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  • error with htseq count and bed tool

    hello every one,

    as i am working on count based differential analysis and for that i am trying to use HTSEQ and bedtools
    1. I am using Bedtool to count read in as
    Code:
    bedtools multicov -bams sample1.bam sample2.bam sample3.bam -bed all.gff3
    here in spite of bed file i am using reference genome file all.gff3. is it correct to use it ?
    Because I am not sure that I will get proper result with these gff3 file or not
    2. I am getting error with ht-seq as it is already installed in my machine but still it is showing that

    Code:
    [root@localhost ~]# htseq-count
    bash: htseq-count: command not found...
    Kindly reply me

    Thanks
    Last edited by meghavarshney; 07-01-2015, 09:16 PM. Reason: error

  • #2
    1) It may be installed, but it's not in your path. Look at where it was installed and either change your $PATH variable or use the full path to specify the executable.
    2) You shouldn't be running things like this as root.

    Comment


    • #3
      I had installed it in this location and still m not able to access it
      Code:
      [root@localhost HTSeq-0.6.1]# python setup.py install --user
      running install
      running bdist_egg
      running egg_info
      writing HTSeq.egg-info/PKG-INFO
      writing top-level names to HTSeq.egg-info/top_level.txt
      writing dependency_links to HTSeq.egg-info/dependency_links.txt
      reading manifest file 'HTSeq.egg-info/SOURCES.txt'
      reading manifest template 'MANIFEST.in'
      no previously-included directories found matching 'example_data'
      no previously-included directories found matching 'test'
      warning: no previously-included files found matching 'todo.txt'
      writing manifest file 'HTSeq.egg-info/SOURCES.txt'
      installing library code to build/bdist.linux-x86_64/egg
      running install_lib
      running build_py
      running build_ext
      creating build/bdist.linux-x86_64/egg
      creating build/bdist.linux-x86_64/egg/HTSeq
      copying build/lib.linux-x86_64-2.7/HTSeq/__init__.py -> build/bdist.linux-x86_64/egg/HTSeq
      copying build/lib.linux-x86_64-2.7/HTSeq/_HTSeq_internal.py -> build/bdist.linux-x86_64/egg/HTSeq
      copying build/lib.linux-x86_64-2.7/HTSeq/StepVector.py -> build/bdist.linux-x86_64/egg/HTSeq
      copying build/lib.linux-x86_64-2.7/HTSeq/_version.py -> build/bdist.linux-x86_64/egg/HTSeq
      creating build/bdist.linux-x86_64/egg/HTSeq/scripts
      copying build/lib.linux-x86_64-2.7/HTSeq/scripts/__init__.py -> build/bdist.linux-x86_64/egg/HTSeq/scripts
      copying build/lib.linux-x86_64-2.7/HTSeq/scripts/qa.py -> build/bdist.linux-x86_64/egg/HTSeq/scripts
      copying build/lib.linux-x86_64-2.7/HTSeq/scripts/count.py -> build/bdist.linux-x86_64/egg/HTSeq/scripts
      copying build/lib.linux-x86_64-2.7/HTSeq/_HTSeq.so -> build/bdist.linux-x86_64/egg/HTSeq
      copying build/lib.linux-x86_64-2.7/HTSeq/_StepVector.so -> build/bdist.linux-x86_64/egg/HTSeq
      byte-compiling build/bdist.linux-x86_64/egg/HTSeq/__init__.py to __init__.pyc
      byte-compiling build/bdist.linux-x86_64/egg/HTSeq/_HTSeq_internal.py to _HTSeq_internal.pyc
      byte-compiling build/bdist.linux-x86_64/egg/HTSeq/StepVector.py to StepVector.pyc
      byte-compiling build/bdist.linux-x86_64/egg/HTSeq/_version.py to _version.pyc
      byte-compiling build/bdist.linux-x86_64/egg/HTSeq/scripts/__init__.py to __init__.pyc
      byte-compiling build/bdist.linux-x86_64/egg/HTSeq/scripts/qa.py to qa.pyc
      byte-compiling build/bdist.linux-x86_64/egg/HTSeq/scripts/count.py to count.pyc
      creating stub loader for HTSeq/_HTSeq.so
      creating stub loader for HTSeq/_StepVector.so
      byte-compiling build/bdist.linux-x86_64/egg/HTSeq/_HTSeq.py to _HTSeq.pyc
      byte-compiling build/bdist.linux-x86_64/egg/HTSeq/_StepVector.py to _StepVector.pyc
      creating build/bdist.linux-x86_64/egg/EGG-INFO
      installing scripts to build/bdist.linux-x86_64/egg/EGG-INFO/scripts
      running install_scripts
      running build_scripts
      creating build/bdist.linux-x86_64/egg/EGG-INFO/scripts
      copying build/scripts-2.7/htseq-qa -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
      copying build/scripts-2.7/htseq-count -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
      changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/htseq-qa to 755
      changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/htseq-count to 755
      copying HTSeq.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
      copying HTSeq.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
      copying HTSeq.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
      copying HTSeq.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
      writing build/bdist.linux-x86_64/egg/EGG-INFO/native_libs.txt
      zip_safe flag not set; analyzing archive contents...
      HTSeq.StepVector: module references __file__
      creating 'dist/HTSeq-0.6.1-py2.7-linux-x86_64.egg' and adding 'build/bdist.linux-x86_64/egg' to it
      removing 'build/bdist.linux-x86_64/egg' (and everything under it)
      Processing HTSeq-0.6.1-py2.7-linux-x86_64.egg
      removing '/root/.local/lib/python2.7/site-packages/HTSeq-0.6.1-py2.7-linux-x86_64.egg' (and everything under it)
      creating /root/.local/lib/python2.7/site-packages/HTSeq-0.6.1-py2.7-linux-x86_64.egg
      Extracting HTSeq-0.6.1-py2.7-linux-x86_64.egg to /root/.local/lib/python2.7/site-packages
      Removing HTSeq 0.6.1p1 from easy-install.pth file
      Adding HTSeq 0.6.1 to easy-install.pth file
      Installing htseq-qa script to /root/.local/bin
      Installing htseq-count script to /root/.local/bin
      
