Re: Something broke from 20140622 to 20140822

[Ole Tange]

On Tue, Sep 23, 2014 at 12:53 PM, Vestergaard, Gisle Alberg
<gisle.vestergaard@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