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New version MaSuRCA release 3.2.2

Today I posted a new version that I can finally call a "release" version 3.2.2.  You can get it here ftp://ftp.genome.umd.edu/pub...

Tuesday, December 13, 2016

New version 3.2.1_12132016

I just posted a new MaSuRCA version on the alternative download site: ftp://ftp.genome.umd.edu/pub/MaSuRCA/latest/.  This version improves speed by running delta-filter in parallel after Nucmer in the deduplication of contigs and unitigs.  The new script is called parallel_delta-filter.sh and its usage is:


parallel_delta-filter delta-prefix "switches" num_processes


the output is the filtered delta-prefix.fdelta file.  delta-prefix is the delta file name without .delta. "switches" are command line parameters for delta-filter, e.g. "-q -I 95 -l 100".  num_processes is a number of processes that you wish to run.

2 comments:

  1. Hi Dr. Zimin,
    I got the following message with ~20x pacbio reads and >100x illumina.

    ERROR: the runCA option ovlMemory is not recognized.
    This runCA functionality changed in CABOG version 7.
    Here are suggestions for new runCA option values:
    ovlHashBits=23
    ovlHashBlockLength= 30000000
    (replaces ovlMemory=2GB)
    ovlHashBits=24
    ovlHashBlockLength=110000000
    (replaces ovlMemory=4GB)
    ovlHashBits=25
    ovlHashBlockLength=180000000
    (replaces ovlMemory=8GB)
    ERROR: the runCA option ovlMemory is not recognized.
    This runCA functionality changed in CABOG version 7.
    Here are suggestions for new runCA option values:
    ovlHashBits=23
    ovlHashBlockLength= 30000000
    (replaces ovlMemory=2GB)
    ovlHashBits=24
    ovlHashBlockLength=110000000
    (replaces ovlMemory=4GB)
    ovlHashBits=25
    ovlHashBlockLength=180000000
    (replaces ovlMemory=8GB)

    Therefore I modified my runCA.spec by replacing ovlMemory=4GB.
    Then it's running okay now.

    Ching-Ho Chang

    ReplyDelete
  2. Thank you for your comment. Please see my latest post.

    ReplyDelete