On Wed, Jan 15, 2014 at 7:51 AM, Jennifer Jackson <jen@bx.psu.edu> wrote:

Hello Rui,

The problems you are describing have to do with the format of the input wig dataset.

It looks as if you have corrected the chromosome names to be identical to the reference genome build used (required). There are options to overcome the other issues:

1. verify that your data has no browser lines, and has track and definition lines in the correct format. UCSC is the definitive source for this info, as both the underlying tool and this format were developed by them. Links to their information and the general format rules in Galaxy can be found here
https://wiki.galaxyproject.org/Learn/Datatypes#Wig_and_bigWig

2. send only a single wig file to the tool at a time, when using the Galaxy wrapper.

3. use the 'full parameter' option 'Clip chromosome positions:' to removing overhanging coordinates (known to be produced by several common tools). This is after confirming that the build is correct - overhanging coordinates can be a clue that there is a genome mismatch problem.
https://wiki.galaxyproject.org/Support#Reference_genomes

4. note that variable step data comes in two formats fixed and variable - and that variable has two format versions, those with a a span definition and those without (see examples in wig examples in #1). I have only seen this tool run successfully, in Galaxy, on the type without "span" included. If you find that the span variable is problematic after correcting any other format issue issues, switch to the format without span.

Good luck,

Jen
Galaxy team

On 1/14/14 9:52 PM, ruiwang.sz wrote:
Hi All,

I'm having an error at this:

Dataset 18: Wig/BedGraph-to-bigWig on data 12
Tool execution generated the following error message:
grep: writing output: Broken pipe

grep: writing output: Broken pipe

grep: writing output: Broken pipe

grep: writing output: Broken pipe
..
put: Broken pipe
grep: writing output: Broken pipe
grep: writing output: Broken pipe
..

grep: writing output: Broken pipe

grep: write error

Error running wigToBigWig.
The tool produced the following additional output:

hashMustFindVal: '1' not found

I searched and found this link:

http://redmine.soe.ucsc.edu/forum/index.php?t=msg&goto=10745&S=2a335135e76cf9b7160c0e9d41353767

which says that there is a naming convention difference.

I followed what he did and replaced chrom=1 to chrom=chr1 etc, now it goes further, but

still dies with error:

line 18020168 of /tmp/t3: chromosome chr1 has 195276750 bases, but item ends at 195276760

line 18020169 of /tmp/t3: chromosome chr1 has 195276750 bases, but item ends at 195276770

line 18020170 of /tmp/t3: chromosome chr1 has 195276750 bases, but item ends at 195276780

line 18020171 of /tmp/t3: chromosome chr1 has 195276750 bases, but item ends at 195276790

line 18020172 of /tmp/t3: chromosome chr1 has 195276750 bases, but item ends at 195276800

line 18020173 of /tmp/t3: chromosome chr1 has 195276750 bases, but item ends at 195276810

line 18020174 of /tmp/t3: chromosome chr1 has 195276750 bases, but item ends at 195276820

line 18020175 of /tmp/t3: chromosome chr1 has 195276750 bases, but item ends at 195276830

line 18020176 of /tmp/t3: chromosome chr1 has 195276750 bases, but item ends at 195276840

line 18020177 of /tmp/t3: chromosome chr1 has 195276750 bases, but item ends at 195276850

line 18020178 of /tmp/t3: chromosome chr1 has 195276750 bases, but item ends at 195276860

line 18020179 of /tmp/t3: chromosome chr1 has 195276750 bases, but item ends at 195276870

line 18020180 of /tmp/t3: chromosome chr1 has 195276750 bases, but item ends at 195276880

Unrecognized line 18020181 of /tmp/t3:

variableStep chr10 span=10

Error running wigToBigWig.

The command line is: wigToBigWig /tmp/t3 /home/bioinfoadmin/app/galaxy-dist/tool-data/shared/ucsc/chrom/ucsc_gg4.len /home/bioinfoadmin/app/galaxy-dist/database/files/000/dataset_769.dat -clip 2>&1 || echo "Error running wigToBigWig." >&2

Quite puzzled...wondering if anyone has seen it before and could give me a hand. :-) I'll really appreciate!

Thanks,

Rui
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