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