Re: GNU Parallel Bug Reports Job log bug

[Ole Tange]

I do not have multiRunTools nor
/home/anjan/Desktop/TessArae/projects/Next_Gen_RDM/lindel_db_data/egl_ref_seq/egl_mpx.6.3.reference.sequences.fasta.v.3.0.raw.2.0
so it is impossible for me to reproduce. Please follow the guide for
reporting bugs from the man page:

       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.

       · 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:).

       If you suspect the error is dependent on your environment or
       distribution, please see if you can reproduce the error on one
       of these VirtualBox images:
       http://sourceforge.net/projects/virtualboximage/files/

       Specifying the name of your distribution is not enough as you
       may have installed software that is not in the VirtualBox
       images.

       If you cannot reproduce the error on any of the VirtualBox
       images above, you should assume the debugging will be done
       through you. That will put more burden on you and it is extra
       important you give any information that help.

/Ole


On Wed, Dec 18, 2013 at 9:41 PM, Anjan Purkayastha
<address@hidden> wrote:
> Hi,
> I'm running GNU parallel version 20121122 on my Ubuntu machine. The --joblog
> <log.file.name> creates a file with a header line, but without any log
> entries.
> Here is a sample command from my perl master program:
> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> my $joblog= $ARGV[0]."\.log";
>
> system("parallel --joblog $joblog -a $ARGV[0] --colsep '\t' multiRunTools
> --task align --file1 \{1\} --out \{2\}  --ref
> /home/anjan/Desktop/TessArae/projects/Next_Gen_RDM/lindel_db_data/egl_ref_seq/egl_mpx.6.3.reference.sequences.fasta.v.3.0.raw.2.0");
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> Any ideas?
> Thanks,
> Anjan
>
> --
> ============================
> Anjan Purkayastha, PhD
> Senior Computational Biologist
> TessArae LLC
> 46090 Lake Center Plaza | Suite 304
> Potomac Falls | VA 20165
> 703.444.7188 ext 116 (phone)
> 703.740.6939 (mobile)
> address@hidden