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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