      Installed /root/.local/lib/python2.7/site-packages/HTSeq-0.6.1-py2.7-linux-x86_64.egg
      Processing dependencies for HTSeq==0.6.1
      Finished processing dependencies for HTSeq==0.6.1
      as i had tried it in these ways
      Code:
      [pinky@localhost HTSeq-0.6.1]$ htseq-count
      bash: htseq-count: command not found...
      [pinky@localhost HTSeq-0.6.1]$ python htseq-count
      python: can't open file 'htseq-count': [Errno 2] No such file or directory
      [pinky@localhost HTSeq-0.6.1]$ python /home/pinky/Downloads/HTSeq-0.6.1/htseq-count
      python: can't open file '/home/pinky/Downloads/HTSeq-0.6.1/htseq-count': [Errno 2] No such file or directory
      but still the problem remains same.

      Comment


      • #4
        Normally python programs end up in ~/.local/bin when you install them like this. Have a look there and add that to your path.

        Comment


        • #5
          i had checked but still i didn't find
          Code:
          [pinky@localhost bin]$ htseq-count
          bash: htseq-count: command not found...
          as from root this folder contain
          Code:
          [root@localhost bin]# ls
          annotateBed                                  getOverlap
          bam2bed                                      gff2bed
          bam2bed_gnuParallel                          gff2starch
          bam2bed_sge                                  groupBy
          bam2starch                                   gtf2bed
          bam2starch_gnuParallel                       gtf2starch
          bam2starch_sge                               gvf2bed
          bamToBed                                     gvf2starch
          bamToFastq                                   intersectBed
          bed12ToBed6                                  linksBed
          bedextract                                   mapBed
          bedmap                                       maskFastaFromBed
          bedops                                       mergeBed
          bedpeToBam                                   multiBamCov
          bedToBam                                     multiIntersectBed
          bedToIgv                                     nucBed
          bedtools                                     pairToBed
          closestBed                                   pairToPair
          closest-features                             psl2bed
          clusterBed                                   psl2starch
          complementBed                                R
          convert2bed                                  randomBed
          coverageBed                                  rmsk2bed
          expandCols                                   rmsk2starch
          fasta_clipping_histogram.pl                  Rscript
          fasta_formatter                              sam2bed
          fastaFromBed                                 sam2starch
          fasta_nucleotide_changer                     shuffleBed
          fastq_masker                                 slopBed
          fastq_quality_boxplot_graph.sh               sort-bed
          fastq_quality_converter                      sortBed
          fastq_quality_filter                         starch
          fastq_quality_trimmer                        starchcat
          fastq_to_fasta                               starchcluster_gnuParallel
          fastx_artifacts_filter                       starchcluster_sge
          fastx_barcode_splitter.pl                    subtractBed
          fastx_clipper                                tagBam
          fastx_collapser                              trimmomatic-0.30.jar
          fastx_nucleotide_distribution_graph.sh       unionBedGraphs
          fastx_nucleotide_distribution_line_graph.sh  unstarch
          fastx_quality_stats                          vcf2bed
          fastx_renamer                                vcf2starch
          fastx_reverse_complement                     wig2bed
          fastx_trimmer                                wig2starch
          fastx_uncollapser                            windowBed
          flankBed                                     windowMaker
          genomeCoverageBed
          [root@localhost bin]#
          so is their any other way to tackle this problem.

          Comment


          • #6
            That looks like ~/bin, not ~/.local/bin. The installation log you posted even showed that that's where it put the executables.

            Comment


            • #7
              Originally posted by meghavarshney View Post
              I had installed it in this location and still m not able to access it
              Code:
              [root@localhost HTSeq-0.6.1]# python setup.py install --user
              ...
              Installing htseq-qa script to /root/.local/bin
              Installing htseq-count script to /root/.local/bin
              I think you have done something weird here: You have installed the packages as root using the option --user. This installed htseq-count in the root home directory,/root/.local/bin. As regular user you can't access /root/.local/bin as it's not on path.

              If you execute python setup.py install --user as regular user you should be fine and see htseq-count in ~/.local/bin/.

              Comment


              • #8
                thnkxx

                thnkx to both of you . i got solution as for this i reinstalled HTSeq again as a regular user and now its properly working for me .


                thankx again

                Comment

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