Hi Michael,

This particular .wig file has a data format problem that is the root cause of the conversion error. Specifically, there is an extra track line in the file. This can be found using unix tools with a grep or in Galaxy with the tool "Filter and Sort -> Select" by matching the pattern "track".


Ideally this would be corrected and resubmitted by the data author before use, since how/why this was inserted and what impact it has would need to be examined.

Since you noticed problems with other GEO files (conversion problems), verifying the .wig format and making any necessary corrections would also be advised.

Hopefully this helps!

Best,

Jen
Galaxy team

On 4/13/12 6:19 AM, Michael Sikes 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 <https://main.g2.bx.psu.edu/history>
~960,000 lines
format: wig, database: mm8
Info: uploaded wig file
<https://main.g2.bx.psu.edu/datasets/47465bc44dbd111e/display?to_ext=wig><https://main.g2.bx.psu.edu/datasets/47465bc44dbd111e/show_params><https://main.g2.bx.psu.edu/tool_runner/rerun?id=4746000><https://main.g2.bx.psu.edu/history>
<https://main.g2.bx.psu.edu/tag/retag?item_id=47465bc44dbd111e&item_class=HistoryDatasetAssociation><https://main.g2.bx.psu.edu/dataset/annotate?id=47465bc44dbd111e>
display at UCSC main
<https://main.g2.bx.psu.edu/datasets/4746000/display_at/ucsc_main?redirect_url=http%3A%2F%2Fgenome.ucsc.edu%2Fcgi-bin%2FhgTracks%3Fdb%3Dmm8%26position%3Dchr11%3A3000251-3023451%26hgt.customText%3D%25s&display_url=https%3A%2F%2Fmain.g2.bx.psu.edu%2Froot%2Fdisplay_as%3Fid%3D4746000%26display_app%3Ducsc%26authz_method%3Ddisplay_at>


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
<https://main.g2.bx.psu.edu/datasets/47465bc44dbd111e/stdout>
Tool Standard Error:    stderr
<https://main.g2.bx.psu.edu/datasets/47465bc44dbd111e/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 <https://main.g2.bx.psu.edu/history>
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/
<https://main.g2.bx.psu.edu/dataset/errors?id=6041022><https://main.g2.bx.psu.edu/datasets/a2b45d5d5a106890/show_params><https://main.g2.bx.psu.edu/tool_runner/rerun?id=6041022>
<https://main.g2.bx.psu.edu/datasets/48bd55b0d18aebad/display/?preview=True><https://main.g2.bx.psu.edu/datasets/48bd55b0d18aebad/edit><https://main.g2.bx.psu.edu/datasets/48bd55b0d18aebad/delete?show_deleted_on_refresh=False>

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
<https://main.g2.bx.psu.edu/datasets/a2b45d5d5a106890/stdout>
Tool Standard Error:    stderr
<https://main.g2.bx.psu.edu/datasets/a2b45d5d5a106890/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





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