Which Concatenate tool help with an error in wig to BigWig conversion

Question: Which Concatenate tool help with an error in wig to BigWig conversion

2.3 years ago by

hss • 20

United States

hss • 20 wrote:

Hi there, I am not sure which concatenate tool to use to combine individual chromosome wig files into 1 file so that I can convert this merged file into 1 large BigWig file.

I see two concatenate utilities on Galaxy: tail to head,

and tail to head (cat) NEW

I used the first utility yesterday and then tried to create a bigwig file with the concatenated file and I received an error message:

"There's more than one value for chr1 base 3000321 (in coordinates that start with 1). Fatal error: Matched on Error Error running wigToBigWig"

I checked the chr 1 wig file and there was only 1 entry for base 3000321, So I am not sure why the error occurred. Seeing that it takes 24 hours to convert a concatenated file to a BigWig file , I am hoping to get this set up correctly.

Many thanks,

Scott

error galaxy wig-to-bigwig • 801 views

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modified 2.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.3 years ago by hss • 20

2.3 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello Scott,

Cat will not work for this particular use case. And the Wig-to-BigWig error is likely due to inputs: format, content, or form usage.

Would you please send in a bug report for this error and we can provide specific feedback for your data/account, including any account issues and/or tool issues discovered with a ticket for any needed fixes (by direct email). This is how: https://wiki.galaxyproject.org/Support#Reporting_tool_errors Please be sure to leave all inputs in the analysis thread undeleted. Include a link to this post in the comments so we can link the two together.

We will post back the abstracted solution to the problem, including workarounds and discovered tool/server issues when present/possible, but we never every share private data sent in through a bug report back to this public forum (or anywhere public, such as github issues).

Thanks for reporting again & let's get this resolved. Jen, Galaxy team

ADD COMMENT • link modified 2.3 years ago • written 2.3 years ago by Jennifer Hillman Jackson ♦ 25k

2.3 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Thanks for sending in the bug report. The error message suggests that the inputs are malformed - specifically, the track line is missing from at least one of them. This is required. To double check format, this is the specification for wig data: http://genome.ucsc.edu/goldenPath/help/wiggle.html

It is also important that wig datasets used with this tool contain one track of data (not multiple - do not use concatenate first). If the goal is to have these grouped when visualizing in Trackster (within Galaxy, under Visualization) or UCSC (http://genome.ucsc.edu) - both web tools permit the grouping of multiple tracks.

Should the tool fail again after correcting the inputs and a different error message is generated, please send in a new bug report from an active history, not deleted, will all inputs and the error datasets undeleted. It would be a good choice to do this test in a new history, without another analysis, as very large histories are difficult to import and review/test with.

Others are still welcome to comment/clarify to help Scott.

Thanks, Jen, Galaxy team

ADD COMMENT • link modified 2.3 years ago • written 2.3 years ago by Jennifer Hillman Jackson ♦ 25k

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