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
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