Tophat sequence aligner does not work properly












0














I am trying to use tophat to align my fastq reads to the reference genome.



I first used bowtie to create index files. I have trimmed my read1 and read2 fastq files. All output files of bowtie index and reads files are in the same directory. Here you can see the screen shot of my directory.



enter image description here



Then I am running the following command to run tophat.



enter image description here
I do not know what I am doing wrong since my command runs but after almost 45 minutes it stops(at the following step).
enter image description here




The tophat output directory(sample_thout) has been created but it contains only the following files.
enter image description here




Inside the log I can see the following:



enter image description here







Inside tmp I can see these files:
enter image description here



I am pretty new to RNa seq and tophat alignment. Is there any body that can help me with the issue that I have?






alignment rna-seq







share|improve this question



























    0














    I am trying to use tophat to align my fastq reads to the reference genome.



    I first used bowtie to create index files. I have trimmed my read1 and read2 fastq files. All output files of bowtie index and reads files are in the same directory. Here you can see the screen shot of my directory.



    enter image description here



    Then I am running the following command to run tophat.



    enter image description here
    I do not know what I am doing wrong since my command runs but after almost 45 minutes it stops(at the following step).
    enter image description here
    



    The tophat output directory(sample_thout) has been created but it contains only the following files.
    enter image description here



    
    Inside the log I can see the following:



    enter image description here



    



    Inside tmp I can see these files:
    enter image description here



    I am pretty new to RNa seq and tophat alignment. Is there any body that can help me with the issue that I have?






    alignment rna-seq







    share|improve this question

























      0












      0








      0







      I am trying to use tophat to align my fastq reads to the reference genome.



      I first used bowtie to create index files. I have trimmed my read1 and read2 fastq files. All output files of bowtie index and reads files are in the same directory. Here you can see the screen shot of my directory.



      enter image description here



      Then I am running the following command to run tophat.



      enter image description here
      I do not know what I am doing wrong since my command runs but after almost 45 minutes it stops(at the following step).
      enter image description here
      



      The tophat output directory(sample_thout) has been created but it contains only the following files.
      enter image description here



      
      Inside the log I can see the following:



      enter image description here



      



      Inside tmp I can see these files:
      enter image description here



      I am pretty new to RNa seq and tophat alignment. Is there any body that can help me with the issue that I have?






      alignment rna-seq







      share|improve this question













      I am trying to use tophat to align my fastq reads to the reference genome.



      I first used bowtie to create index files. I have trimmed my read1 and read2 fastq files. All output files of bowtie index and reads files are in the same directory. Here you can see the screen shot of my directory.



      enter image description here



      Then I am running the following command to run tophat.



      enter image description here
      I do not know what I am doing wrong since my command runs but after almost 45 minutes it stops(at the following step).
      enter image description here
      



      The tophat output directory(sample_thout) has been created but it contains only the following files.
      enter image description here



      
      Inside the log I can see the following:



      enter image description here



      



      Inside tmp I can see these files:
      enter image description here



      I am pretty new to RNa seq and tophat alignment. Is there any body that can help me with the issue that I have?






      alignment rna-seq




      alignment rna-seq






      share|improve this question













      share|improve this question











      share|improve this question




      share|improve this question










      asked Nov 22 at 22:51









      yas.f

      8419




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