Hi all,
I'm trying to run tophat2 on a three paired-end datasets against hg19, but it has taken three days so far! How long do typical runs take for other people??
I've run it with 8 threads on an 8-core machine with 32Gb of RAM and the bowtie2 alignment took about a day to run using all eight cores, but since then it is stuck using 100% of only one core at this step:
There are about 136M read pairs in total.
Oh, and the parameters used are:
I'm trying to run tophat2 on a three paired-end datasets against hg19, but it has taken three days so far! How long do typical runs take for other people??
I've run it with 8 threads on an 8-core machine with 32Gb of RAM and the bowtie2 alignment took about a day to run using all eight cores, but since then it is stuck using 100% of only one core at this step:
[2012-05-19 11:45:52] Searching for junctions via segment mapping
Oh, and the parameters used are:
-p 8 --coverage-search --microexon-search --b2-very-sensitive --mate-inner-dist 200
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