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  • STAR read Mapping

    Hello everybody,

    I kindly need your help again ...

    I want to map my reads on the genome using STAR but for some reason I get an error that I don't know how to solve

    When I type the command line here is what I get:



    Code:
    Patrizios-MBP:processing patrizio$ STAR --genomeDir genome/star/ --runThreadN 4 --readFilesIn clipped/SRR359063_1.fastq.zip clipped/ SRR359063_2.fastq.zip --outFileNamePrefix mapping/star/SRR359063. --outSAMattributes All --outSAMtype BAM SortedByCoordinate --readFileCommand gunzip
    EXITING: FATAL INPUT ERROR: unrecoginzed parameter name "readFileIn" in input "Command-Line-Initial"
    SOLUTION: use correct parameter name (check the manual)

    Feb 19 18:49:56 ...... FATAL ERROR, exiting[/B]

    I also tried to process unzipped files and remove the command to execute each single input file --readFileCommand, but still I can't go further,

    I have a MacOs terminal,


    thank you

    Patrizio
    Last edited by GenoMax; 02-19-2019, 10:16 AM. Reason: Added [code] tags

  • #2
    STAR requires a lot of RAM depending on genome size. e.g. human genome will need ~30G of free RAM which you may not have available on your Mac. If that is true, you will not be able to do this on your local mac.

    Comment


    • #3
      Do you think that this is the reason why I have this error? this is a nematode genome so I thought the process would have been faster than human

      I will scan the command, I found an error probably I didn't type correctly the command

      later I will also try with topHat, it should be feasible because requires less RAM

      thank you
      Last edited by NDUFB11; 02-19-2019, 10:07 AM.

      Comment


      • #4
        Oops. I should have looked at the error carefully. You are correct.

        Edit: Found the problem. You have a space between clipped and file name here (clipped/ SRR359063_2.fastq.zip ). Remove that.

        Comment


        • #5
          It's working !!!! holeee'!

          have a look

          Code:
          Patrizios-MBP:processing patrizio$ STAR --genomeDir genome/star/ --runThreadN 4 --readFilesIn clipped/SRR359063_1.fastq clipped/SRR359063_2.fastq --outFileNamePrefix mapping/star/SRR359063. --outSAMattributes All --outSAMtype BAM SortedByCoordinate 
          Feb 19 19:22:44 ..... started STAR run
          Feb 19 19:22:44 ..... loading genome
          Feb 19 19:22:49 ..... started mapping
          Feb 19 19:23:50 ..... finished mapping
          Feb 19 19:23:50 ..... started sorting BAM
          Feb 19 19:23:54 ..... finished successfully
          Patrizios-MBP:processing patrizio$
          I can go further with the process !

          Thank you GenoMax

          at some point I will ship a bottle of wine to you

          -P
          Last edited by GenoMax; 02-19-2019, 10:33 AM. Reason: Added [code] tags

          Comment


          • #6
            Looks good!

            Comment


            • #7
              Just a quick comment-- STAR does come with RAM limiting arguments: --limitGenomeGenerateRAM, --limitIObufferSize , --genomeSAsparseD

              Comment

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