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Old 04-04-2014, 08:29 AM   #1
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Location: Redwood City, CA

Join Date: Oct 2010
Posts: 4
Default BEDTools coverageBed error

Recently I have been getting the following persistent error when runnng BEDTools coverageBed (ver 2.16.2 or 2.12.0):

/mnt/ngs/analysis/software/BEDTools-Version-2.16.2/bin/coverageBed: line 2: 32662 Killed ${0%/*}/bedtools coverage "$@"

I suspected this is was a file format problem but one of my inputs is the product of intersectBed and the other works fine with intersectBed. I've tried dos2unix to make sure there are no extraneous characters mucking me up but that has not helped.

I have used coverageBed successfully in the past so I tried to narrow down which input file was the culprit by swapping them out but BOTH files can be made to work as input depending on what file they are paired with!

Any thoughts?


Last edited by JMorlan; 04-04-2014 at 08:41 AM.
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Old 04-22-2018, 11:17 PM   #2
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Location: China

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Hi JMorlan,

Have you solved this problem?
I met the similar problem, so if you have handled it, may you please provide some advice?


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bedtools, coveragebed

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