On Tue, Sep 23, 2014 at 12:53 PM, Vestergaard, Gisle Alberg
<gisle.vesterga...@helmholtz-muenchen.de> wrote:
Congrats on your new email address.
> This works (parallel version 20140622):
> cat 10000_illumina_reads.trimmed_and_processed.sortbylength.fa |
> ~/bin/Programs/Parallel/parallel-20140622/src/parallel --block 100k
> --recstart '>' --pipe "cat > {#}; usearch -cluster_fast {#} -id 0.9
> -centroids {#}.out; cat {#}.out >> tyt; rm {#} {#}.out"
>
> This does not with (parallel-20140822)
>
> cat 10000_illumina_reads.trimmed_and_processed.sortbylength.fa |
> ~/bin/Programs/parallel-20140822/src/parallel --block 100k --recstart '>'
> --pipe "cat > {#}; usearch -cluster_fast {#} -id 0.9 -centroids {#}.out; cat
> {#}.out >> tyt2; rm {#} {#}.out"
>From man parallel:
Your bug report should always include:
· The error message you get (if any).
· The complete output of parallel --version. If you are not running
the latest released version you should specify why you believe the
problem is not fixed in that version.
· A complete example that others can run that shows the problem. This
should preferably be small and simple. A combination of yes, seq,
cat, echo, and sleep can reproduce most errors. If your example
requires large files, see if you can make them by something like
seq 1000000 > file or yes | head -n 10000000 > file. If your
example requires remote execution, see if you can use localhost -
maybe using another login.
· The output of your example. If your problem is not easily
reproduced by others, the output might help them figure out the
problem.
· Whether you have watched the intro videos
(http://www.youtube.com/playlist?list=PL284C9FF2488BC6D1), walked
through the tutorial (man parallel_tutorial), and read the EXAMPLE
section in the man page (man parallel - search for EXAMPLE:).
It is hard to see what is going on without an example that others can run.
But I fixed a bug related to {#} and {%} yesterday which was
introduced 20140722, so try the git version and see if that solved
your issue, too:
git clone git://git.savannah.gnu.org/parallel.git
If not: Please provide an example as described above.
/Ole
