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rogerjms / bedtools

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bamtobed hangs with large file #105

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1.Merge 100 sorted bam files into single bam file using samtools merge command 
with a total of 1.7 billion read pairs.
2.Try to convert it to bed file using bamtobed tool (24GB RAM, 8 processors)
3.Program runs and creates output file but hangs halfway through

What is the expected output? What do you see instead?
The entire bam file converted to bed file or error. But it just stops after 
producing part of the output.

What version of the product are you using? On what operating system?
Program: bamToBed (v2.11.2)
Scientific Linux, a Red Hat Enterprise Linux, recompiled from source

Please provide any additional information below.

Original issue reported on code.google.com by arjun53s...@gmail.com on 27 Dec 2011 at 4:58

GoogleCodeExporter commented 9 years ago 
Have you tested this with the latest version of BEDTools?  Also, have you 
attempted to identify and remove the problematic BAM in order to ensure that 
this is not actually an input issue?

Original comment by aaronqui...@gmail.com on 27 Dec 2011 at 9:27

GoogleCodeExporter commented 9 years ago

Original comment by aaronqui...@gmail.com on 9 Feb 2012 at 11:13