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  • Cuffmerge command giving error- TypeError: 'str' object is not callable

    Hi all
    I am merging the 1 test sample transcripts.gtf and 1 control sample transcripts.gtf files through cuffmerge via this command :

    cufflinks-2.0.0.Linux_x86_64/cuffmerge -s ref-genomes/hg19.fa assemblies.txt

    where hg19.fa is reference genome which I used to align the raw reads. I am not giving reference GTF file for the moment.
    assemblies.txt contains 2 lines:
    /home/kumardeep/ngs/control/transcripts.gtf
    /home/kumardeep/ngs/test/transcripts.gtf

    The error i am getting is as :
    [Fri May 11 10:09:51 2012] Beginning transcriptome assembly merge
    -------------------------------------------

    [Fri May 11 10:09:51 2012] Preparing output location ./merged_asm/
    Warning: no reference GTF provided!
    [Fri May 11 10:09:54 2012] Converting GTF files to SAM
    Traceback (most recent call last):
    File "cufflinks-2.0.0.Linux_x86_64/cuffmerge", line 576, in ?
    sys.exit(main())
    File "cufflinks-2.0.0.Linux_x86_64/cuffmerge", line 554, in main
    sam_input_files = convert_gtf_to_sam(gtf_input_files)
    File "cufflinks-2.0.0.Linux_x86_64/cuffmerge", line 287, in convert_gtf_to_sam
    sam_out = gtf_to_sam(line)
    File "cufflinks-2.0.0.Linux_x86_64/cuffmerge", line 252, in gtf_to_sam
    exit(1)
    TypeError: 'str' object is not callable


    Please suggest the useful
    Thanks
    Kumardeep

  • #2
    Hi Kumardeep,

    Could it be that you left out gtf_to_sam from you PATH?

    the code looks light it might be something to do with this.

    David
    Last edited by davidblaney; 05-21-2012, 04:50 AM.

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