Question: Tophat_Reports "Failed" Error
gravatar for vinay kumar
6.7 years ago by
vinay kumar0 wrote:

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.

tophat fusion • 3.2k views
ADD COMMENTlink modified 6.7 years ago • written 6.7 years ago by vinay kumar0

I ran the same version last week without problems in several 4 gb pe 100b reads in a linux64 machine with 16gb RAM, this was my command: tophat --bowtie1 -p 8 --coverage-search --fusion-search -G hs37.64.gtf -M hg37.64 $FQ1 $FQ2

ADD REPLYlink written 6.7 years ago by JC7.6k
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