Thank you, John. After updating to the current version of samtools, it
solved my issue.
On Fri, Aug 18, 2017 at 3:12 AM, John Marshall <
john.w.marsh...@glasgow.ac.uk> wrote:
> On 17 Aug 2017, at 22:38, Yan Li <li.y...@gene.com> wrote:
> > 2. But after I executed the following command, no output file is founded
> > > samtools sort -n HBS0001.bam -o HBS0001.namSort.bam
> >
> > 3. my large log file contains the following non-readable characters
> > > head log.0.o183860
> > [bam_sort_core] merging from 104 files...
> > ?BCsmV]??E>?mn~[XAEADD7!-3s??}) [snip]
>
> i.e., the BAM file output has ended up in your log file.
>
> You have written your command line following the current samtools
> documentation, but the samtools executable being run is an old 0.1.18 or so
> version. You should install the current version of samtools -- or if you
> already have, you should ensure your $PATH is set up such that the samtools
> executable you're expecting to be used really is the one being used.
>
> John
>
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