On Wed, Apr 05, 2017 at 03:25:48PM -0500, Zhiliang Hu wrote:
> > samtools view -bhS mapped.sam | samtools sort - mapped.sam.sorted
> (to prepare data for variant calls) when I see this error on all 4 sets of
> our sequences (i.e. reproducible):
>
> [bam_header_read] EOF marker is absent. The input is probably truncated
I doubt this is a BWA issue as it's outputting SAM which doesn't have
EOF blocks anyway.
I wonder which of the two samtools is producing this warning? You
could check by outputting to a file rather than using a pipe and
executing it in two parts. If it's the former then it's simply a
rogue warning from samtools complaining about no EOF on the input SAM
(which is true, but pointless as SAM never has an EOF marker).
Regardless it appears you are using an outdated version of samtools.
The newer samtools (1.4) has a different command line syntax for the
sort command. "... | samtools sort -o mapped.sam.sorted". I checked
with 1.4 and I don't get these warning messages. (I didn't check with
1.3)
James
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| Plurima gyrabant gymbolitare vabo;
A Staden Package developer: | Et Borogovorum mimzebant undique formae,
https://sf.net/projects/staden/ | Momiferique omnes exgrabure Rathi.
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