Question: (No Subject)
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Michael Sikes • 40 wrote:
Hi,
I have hit a brick wall when trying to convert wig files from the GEO
to bigwig files. Each time I try (and I have tried many times since
October), I get the same error. For example, here is a downloaded wig
file, that I assigned to the mouse mm8 genome, and the error I got
when I tried to convert it to a bigwig file. The dataset came from
Bing Ren's lab, and its GEO record is here:
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM560344
The wig file was uploaded to Galaxy Dec. 8, 2011, and I assigned mm8
rather than mm9 based on the GEO record:
49: GSM560344_03112009_313D2AAXX_B7.wi
~960,000 lines
format: wig, database: mm8
Info: uploaded wig file
display at UCSC main
The details for this upload are as follows:
Tool: Upload File
Name: GSM560344_03112009_313D2AAXX_B7.wi
Created: Dec 08, 2011
Filesize: 12.1 Mb
Dbkey: mm8
Format: wig
Tool Version:
Tool Standard Output: stdout
Tool Standard Error: stderr
Input Parameter Value
File Format auto
Genome
Conditional (files_metadata) 32
Inheritance Chain
GSM560344_03112009_313D2AAXX_B7.wi
The wig-to-bigWig conversion on data 49 (using the wig to bigwig
conversion tool in the convert formats toolbox) was run on March 21,
2012 and gave the following error:
77: Wig-to-bigWig on data 49
0 bytes
An error occurred running this job:line 152351 of stdin: chromosome
chr13 has 120614378 bases, but item ends at 120614600
line 298005 of stdin: chromosome chr17 has 95177420 bases, but item
ends at 95177625
line 325066 of stdin: chromosome chr16 has 98252459 bases, but item
ends at 9825252
The details for this operation are as follows:
Tool: Wig-to-bigWig
Name: Wig-to-bigWig on data 49
Created: Mar 21, 2012
Filesize: 0 bytes
Dbkey: mm8
Format: bigwig
Tool Version:
Tool Standard Output: stdout
Tool Standard Error: stderr
Input Parameter Value
Convert 49: GSM560344_03112009_313D2AAXX_B7.wi
Conditional (settings) 1
Items to bundle in r-tree 256
Data points bundled at lowest level 1024
Clip chromosome positions True
Do not use compression True
Inheritance Chain
Wig-to-bigWig on data 49
I gather that the chromosome ends are not being snipped off, even
though I toggle this option on the galaxy conversion tool. And I know
it's doing something, because if I toggle that option off, I get an
error that includes "broken pipe" and simply aborts. I apologize for
knowing so little about the bioinformatics involved here. And I'm sure
I've overlooked something that is likely obvious to others and/or
failed to provide some critical bit of info in this email. But any
help would be greatly appreciated.
Thanks,
Mike