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  • another tophat "could not execute prep_reads" error

    Hi,

    Im getting this error:
    Code:
    tophat -o RNA-seq-14.11.10/tophat_out_0H -G maygtf.gtf --no-novel-juncs --solexa1.3-quals indexes/_May_2009-masked reads/RNA-seq/R43s_1_sequence_0H.fastq
    
    
    [Mon Nov 15 12:52:59 2010] Beginning TopHat run (v1.1.0)
    -----------------------------------------------
    [Mon Nov 15 12:52:59 2010] Preparing output location RNA-seq-14.11.10/tophat_out_0H//
    [Mon Nov 15 12:52:59 2010] Checking for Bowtie index files
    [Mon Nov 15 12:52:59 2010] Checking for reference FASTA file
    [Mon Nov 15 12:52:59 2010] Checking for Bowtie
    	Bowtie version:			 0.12.7.0
    [Mon Nov 15 12:52:59 2010] Checking for Samtools
    	Samtools version:		 0.1.9.0
    [Mon Nov 15 12:52:59 2010] Checking reads
    	min read length: 36bp, max read length: 36bp
    	format:		 fastq
    	quality scale:	 phred64 (reads generated with GA pipeline version >= 1.3)
    [Mon Nov 15 12:55:49 2010] Reading known junctions from GTF file
    	[FAILED]
    Error: could not execute prep_reads
    I check the log file for prep_reads it has:

    prep_reads v1.1.3 (1680)
    ---------------------------
    prep_reads: unrecognized option `--gtf-annotations'

    Anybody had this error? or can help? Thanks James

  • #2
    I got the same error for my dataset today, without those options:

    tophat -o Mytophat_out -G mygtf.gtf indexes/myindex reads/myreads.fasta

    The error message is :

    [FAILED]
    Error: could not execute prep_reads


    and in the prep_reads.log is:

    prep_reads v1.1.3 (1680)
    ---------------------------
    somedir/prep_reads: unrecognized option `--gtf-annotations'


    Hope someone can help.


    Originally posted by James View Post
    Hi,

    Im getting this error:
    Code:
    tophat -o RNA-seq-14.11.10/tophat_out_0H -G maygtf.gtf --no-novel-juncs --solexa1.3-quals indexes/_May_2009-masked reads/RNA-seq/R43s_1_sequence_0H.fastq
    
    
    [Mon Nov 15 12:52:59 2010] Beginning TopHat run (v1.1.0)
    -----------------------------------------------
    [Mon Nov 15 12:52:59 2010] Preparing output location RNA-seq-14.11.10/tophat_out_0H//
    [Mon Nov 15 12:52:59 2010] Checking for Bowtie index files
    [Mon Nov 15 12:52:59 2010] Checking for reference FASTA file
    [Mon Nov 15 12:52:59 2010] Checking for Bowtie
    	Bowtie version:			 0.12.7.0
    [Mon Nov 15 12:52:59 2010] Checking for Samtools
    	Samtools version:		 0.1.9.0
    [Mon Nov 15 12:52:59 2010] Checking reads
    	min read length: 36bp, max read length: 36bp
    	format:		 fastq
    	quality scale:	 phred64 (reads generated with GA pipeline version >= 1.3)
    [Mon Nov 15 12:55:49 2010] Reading known junctions from GTF file
    	[FAILED]
    Error: could not execute prep_reads
    I check the log file for prep_reads it has:

    prep_reads v1.1.3 (1680)
    ---------------------------
    prep_reads: unrecognized option `--gtf-annotations'

    Anybody had this error? or can help? Thanks James
    Last edited by SongLi; 11-16-2010, 11:21 AM.

    Comment


    • #3
      I fixed this problem. It may have been two things:

      It may have been calling an older prep_reads I had lurking in my path.

      It said I was calling tophat v1.1.0 even though I downloaded v1.1.3. I just re-downloaded the binaries and replaced them. Now it tells me I'm running v1.1.3.

      I'm running Mac OSX 10.5.8. by the way.

      Comment


      • #4
        Thank you James,

        However, it may not be the reason, because in the log file you posted, it says v1.1.3 there.

        I still have the problem on my side.



        Originally posted by James View Post
        I fixed this problem. It may have been two things:

        It may have been calling an older prep_reads I had lurking in my path.

        It said I was calling tophat v1.1.0 even though I downloaded v1.1.3. I just re-downloaded the binaries and replaced them. Now it tells me I'm running v1.1.3.

        I'm running Mac OSX 10.5.8. by the way.

        Comment


        • #5
          Hi James,

          Since you have solved the problem, would you mind post what the messages you get when the read RTF file passed?

          On my side the error is:
          [Tue Nov 16 17:02:17 2010] Reading known junctions from GTF file
          [FAILED]
          Error: could not execute prep_reads


          That may help me to figure out what's wrong in my case.
          Thanks,



          Originally posted by James View Post
          I fixed this problem. It may have been two things:

          It may have been calling an older prep_reads I had lurking in my path.

          It said I was calling tophat v1.1.0 even though I downloaded v1.1.3. I just re-downloaded the binaries and replaced them. Now it tells me I'm running v1.1.3.

          I'm running Mac OSX 10.5.8. by the way.

          Comment


          • #6
            I have the same problem with tophat 1.1.3, and do not manage to solve the problem.

            I used :
            ./tophat --solexa1.3-quals --no-novel-juncs -G Danio_rerio.Zv9.60.gtf -o /5cq15 Danio_rerio.Zv9.60 5.fastq

            the log file is the same as yours:
            prep_reads v1.1.3 (1680)
            ---------------------------
            /home/olivier/src/illumina_software_version/tophat_113/bin/prep_reads: unrecognized option '--gtf-annotations'

            Funny thing however in the gtf_juncs log file: seems to do something their
            gtf_juncs v1.1.3 (1680)
            ---------------------------
            Extracted 218405 junctions from /Danio_rerio.Zv9.60.gtf

            I tried gtf and gff format and both failed.
            When I run without -G option it works fine...
            Any feedback would be much appreciated

            Cheers

            Oliviera

            Comment


            • #7
              I just tested the new release 1.1.4 and now the problem seems to be fixed!
              Thanx a lot


              Oliviera

              Comment


              • #8
                Thank you TopHat team for the timingly fix!

                Don't know where to post, so I just post here.

                Originally posted by oliviera View Post
                I just tested the new release 1.1.4 and now the problem seems to be fixed!
                Thanx a lot


                Oliviera

                Comment

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