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  • liweixie
    Member
    • Oct 2013
    • 21

    #1

    cuffdiff bus error

    I use cufflinks 2.0.2
    when I run cuffdiff, it gives such error
    cuffdiff -o diff_out -b hg19.fa -L s2,s3 -u merged.gtf s2.bam, s3.bam
    Warning: Your version of Cufflinks is not up-to-date. It is recommended that you upgrade to Cufflinks v2.1.1 to benefit from the most recent features and bug fixes (http://cufflinks.cbcb.umd.edu).
    [00:18:42] Loading reference annotation and sequence.
    No fasta index found for hg19.fa. Rebuilding, please wait..
    Fasta index rebuilt.
    [00:21:45] Inspecting maps and determining fragment length distributions.
    [00:23:03] Modeling fragment count overdispersion.
    > Map Properties:
    > Normalized Map Mass: 1497160.24
    > Raw Map Mass: 704960.07
    > Number of Multi-Reads: 137482 (with 364310 total hits)
    > Fragment Length Distribution: Empirical (learned)
    > Estimated Mean: 108.48
    > Estimated Std Dev: 20.07
    > Map Properties:
    > Normalized Map Mass: 1497160.24
    > Raw Map Mass: 813538.05
    > Number of Multi-Reads: 167211 (with 475929 total hits)
    > Fragment Length Distribution: Empirical (learned)
    > Estimated Mean: 107.13
    > Estimated Std Dev: 19.17
    [00:23:04] Calculating preliminary abundance estimates
    > Processing Locus chr7:75625836-75651212 [********************* ] 85%
    WARNING: Multi-Hit not found (75684299,75687306).
    > Processing Locus chr9:135822455-135826943 [*********************** ] 95%
    WARNING: Multi-Hit not found (135895425,135895543).
    > Processed 21567 loci. [*************************] 100%
    [00:46:04] Learning bias parameters.
    Bus error: 10
    It stops at learning bias and shows bus error.
    Anyone knows how to solve this problem.
    Thank you!

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