Hi, Has anyone get tophat2 to work for the fusion search? I am using tophat-2.0.4 and it terminates "Reporting output tracks" step. The error says: [FAILED] Error running tophat_reports. The machine I am running it on has about 24 gigs of RAM. tophat -o <out_dir> -p 12 --fusion-search --bowtie1 --no-coverage-search --segment-length 20 -r 160 --mate-std-dev 24 --fusion-min-dist 100000 --fusion-anchor-length 13 --fusion-ignore-chromosomes chrM /indexes/hg19 $fq1 $fq2. Also my system log says the program used more than 19gb of memory. I can't understand why there is high requirement of memory for the tophat. The size of my input files is abut 1.5 gb each.
Question: Tophat_Reports "Failed" Error
7.2 years ago by
vinay kumar • 0
vinay kumar • 0 wrote:
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