On 13 Nov 2014, at 12:23, Karel Břinda <[email protected]> wrote:
> I observe a strange problem and I am not able to find out what is the exact
> reason of it. When I use "samtools mpileup | another_program", samtools
> return error code 141.
When a Unix shell reports that a command has an exit status greater than 128,
this usually means the command was terminated by a signal. You don't say what
platform this is on, but typically 141 means signal 141-128 = 13, which is
typically SIGPIPE.
> Everything else is OK (pileup is well created, all data are well processed).
> I observe it when I use "set -o pipefail". The overall return error status is
> 141 and it is really caused by samtools because
> echo "${PIPESTATUS[0]} ${PIPESTATUS[1]}"
> 141 0
>
> It is interesting that this problem appears only with pipes. When I save the
> output of samtools to a file, the error code is 0.
SIGPIPE means that samtools tried to write on a pipe but there was no-one to
read it. So this means that another_program closed its input and exited while
samtools mpileup still had more data to write. Perhaps it was some trivial
trailer or statistics and so doesn't much matter; but perhaps you should check
that another_program really did process all the way to the end of the last
chromosome!
John
--
The Wellcome Trust Sanger Institute is operated by Genome Research
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