On 21 Nov 2016, at 05:20, 陈然 <chen...@kindstar.com.cn> wrote:
> Thank you very much for your reply. I tried the command you advised me, it
> shows like:
>
> $ cd /biotool/samtools-1.3.1
> $ strace -e open ./samtools faidx /data/hg19.fasta
> [...]
> open("/data/hg19.fasta", O_RDONLY) = -1 EOVERFLOW (Value too large
> for defined data type)
> [fai_build] fail to open the FASTA file /data/hg19.fasta
> Could not build fai index /data/hg19.fasta.fai
>
> Does the last log text " EOVERFLOW (Value too large for defined data type)"
> give some hint?
> [...]
> $ uname -a
> Linux ubuntu 3.2.0-110-generic-pae #151-Ubuntu SMP Tue Aug 30 14:20:45 UTC
> 2016 i686 i686 i386 GNU/Linux
As noted in the open(2) manual page, EOVERFLOW here means hg19.fasta.fai is too
large to be opened; in particular, this is because you are on a 32-bit machine
and samtools has not been built with large file support.
You should rebuild samtoools, being sure to run ./configure this time -- see
the INSTALL and NEWS files. Running ./configure produces a number of messages;
on your 32-bit machine you will see
...
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... 64
...
and samtools and htslib will be built to use some extra flag arguments etc that
make that open(2) call succeed.
(Please keep replies on the mailing list.)
John
--
The Wellcome Trust Sanger Institute is operated by Genome Research
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