted best-first chunk memory for read

    when I get this message I have found that the following option makes it go away (doubling the default value)

    --chunkmbs 128

    Comment


    • Out of memory with me as well

      Hi,
      I am also getting:
      C:\bowtie-0.12.5>bowtie -c hg18 ATTCAGTAGGTACTATAAATGGCCGAT --chunkmbs 512
      Out of memory allocating the ebwt[] array for the Bowtie index. Please try
      again on a computer with more memory.
      Command: bowtie -c --chunkmbs 512 hg18 ATTCAGTAGGTACTATAAATGGCCGAT

      I tried the chunkmbs with 32, 128, 256 and 512 on a winXP32bit with 4GB of RAM, the maximum allocated memory is around 1.2 GB. Any other ideas I could try?
      Thanks a lot,

      David

      --edit--:
      I rebooted the system, the task manager shows at least 3.6G of total phys. memory, 2.7GB available and 1.6G cache, I am still getting the request to use a 'computer with more memory'. I thought Bowtie was supposed to run on the human genome with ~ 2GB of RAM?
      --edit2--:
      I got it to work under a VMWare virtual machine running Ubuntu on the above XP system, without any chunkmbs setting, there is definitely something fishy when running under XP
      Last edited by david2; 08-26-2010, 12:06 PM. Reason: Added more info about the system... works under VMWare/Ubuntu

      Comment


      • Hi,
        I am just starting to use Linux and Bowtie so this might be something simple.
        I downloaded Bowtie and just wanted to run the example suggested in the tutorial.
        I am giving the command
        chmod ugo+rwx bowtie e_coli reads/e_coli_1000.fq
        I get an error that says chmod cannot access e_coli No such file or directory.
        Can't figure out what is wrong.
        Help appreciated!
        Thanks.

        Comment


        • The command

          chmod ugo+rwx bowtie e_coli reads/e_coli_1000.fq

          will change permissions (chmod)
          for the user, group and others (ugo)
          to include reading, writing and executing permissions (+rwx)
          for the files bowtie, e_coli and reads/e_coli_1000.fq

          The error is that it can't find a file or directory named e_coli. That will be relative to the directory you are running the command from, so you should try
          ls
          and see if there are any files named e_coli.

          If your filename has a space in it (not recommended) you should be able to put a \ before the space, which should keep the command from thinking you're listing a new file. You could also put the filename with a space in single or double quotes, which may help that same problem.

          Hope that helps.

          Comment


          • Thank you mrawlins.
            That was very helpful. I finally got bowtie up and running.

            Comment


            • Hi All,
              Still trying to figure out Bowtie options.
              How do I get it to align reads allowing more than 3 mismatches?
              Thanks.

              Comment


              • seqniru,

                You might try -v <int>. This ignores quality values and allows up to <int> mismatches. I don't think there's a limit on it, like with -n only going up to 3 mismatches

                I also have a question of my own. I am trying to align some data using Bowtie and keep getting an error:

                Reads file contained a pattern with more than 1024 quality values.
                Please truncate reads and quality values and and re-run Bowtie
                terminate called after throwing an instance of 'int'
                Aborted

                I have looked for solutions to this and tried some but nothing seems to work. My reads and quality strings are the same length, -v does not work.

                Here is a file head:

                @IL2_1423:1:49:708:540
                GTCTCTTTCTTTTAGATGAA
                +
                >>>>>>>>>>>>>>>>>>>>

                I am not sure if this has something to do with the quality string being all >? Any help is appreciated! Thanks.

                Comment


                • Thank you gzentner.
                  I tried -v but it does not work with number greater than 3 either.

                  Comment


                  • Still looking for answer to this question.
                    How do I get it to align reads allowing more than 3 mismatches?
                    Both -n and -v can only be set to a maximum of 3 mismatches.
                    Thanks.

                    Comment


                    • -n 3 allows more mismatches if seed length is less than read length. For more mismatches in the seed you need another aligner like Bfast.

