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  • Bowtie2

    Hello,

    I'm also having trouble installing bowtie2 and its undoubtedly due to my own incompetence!

    I'm using a mac and have downloaded the bowtie2 source file and used the make command to unpack it.

    now here's where my issue is, i have tried to set the PATH as described in this thread but i still get 'command not found' when i try to run bowtie. I am new to command line and reading around there seems to be suggestions of changing either bash_profile or bashrc, but neither seem to make a difference.

    If i navigate to the bowtie2 folder that was populated following the make command, and list the contents, i can see the full list of files and executables including bowtie2. if i type bowtie2 (or .bowtie2) from this folder, i still get the same error 'command not found'.

    I presume its something trivial that ive done wrong. Does anyone have any ideas?

    My mac is not a vanilla setup and was previously used by someone who's then removed all of their programs and files, is it possible something was removed that i need to reinstall?

    Comment


    • Originally posted by lonesome_forager View Post
      Hello,

      I'm also having trouble installing bowtie2 and its undoubtedly due to my own incompetence!

      I'm using a mac and have downloaded the bowtie2 source file and used the make command to unpack it.

      now here's where my issue is, i have tried to set the PATH as described in this thread but i still get 'command not found' when i try to run bowtie. I am new to command line and reading around there seems to be suggestions of changing either bash_profile or bashrc, but neither seem to make a difference.

      If i navigate to the bowtie2 folder that was populated following the make command, and list the contents, i can see the full list of files and executables including bowtie2. if i type bowtie2 (or .bowtie2) from this folder, i still get the same error 'command not found'.

      I presume its something trivial that ive done wrong. Does anyone have any ideas?

      My mac is not a vanilla setup and was previously used by someone who's then removed all of their programs and files, is it possible something was removed that i need to reinstall?
      Make is a utility that compiles/links/makes executables from source code. Assuming that you did not encounter any errors during "make" you should have the binaries available. You may need to add execute permissions to the files before you can use them.

      Code:
      $ chmod u+x bowtie2*
      then try

      Code:
      $ ./bowtie2

      Comment


      • Originally posted by GenoMax View Post
        Make is a utility that compiles/links/makes executables from source code. Assuming that you did not encounter any errors during "make" you should have the binaries available. You may need to add execute permissions to the files before you can use them.

        Code:
        $ chmod u+x bowtie2*
        then try

        Code:
        $ ./bowtie2
        Yes! that worked, thankyou so much! Do you know why that had to be done? will i have to do that whenever i install other softwares too?

        Comment


        • Originally posted by lonesome_forager View Post
          Yes! that worked, thankyou so much! Do you know why that had to be done? will i have to do that whenever i install other softwares too?
          In case the execute permissions are not set on a binary you would need to do that in future for other software.

          Comment


          • Hi,
            Thank you very much. I am facing now an old problem. Again my bowtie, samtools, bcftools commands are not working even after "source" command. What should I do now?

            Best Regards
            Zillur

            Zillur-Rahman:~ ZILLURRAHMAN$ source desktop/1st_semester/bioinformatics/pathcommand_mod.txt
            Zillur-Rahman:~ ZILLURRAHMAN$ type bowtie2
            -bash: type: bowtie2: not found
            Zillur-Rahman:~ ZILLURRAHMAN$ cd desktop/1st_semester/bioinformatics/
            Zillur-Rahman:bioinformatics ZILLURRAHMAN$ ls
            2nd_exam
            An A-Z Index of the Bash command line for Linux | Bash | SS64.com.webarchive
            AtoZCommands.pdf
            Bioinfo
            Books
            Bow-tie
            Canadian_bioinformatics
            Lectures
            NCBI_BLASTexercises.pdf
            Papers
            Project
            SamTools
            Workshop (11-13 Nov, 14)
            bcftools-1.1
            bioinformaticprojectbabesiamicrotipapers
            e_coli
            nohup.out
            path_set
            pathcommand.txt
            pathcommand_mod.txt
            perldoc
            s_cerevisiae_c-2
            Zillur-Rahman:bioinformatics ZILLURRAHMAN$ head pathcommand_mod.txt
            export PATH="/Users/ZILLURRAHMAN/Desktop/Bioinformatics/bow-tie/bowtie2-2.2.3:/Users/ZILLURRAHMAN/Desktop/Bioinformatics/samtools/samtools-1.1:/Users/ZILLURRAHMAN/Desktop/Bioinformatics/bcftools-1.1:$PATH"
            Zillur-Rahman:bioinformatics ZILLURRAHMAN$ source pathcommand_mod.txt
            Zillur-Rahman:bioinformatics ZILLURRAHMAN$ type bowtie2
            -bash: type: bowtie2: not found
            Zillur-Rahman:bioinformatics ZILLURRAHMAN$

            Comment


            • Hi,
              Sorry for the inconvenience. I have found the solution. I just had to add a folder in my path. Now everything is working.

