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
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