Question: (No Subject)
gravatar for Michael Sikes
6.6 years ago by
Michael Sikes40 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: 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
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