              But can you help me about this matter?
              I have to map yeast genome and then find SNP. For this from where I can download genome.


              The Saccharomyces Genome Database (SGD) provides comprehensive integrated biological information for the budding yeast Saccharomyces cerevisiae.

              The Saccharomyces Genome Database (SGD) provides comprehensive integrated biological information for the budding yeast Saccharomyces cerevisiae.


              Where I can find reference genome?

              Best Regards
              Zillur

              Comment


              • Zillur: Save yourself trouble and download one of the genome bundles (NCBI, Ensembl take your pick) from Illumina's iGenomes page. This bundle includes all kinds of indexes (bowtie is one of them) and annotations etc.

                Comment


                • Hi,
                  Thank you very much for your kind reply. I am trying this following ways. but.... May be I am missing something..........

                  Zillur-Rahman:wholegenomefasta ZILLURRAHMAN$ ls
                  GenomeSize.xml genome.dict genome.fa genome.fa.fai
                  Zillur-Rahman:wholegenomefasta ZILLURRAHMAN$ bowtie2 -x saccharomyces -1 genome.fa -2 genome.fa.fai -S eg2.sam
                  Could not locate a Bowtie index corresponding to basename "saccharomyces"
                  Error: Encountered internal Bowtie 2 exception (#1)
                  Command: /Users/ZILLURRAHMAN/Desktop/1st_semester/Bioinformatics/bow-tie/bowtie2-2.2.3/bowtie2-align-s --wrapper basic-0 -x saccharomyces -S eg2.sam -1 genome.fa -2 genome.fa.fai
                  (ERR): bowtie2-align exited with value 1
                  Zillur-Rahman:wholegenomefasta ZILLURRAHMAN$ cd ..
                  Zillur-Rahman:sequence ZILLURRAHMAN$ ls
                  AbundantSequences Bowtie2Index Chromosomes
                  BWAIndex BowtieIndex WholeGenomeFasta
                  Zillur-Rahman:sequence ZILLURRAHMAN$ cd chromosomes
                  Zillur-Rahman:chromosomes ZILLURRAHMAN$ ls
                  I.fa III.fa IX.fa V.fa VII.fa X.fa XII.fa XIV.fa XVI.fa
                  II.fa IV.fa MT.fa VI.fa VIII.fa XI.fa XIII.fa XV.fa
                  Zillur-Rahman:chromosomes ZILLURRAHMAN$ ls
                  IV.fa MT.fa VI.fa VIII.fa XI.fa XIII.fa XV.fa ch_1.fa ch_3.fa
                  IX.fa V.fa VII.fa X.fa XII.fa XIV.fa XVI.fa ch_2.fa
                  Zillur-Rahman:chromosomes ZILLURRAHMAN$ bowtie2 -x saccharomyces ch_1.fa -2 ch_2.fa -3 ch_3.fa -S eg2.sam
                  Error: 1 mate files/sequences were specified with -1, but 0
                  mate files/sequences were specified with -2. The same number of mate files/
                  sequences must be specified with -1 and -2.
                  Error: Encountered internal Bowtie 2 exception (#1)
                  Command: /Users/ZILLURRAHMAN/Desktop/1st_semester/Bioinformatics/bow-tie/bowtie2-2.2.3/bowtie2-align-s --wrapper basic-0 -x saccharomyces -3 ch_3.fa -S eg2.sam -1 -2 ch_1.fa ch_2.fa
                  (ERR): bowtie2-align exited with value 1
                  Zillur-Rahman:chromosomes ZILLURRAHMAN$ bowtie2 -x saccharomyces ch_1.fa -2 ch_2.fa -S eg2.sam
                  Error: 1 mate files/sequences were specified with -1, but 0
                  mate files/sequences were specified with -2. The same number of mate files/
                  sequences must be specified with -1 and -2.
                  Error: Encountered internal Bowtie 2 exception (#1)
                  Command: /Users/ZILLURRAHMAN/Desktop/1st_semester/Bioinformatics/bow-tie/bowtie2-2.2.3/bowtie2-align-s --wrapper basic-0 -x saccharomyces -S eg2.sam -1 -2 ch_1.fa ch_2.fa
                  (ERR): bowtie2-align exited with value 1
                  Zillur-Rahman:chromosomes ZILLURRAHMAN$ bowtie2 -x saccharomyces -1 ch_1.fa -2 ch_2.fa -S eg2.sam
