On Sat, Nov 16, 2013 at 12:27 PM, ruiwang.sz <ruiwang.sz@gmail.com> wrote:
> Hi All,
>
>
> I‘m seeing some weird error messages...I googled but didn't see anything
> useful:
>
>
> So, it is during the wigToBigwig conversion:
>
>
> Dataset generation errors
> Dataset 47: Wig/BedGraph-to-bigWig on data 43
> Tool execution generated the following error message:
> grep: writing output: Broken pipe
> grep: writing output: Broken pipe
> grep: writing output: Broken pipe
> and many more lines of the same error
>
> The tool produced the following additional output:
> Couldn't open tool-data/shared/ucsc/chrom/mm10.len , No such file or
> directory
>
>
> but it is there:
>
>
> ls -l tool-data/shared/ucsc/chrom/mm10.len
>
> -rw-rw-r-- 1 bioinfoadmin bioinfoadmin 1405 Oct  9 11:33
> tool-data/shared/ucsc/chrom/mm10.len

Hi Rui,

Jobs run in a working directory based on the job id under whatever is
configured as job_working_directory in universe_wsgi.ini.  Thus, from
that directory, tool-data/shared/ ... does not exist.  To fix this,
set len_file_path in universe_wsgi.ini to an absolute path.

--nate

>
>
> From the Galaxy server log, I found these:
>
>
> galaxy.tools WARNING 2013-11-15 17:46:43,200 Failed to resolve dependency on
> 'ucsc_tools', ignoring
>
> galaxy.jobs.runners.local DEBUG 2013-11-15 17:46:43,255 (216) executing:
> grep -v "^track"
> /home/bioinfoadmin/app/galaxy-dist/database/files/000/dataset_458.dat |
> wigToBigWig stdin tool-data/shared/ucsc/chrom/mm10.len
> /home/bioinfoadmin/app/galaxy-dist/database/files/000/dataset_473.dat
> -blockSize=256 -itemsPerSlot=1024 -clip      2>&1 || echo "Error running
> wigToBigWig." >&2
>
>
> and then, setmetadata set the dataset state to ERROR.
>
>
> I did verify that the result dataset_473.dat has a size 0.
>
>
> However, when I run the command alone:
>
>
> grep -v "^track"
> /home/bioinfoadmin/app/galaxy-dist/database/files/000/dataset_458.dat |
> wigToBigWig stdin tool-data/shared/ucsc/chrom/mm10.len
> /home/bioinfoadmin/app/galaxy-dist/database/files/000/dataset_473.dat
> -blockSize=256 -itemsPerSlot=1024 -clip
>
>
> it successfully generated the dataset_473.dat.
>
>
> also, I look into the wig_to_Bigwig.xml in tools/filters, the command is:
>
>
> grep -v "^track" $input1 | wigToBigWig stdin $chromInfo $out_file1
>
>
> however, I don't see where this "$chromInfo" was defined, yet it indeed
> found the
>
> the correct value: tool-data/shared/ucsc/chrom/mm10.len. how does that
> happen?
>
>
> it is very puzzling...I'm not sure if anyone has seen this before, please
> let me know!
>
>
> Thanks,
>
> Rui
>
>
>

> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/