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  • seq_GA
    Senior Member
    • Feb 2009
    • 124
    #1

    Bowtie warning

    Hi
    I am getting warning when I try to map fastq format files as below though I am seeing it for the first time.

    Code:
    Warning: Exhausted best-first chunk memory for read SRR019562.3744420 SOLEXA2_1:1:18:1322:2002 length=36 (patid 3738898); skipping read
    May I know the reason.
    Tags: None
  • macrowave
    Member
    • May 2010
    • 13
    #2
    I think you need to bump up '--chunkmbs' value, actually this was well explained in the manual.

    Comment

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