Error: segment-based junction search failed with err = -9

Albert Cheng · 08-19-2010, 08:05 AM

Hi,

I get this error running tophat. I got this from only one of the job. Other jobs are successful. May I know how I could avoid that?

Error: segment-based junction search failed with err = -9

Thanks!
Albert

fkrueger · 08-19-2010, 09:24 AM

I had the same error message today when I tried to align some human sequences that had been spiked into the phiX lane (around 5%). When I aligned the sequences to phiX first and ran tophat again with just the unmapped sequences it did work eventually.

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08-19-2010, 08:05 AM	#1
Albert Cheng Junior Member Location: Boston Join Date: Aug 2010 Posts: 1	Error: segment-based junction search failed with err = -9 Hi, I get this error running tophat. I got this from only one of the job. Other jobs are successful. May I know how I could avoid that? Error: segment-based junction search failed with err = -9 Thanks! Albert

08-19-2010, 09:24 AM	#2
fkrueger Senior Member Location: Cambridge, UK Join Date: Sep 2009 Posts: 625	I had the same error message today when I tried to align some human sequences that had been spiked into the phiX lane (around 5%). When I aligned the sequences to phiX first and ran tophat again with just the unmapped sequences it did work eventually.