                  Could not locate a Bowtie index corresponding to basename "saccharomyces"
                  Error: Encountered internal Bowtie 2 exception (#1)
                  Command: /Users/ZILLURRAHMAN/Desktop/1st_semester/Bioinformatics/bow-tie/bowtie2-2.2.3/bowtie2-align-s --wrapper basic-0 -x saccharomyces -S eg2.sam -1 ch_1.fa -2 ch_2.fa
                  (ERR): bowtie2-align exited with value 1
                  Zillur-Rahman:chromosomes ZILLURRAHMAN$ bowtie2 -x chromosomes -1 ch_1.fa -2 ch_2.fa -S eg2.sam
                  Could not locate a Bowtie index corresponding to basename "chromosomes"
                  Error: Encountered internal Bowtie 2 exception (#1)
                  Command: /Users/ZILLURRAHMAN/Desktop/1st_semester/Bioinformatics/bow-tie/bowtie2-2.2.3/bowtie2-align-s --wrapper basic-0 -x chromosomes -S eg2.sam -1 ch_1.fa -2 ch_2.fa
                  (ERR): bowtie2-align exited with value 1
                  Zillur-Rahman:chromosomes ZILLURRAHMAN$ bowtie2 -x genome -1 ch_1.fa -2 ch_2.fa -S eg2.sam
                  Could not locate a Bowtie index corresponding to basename "genome"
                  Error: Encountered internal Bowtie 2 exception (#1)
                  Command: /Users/ZILLURRAHMAN/Desktop/1st_semester/Bioinformatics/bow-tie/bowtie2-2.2.3/bowtie2-align-s --wrapper basic-0 -x genome -S eg2.sam -1 ch_1.fa -2 ch_2.fa
                  (ERR): bowtie2-align exited with value 1
                  Zillur-Rahman:chromosomes ZILLURRAHMAN$ bowtie2 -x ..genome -1 ch_1.fa -2 ch_2.fa -S eg2.sam
                  Could not locate a Bowtie index corresponding to basename "..genome"
                  Error: Encountered internal Bowtie 2 exception (#1)
                  Command: /Users/ZILLURRAHMAN/Desktop/1st_semester/Bioinformatics/bow-tie/bowtie2-2.2.3/bowtie2-align-s --wrapper basic-0 -x ..genome -S eg2.sam -1 ch_1.fa -2 ch_2.fa
                  (ERR): bowtie2-align exited with value 1
                  Zillur-Rahman:chromosomes ZILLURRAHMAN$ pwd
                  /Users/ZILLURRAHMAN/desktop/phd/saccharomyces/saccharomyces_cerevisiae_ensembl_r64-1-1/saccharomyces_cerevisiae/ensembl/r64-1-1/sequence/chromosomes
                  Zillur-Rahman:chromosomes ZILLURRAHMAN$

                  Comment


                  • You are in (using) the wrong folder (you are is plain sequence folder = WholeGenomeFasta). You want to use the index files in the Bowtie2Index folder.

                    Comment


                    • Thank you very much for your kind reply. May be I am annoying. But what is the base name means?

                      Best Regards
                      Zillur

                      Zillur-Rahman:bowtie2index ZILLURRAHMAN$ bowtie2 -x saccharomyces -1 ../chromosomes/ch_1.fa -2 ../chromosomes/ch_2.fa -S eg2.sam
                      Could not locate a Bowtie index corresponding to basename "saccharomyces"
                      Error: Encountered internal Bowtie 2 exception (#1)
                      Command: /Users/ZILLURRAHMAN/Desktop/1st_semester/Bioinformatics/bow-tie/bowtie2-2.2.3/bowtie2-align-s --wrapper basic-0 -x saccharomyces -S eg2.sam -1 ../chromosomes/ch_1.fa -2 ../chromosomes/ch_2.fa
                      (ERR): bowtie2-align exited with value 1
                      Zillur-Rahman:bowtie2index ZILLURRAHMAN$ pwd
                      /Users/ZILLURRAHMAN/desktop/phd/saccharomyces/saccharomyces_cerevisiae_ensembl_r64-1-1/saccharomyces_cerevisiae/ensembl/r64-1-1/sequence/bowtie2index
                      Zillur-Rahman:bowtie2index ZILLURRAHMAN$

                      Comment


                      • If you downloaded the iGenomes files the Bowtie2index will have a generic "base" name. It is going to be "genome". This is the prefix (part before the first period in file name) from the index files.

