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  • CNVer error

    Hello all,

    I am new to NGS and genomic analysis, and I am having problems running the CNVer tool. When I run the run_pipeline.sh script I get errors such as:

    Converged after 64 iterations
    num_edges: 4463
    num_nodes: 12760
    bwtie_concise_to_binary: bwtie_concise_to_binary.c:99: main: Assertion `read_in==4' failed.
    /Data/projects/cnver_test/cnver-0.7.2/src/run_pipeline.sh: line 132: 23573 Broken pipe cat ${FILE}
    23574 Aborted (core dumped)
    ....
    Using window_size 200, num_bins 50
    make_gc_map: make_gc_map.c:324: main: Assertion `bin<num_bins && bin>=0' failed.
    /Data/projects/cnver_test/cnver-0.7.2/src/run_pipeline.sh: line 171: 23722 Done cat $f
    23723 Aborted (core dumped) | ${CNVER_FOLDER}/make_gc_map ${FASTA_FILES_FOLDER}/${CONTIG}.fa ${CONTIG}.masks - ${CONTIG} 200 50

    I have attached more of the error message.

    If anyone has any suggestions that would help me identify the problem, I would greatly appreciate the help.

    Thanks alot,

    Michael
    Attached Files

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