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Old 11-17-2011, 05:37 AM   #1
Location: LA

Join Date: May 2008
Posts: 78
Default Bowtie Error while flushing and closing output

Here is what I got with Bowtie while mapping two 20 Gb paired-end reads files:
Error while flushing and closing output
terminate called after throwing an instance of 'int'
Previously it was working fine with the same settings on the same machine. Any ideas what goes wrong? Thanks!
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Old 02-09-2012, 05:34 AM   #2
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Location: Venice

Join Date: Feb 2012
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I had the same message. It was caused by no space left on the disk.
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Old 06-09-2014, 09:51 AM   #3
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Location: Dallas

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It has been caused due to lack of storage space.
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Old 06-17-2014, 12:39 AM   #4
Location: Sweden

Join Date: Jun 2014
Posts: 86

I have received this error as well, but since I have 160 GB left on my hard drive, it shouldn't be that that's the problem. I've been googling a lot for ways to fix this problem, all to no avail.

I'm using the pre-built executables of Tophat, and I'm trying to run the test in the Tophat manual ("Testing the installation"), which is where I get the error.

Any other ideas on how to solve it? All help is greatly appreciated!
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Old 06-18-2014, 02:43 AM   #5
Location: UK

Join Date: May 2013
Posts: 10

I had this problem when I was using the latest version of Bowtie. Try downgrading to Bowtie2 v2.2.1.
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Old 07-22-2014, 05:41 AM   #6
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Location: Maryland, USA

Join Date: Dec 2012
Posts: 7

If you are using bowtie through tophat and getting this error, here is a work-around for the issue:
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