Hi Mike,

I apologize if I wasn't clear, but the 'Select' was to show you how to identify the multi-track group wig files. I wanted to give you a way to screen similar files going forward.


The wig-to-bigWig program in Galaxy comes from UCSC. It accepts .wig files with a single track group as input:
http://genome.ucsc.edu/goldenPath/help/bigWig.html (see step #1)

The data author lab can either submit the data as single track group .wig files, or, if you are confident that the multiple track group .wig format is expected and OK from this source, split the file. There are no specific tools in Galaxy to do this, but something like this would work:

 - Text Manipulation -> "Add column", "1", Iterate? = yes
 - "Select", "track"
 - note the line number of track lines
- "Remove beginning of a file", using line numbers, and the -original- .wig file, to break up into individual .wig files.

Good luck!

Jen
Galaxy team

On 4/16/12 6:57 AM, Michael Sikes wrote:
Jennifer,

Thanks for your help. I ran the filter and sort tool as advised, and
then ran the wig to bigwig on the new history item generated by the
filter. This time I got a different error:
84: Wig-to-bigWig on data 83 <https://main.g2.bx.psu.edu/history>
0 bytes
An error occurred running this job:/stdin is empty of data
Error running wigToBigWig.
/
<https://main.g2.bx.psu.edu/dataset/errors?id=6818347><https://main.g2.bx.psu.edu/datasets/0f70746579b165e2/show_params><https://main.g2.bx.psu.edu/tool_runner/rerun?id=6818347>
<https://main.g2.bx.psu.edu/datasets/b4fb2e8c767b4258/display/?preview=True><https://main.g2.bx.psu.edu/datasets/b4fb2e8c767b4258/edit><https://main.g2.bx.psu.edu/datasets/b4fb2e8c767b4258/delete?show_deleted_on_refresh=False>
83: Select on data 49 <https://main.g2.bx.psu.edu/history>
1 line, 1 comments
format: wig, database: mm8
Info: Matching pattern: track
<https://main.g2.bx.psu.edu/datasets/b4fb2e8c767b4258/display?to_ext=wig><https://main.g2.bx.psu.edu/datasets/b4fb2e8c767b4258/show_params><https://main.g2.bx.psu.edu/tool_runner/rerun?id=6818275><https://main.g2.bx.psu.edu/history>
<https://main.g2.bx.psu.edu/tag/retag?item_id=b4fb2e8c767b4258&item_class=HistoryDatasetAssociation><https://main.g2.bx.psu.edu/dataset/annotate?id=b4fb2e8c767b4258>


Again, I'm sure I left off something obvious. Could you tell me what I
did wrong?

Thanks,
Mike

On Apr 13, 2012, at 1:27 PM, Jennifer Jackson wrote:

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/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
<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 ParameterValue
File Formatauto
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 ParameterValue
Convert49: GSM560344_03112009_313D2AAXX_B7.wi
Conditional (settings)1
Items to bundle in r-tree256
Data points bundled at lowest level1024
Clip chromosome positionsTrue
Do not use compressionTrue


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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--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org
http://galaxyproject.org/wiki/Support

Michael Sikes, Ph.D.
Associate Professor of Immunology
North Carolina State University
Microbiology Department
4524A Gardner Hall
Campus Box 7615
Raleigh, NC 27695
Ph: 919-513-0528
Fax: 919-515-7867
email: mlsi...@ncsu.edu <mailto:mlsi...@ncsu.edu>


--
Jennifer Jackson
http://galaxyproject.org
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
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use the Galaxy Development list:

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