On 16 Mar 2016, at 11:20, Wybouw, Nicky <[email protected]> wrote:
> I get this output
>
> [E..hts_open_format] fail to open file '.bam'
> [mpileup] failed to open '.bam': Value too large for defined data type
>
> The input BAM files worked fine using the old version and are only 8.2GB big.
You are running samtools on a 32-bit machine or some other machine on which
programs cannot by default access files larger than 2GB. The htslib-1.3 build
scripts do not activate the Large File Support needed on your machine to access
such files.
This is already fixed in development [1] and will be fixed in the next release.
In the meantime, you can fix this by adding
-D_FILE_OFFSET_BITS=64
to the end of the "CFLAGS = -g -Wall -O2" line in
samtools-1.3/htslib-1.3/Makefile and recompiling everything (either start from
a freshly unpacked samtools-1.3 directory, or use "make clean-all; make").
John
[1]
https://github.com/samtools/htslib/commit/f1327a703583bf61e2e7ffd11198487fee2a8422
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