On Mon, Nov 28, 2016 at 11:16:55AM +1100, hans.daetwy...@ecodev.vic.gov.au
wrote:
> XXX.bam is the 1995th file, and YYY.bam is the 1996th. When YYY.bam
> becomes the 1995th (because I removed an earlier bam file in the list)
> file the error passes XXX.bam and prints at YYY.bam.
Try the linux "ulimit -a" command to see if this is an OS imposed
limitation.
Hopefully "ulimit -n" will permit you to adjust the number of open
files.
If you're unable to raise it, about the only course of action left is
to merge groups of, say, 100 files into intermediaries first. (I'm not
sure whether this has any impact on mpileup & bcftools results though.)
James
--
James Bonfield (j...@sanger.ac.uk) | Hora aderat briligi. Nunc et Slythia Tova
| Plurima gyrabant gymbolitare vabo;
A Staden Package developer: | Et Borogovorum mimzebant undique formae,
https://sf.net/projects/staden/ | Momiferique omnes exgrabure Rathi.
--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
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