                        Comment


                        • Your command can be as follows:
                          Code:
                          $ bowtie2 -x /path_to_bowtie2index_dir/genome -1 Sample_R1.fastq -2 Sample_R2.fastq -S eg2.sam
                          Last edited by GenoMax; 12-10-2014, 02:06 PM. Reason: Corrected command line example

                          Comment


                          • Thank you very much for your kind reply. I have tried this...

                            Zillur-Rahman:sequence ZILLURRAHMAN$ ls
                            AbundantSequences Bowtie2Index Chromosomes
                            BWAIndex BowtieIndex WholeGenomeFasta
                            Zillur-Rahman:sequence ZILLURRAHMAN$ cd bowtie2index
                            Zillur-Rahman:bowtie2index ZILLURRAHMAN$ ls
                            eg2.sam genome.3.bt2 genome.fa.fai
                            genome.1.bt2 genome.4.bt2 genome.rev.1.bt2
                            genome.2.bt2 genome.fa genome.rev.2.bt2
                            Zillur-Rahman:bowtie2index ZILLURRAHMAN$ bowtie2 -x genome -1 ../chromosomes/ch_1.fa -2 ../chromosomes/ch_2.fa -S eg2.sam
                            Error: reads file does not look like a FASTQ file
                            libc++abi.dylib: terminating with uncaught exception of type int
                            (ERR): bowtie2-align died with signal 6 (ABRT)
                            Zillur-Rahman:bowtie2index ZILLURRAHMAN$


                            What should I do if I want to map all chromosomes together? There are 16 chromosomes

                            Best Regards
                            Zillur

                            Comment


                            • You need to use fastq format files (which would be your sample) against the yeast genome to do the mapping. In the command line you had posted above you are using yeast chromosome files (which does not make any sense). Replace them with your sample fastq files.

                              "genome" ==> Entire yeast genome/all chromosomes together.

                              If you have paired end data:

                              Code:
                              $ bowtie2 -x /path_to_bowtie2index_dir/genome -1 Sample_R1.fastq -2 Sample_R2.fastq -S eg2.sam

                              Comment


                              • Thank you very much for your kind reply. But where I get the sample fast files?

                                Best Regards
                                Zillur

                                Zillur-Rahman:bowtie2index ZILLURRAHMAN$ ls
                                eg2.sam genome.3.bt2 genome.fa.fai
                                genome.1.bt2 genome.4.bt2 genome.rev.1.bt2
                                genome.2.bt2 genome.fa genome.rev.2.bt2
                                Zillur-Rahman:bowtie2index ZILLURRAHMAN$ $ bowtie2 -x genome -1 Sample_R1.fastq -2 Sample_R2.fastq -S eg2.sam
                                -bash: $: command not found
                                Zillur-Rahman:bowtie2index ZILLURRAHMAN$ bowtie2 -x genome -1 Sample_R1.fastq -2 Sample_R2.fastq -S eg2.sam
                                Warning: Could not open read file "Sample_R1.fastq" for reading; skipping...
                                Error: No input read files were valid
                                (ERR): bowtie2-align exited with value 1
                                Zillur-Rahman:bowtie2index ZILLURRAHMAN$ bowtie2 -x genome -1 ../Sample_R1.fastq -2 ../Sample_R2.fastq -S eg2.sam
                                Warning: Could not open read file "../Sample_R1.fastq" for reading; skipping...
                                Error: No input read files were valid
                                (ERR): bowtie2-align exited with value 1
                                Zillur-Rahman:bowtie2index ZILLURRAHMAN$ pwd
                                /Users/ZILLURRAHMAN/desktop/phd/saccharomyces/saccharomyces_cerevisiae_ensembl_r64-1-1/saccharomyces_cerevisiae/ensembl/r64-1-1/sequence/bowtie2index
                                Zillur-Rahman:bowtie2index ZILLURRAHMAN$

                                Comment

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