Hello,
thanks a lot for this excellent answer. Thanks to it I found where
originally the problem started.
So as I realized, it appeared only with FASTA files containing space in the
first line (i.e., with a sequence description). The program mentioned in my
previous e-mail as "another_program" considered whole strings after > as a
sequence name (did not remove the description from it). Since samtools
mpileup (unfortunately) skips some of uncovered positions (as it has been
discussed recently in this conference), "another_program" had to process
the PILEUP file concurrently with the FASTA file (to complet missing
information). So it considered the chromosomes in FASTA to be uncovered by
the PILEUP since the chromosome names were differing. And after iterating
over the whole FASTA file, it was still on the second line of the PILEUP
file.
An idea to the end -- would it be possible to add a new parameter to samtools
mpileup, which would ensure that all FASTA positions will be mentioned in
the PILEUP (even with zero coverage)?
Thanks again!
Karel
2014-11-13 14:07 GMT+01:00 John Marshall <j...@sanger.ac.uk>:
> On 13 Nov 2014, at 12:23, Karel Břinda <karel.bri...@gmail.com> 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
> Limited, a charity registered in England with number 1021457 and a
> company registered in England with number 2742969, whose registered
> office is 215 Euston Road, London, NW1 2BE.
>
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