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  • amos2ace gives up at 2Gb?

    Has anyone successfully converted an .afg assembly file (>= 3Gb) to .ace using amos2ace? I am unable to do this on a macbook pro (8 Gb RAM) as the output .ace file is truncated.

    Details:
    I have been given an .afg file assembly, and can convert it to .bnk (with hawkeye), but when I want to convert to .ace (using amos2ace) the resulting .ace file is truncated part way through the phd file descriptions. So when I try and import into Consed, it very rightly complains that there are very many missing .phd files.
    The original .afg is 3 Gb, and amos2ace gives a (truncated) .ace file of 1.93 Gb. When I look inside it, it looks fine until it just stops (see below).
    - Mike DS

    -----------------------just the last bit below-----------------
    QA 1 251 1 251
    DS CHROMAT_FILE: 5387375 PHD_FILE: 5387375.phd.1 TIME: Thu Dec 12 00:14:39 2013
    RD 5393237 228 0 0
    CTGGCTGTCTATGCCTTCCCACATCGTTTCCCACTTAACCATGACTTTGG
    GACCTTAGCTGGCGGTCTGGGTTGTTTCCCTCTTCACGACGGACGTTAGC
    ACCCGCCGTGTGTCTCCCGTGATAACATTCTTCGGTATTCGGAGTTTGCA
    TCGAGTTGGTAAGCCGGGATGGCCCCCTAGTCGAAACAGTGCTCTACCCC
    CGAAGATGAATTCACGAGGCGCTACCTA

    QA 1 228 1 228
    DS CHROMAT_FILE: 5393237 PHD_FILE: 5393237.phd.1 TIME: Thu Dec 12 00:14:40 2013

    Wamos2ace $Revision$
    Run by root on Thu 12 Dec 2013 00:15:39 EST
    }

  • #2
    follow up - converted to BAM

    So, I gave up trying to get an .ace file. I converted the .afg to .bnk format, then .bnk to SAM, then SAM to BAM, and can now view the assembly very nicely in Tablet.
    Now I can see the velvet assemblies, I notice many have crazy alignments for the first 250 nt; then an abrupt change to perfect alignment.
    - Mike DS

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