I'm just trying to use samtools mpileup and it is aborting with out showing any error for some bacterial genomes, with the file given there are two variants and the program dies.

The error is just:

```
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
Aborted (core dumped)
```

The reference file (indexed with bwa) is: https://drive.google.com/file/d/0BzPjZ1hM-XWPMmxucnpDUjdpUFE/view?usp=sharing
The sorted bam file is: https://drive.google.com/file/d/0BzPjZ1hM-XWPUWw4NkdhM0E3Vm8/view?usp=sharing

The call is:

    samtools mpileup -uf SaureusTCH1516_nt_genome.fasta 446.srt.bam

To obtained the sorted bam file:

First I trimmed pair end reads by quality and if adapters were found.

Second the trimmed reads are splitted in two different files, one for each end of the sequencing data, resulting in files without quality information.

Third I aligned the reads files to the reference with bwa aln and bwa sampe

Fourth I created the sam file with samtools view | sort

And finally I indexed the sorted bam file resulting in the file given in the link.

The version of samtools I'm using is 1.1 using htslib 1.1

Any hints on what I could be doing wrong, or what may be happening?

Thanks in advance
<p>You have a corrupted alignment (for read #1 of HISEQ:185:HBB8WADXX:2:1105:8685:78337). I haven&#39;t determined what&#39;s actually wrong with its encoding (well, it&#39;s with the auxiliary tags), but you can simply avoid the problem with</p>

<pre>
samtools mpileup -Ruf SaureusTCH1516_nt_genome.fasta 446.srt.bam</pre>
