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.
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.
Hi Dr. Zimin,
ReplyDeleteI 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
Thank you for your comment. Please see my latest post.
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