                      Comment


                      • Reverse complement matches

                        I have some questions about mapping Illumina reads to a genome with bowtie and I really appreciate if you could help me.
                        My reads are single read and strand-specific, so I did the alignment with bowtie and I realised that there were a lot of reads that aligned to the genome but they were transformed into the reverse complement.
                        eg:
                        B1:000000010#0x37397/1 16 chr3 281135 255 22M * 0 0 TGCCGACTTCCCTGAGTGTACC
                        B1:000000010#0x37397/1 0 chr4 375688 255 22M * 0 0 GGTACACTCAGGGAAGTCGGCA

                        I would like to align the reads to the forward and the reverse complement of the reference genome but I don't want to align the reverse complement of the reads.
                        I don't know if there is an option for this.
                        I'm running bowtie with these parameters:
                        bowtie -v3 -a -m3 --best --strata -p4 -t -S

                        Thanks in advance
                        Best regards


                        alv

                        Comment


                        • Hi alv,

                          "To align the reverse complement of the reads" is equivalent "to align the reads to the reverse complement of the reference genome", and the alignment results are the same. You can BLAST or BLAT the read to check the given results.


                          Originally posted by alvin View Post
                          I have some questions about mapping Illumina reads to a genome with bowtie and I really appreciate if you could help me.
                          My reads are single read and strand-specific, so I did the alignment with bowtie and I realised that there were a lot of reads that aligned to the genome but they were transformed into the reverse complement.
                          eg:
                          B1:000000010#0x37397/1 16 chr3 281135 255 22M * 0 0 TGCCGACTTCCCTGAGTGTACC
                          B1:000000010#0x37397/1 0 chr4 375688 255 22M * 0 0 GGTACACTCAGGGAAGTCGGCA

                          I would like to align the reads to the forward and the reverse complement of the reference genome but I don't want to align the reverse complement of the reads.
                          I don't know if there is an option for this.
                          I'm running bowtie with these parameters:
                          bowtie -v3 -a -m3 --best --strata -p4 -t -S

                          Thanks in advance
                          Best regards


                          alv
                          Xi Wang

                          Comment


                          • Hi, all
                            I am newer for using the bowtie program to map the short reads.
                            could someone give me what the parameters (--best --strata -m) stand?

                            Because when map the short reads to reference genome with the default parameter, in my surprise, there is low ratio.

                            thanks.

                            Comment


                            • @Xi Wang

                              Thank you for your response. You are absolutely right!
                              Best Regards

                              Originally posted by masylichu View Post
                              Hi, all
                              I am newer for using the bowtie program to map the short reads.
                              could someone give me what the parameters (--best --strata -m) stand?
                              Have you taken a look at the bowtie's Manual?



                              Originally posted by masylichu View Post
                              Hi, all
                              Because when map the short reads to reference genome with the default parameter, in my surprise, there is low ratio.
                              What are the optimal parameters?

                              Depends on the objective of your sequencing and technology that you are using, each one has different cons. E.g. Illumina tend to introduce mismatches in general terms. Roche 454 tend to introduce indels, etc.
                              Try with -y and -a.
                              Hope this help

                              Comment


                              • M1

                                I realized that the -m and -M options are not compatible.
                                I think it would be useful if we could use both parameters at the same time.
                                E.g.
                                If we run the program with this parameters
                                $ ./bowtie -a -m3 --best --strata

                                Specifying -m 3 instructs bowtie to refrain from reporting any alignments for reads having more than 3 reportable alignments, --best , best-to-worst order and
                                specifying --strata in addition to -a and --best causes bowtie to report only those alignments having the least number of mismatches...but what if some read maps twice or three times with the same numer of mismatches?
                                Bowtie will report all the alignments for this read because they pass the -a -m3 --best --strata filters, so, I think it would be useful if we could add the -M1 option. Then only one alignment (random) will be informed when this happens, so in this way leading to the "uniqness".

                                Comment

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