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/ ___________________________________________________________ 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/
