Re: [Samtools-help] Reporting on samtools-0.1.18 sort producing a huge file and taking a long time

[James B. <jk...@sa...>]

On Mon, Jul 06, 2015 at 09:29:26AM +0100, Albert Vilella wrote:
> I am just reporting on something I saw over the weekend. A samtools
> sort command executed on Friday was still running this morning on a
> file that should have taken a relatively short time to sort.
> 
> The input file is about 241M, and this morning, samtools-0.1.18 sort
> was producing a file that was 1000x bigger, 236G and growing when I
> killed it.

Wow! What was in the file it was creating? Any clues as to what the
bulk was?

Of more interest is whether this same input file still causes problems
with the newest Samtools.  If not then it's unlikely to get fixed, at
least officially.  (Some linux releases may patch it if there is a fix
for the 0.1.19+ I guess.)

James

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