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  • Cuffmerge Error Allocating Memory

    Hi,

    I am encountering error during Cuffmerge execution. The command I executed is:

    ./cuffmerge -s /extdata1/soft/TOPHAT2/hg19.fa -g UCSC-Ensembl.gtf assemblies.txt

    Assemblies.txt contains two lines:
    SAMPLE1/transcripts.gtf
    SAMPLE2/transcripts.gtf

    After running it gave me this error:

    [15:16:59] Assembling transcripts and estimating abundances.

    chr21:38435145-45747259 Warning: Skipping large bundle.
    Processed 33389 loci.
    [Sun May 27 16:57:47 2012] Comparing against reference file UCSC-Ensembl.gtf
    Warning: Could not connect to update server to verify current version. Please check at the Cufflinks website (http://cufflinks.cbcb.umd.edu).
    Error allocating memory.
    [FAILED]

    Error: could not execute cuffcompare
    Traceback (most recent call last):
    File "./cuffmerge", line 576, in ?
    sys.exit(main())
    File "./cuffmerge", line 559, in main
    compare_meta_asm_against_ref(params.ref_gtf, params.fasta, output_dir+"/transcripts.gtf")
    File "./cuffmerge", line 406, in compare_meta_asm_against_ref
    tmap = compare_to_reference(gtf_input_file, ref_gtf, fasta_file)
    File "./cuffmerge", line 342, in compare_to_reference
    exit(1)
    TypeError: 'str' object is not callable


    It also gave me many warnings regarding the version of cufflinks (I think, It is ignorable).

    I have enough memory in the server, I don't know why it is giving me this memory error. I am running two more processes of Tophat alternatively. Is that the reason it gave me this error?

    Thanking you!
    Aso

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