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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