Hi Nate, Thanks for the note!
So may I ask whether this is expected? I mean, the len_file_path points to tool-data/..., which is right inside galaxy-dist, and it is natural. I didn't realize that this path is relative to the individual job working dir. Are there any other similar cases? Best, Rui On Mon, Nov 18, 2013 at 10:40 AM, Nate Coraor <n...@bx.psu.edu> wrote: > On Sat, Nov 16, 2013 at 12:27 PM, ruiwang.sz <ruiwang...@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/ >
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