Re: [Gmod-ajax] JBrowse 1.2 problem generating JSON data from bed files?

[Mitch S. <mit...@be...>]

Thanks for the reports, these are my top priority right now.  I'll 
follow up to the list when they're fixed.

Mitch

On 02/18/2011 08:32 AM, Brenton Graveley wrote:
> I am having issues with JBrowse 1.2 as well, though they seem different.
>
> First, when using bin/flatfile-to-json.pl on a bed file that worked 
> previously I get the following:
>
> bin/flatfile-to-json.pl --bed FlyBase_FBtr_r5_12_annotations.nochr.bed 
> --tracklabel FlyBase_5.12 --key "FlyBase_5.12" --getLabel 
> --autocomplete label --cssclass transcript --subfeatureClasses 
> '{"UTR": "transcript-UTR", "CDS": "transcript-CDS"}' --getSubs 
> --arrowheadClass transcript-arrowhead
> Operation "cmp": no method found,
> left argument in overloaded package Bio::Annotation::SimpleValue,
> right argument in overloaded package Bio::Annotation::SimpleValue at 
> bin/flatfile-to-json.pl line 169, <GEN1> line 22309.
>
> Second, when loading wiggle tracks in using wig-to-json.pl 
> <http://wig-to-json.pl>, the process takes very long (4 hours so far) 
> for a wiggle track that took about 20 minutes with the previous version.
>
> Brent
>
>
> On Feb 18, 2011, at 11:23 AM, Gregg Helt wrote:
>
>> With the updated JBrowse 1.2, I'm getting "Segmentation fault" errors 
>> when trying to process bed files with flatfile-to-json.pl 
>> <http://flatfile-to-json.pl/>
>>
>> With minimal parameters I just get the seg fault message:
>> bin/flatfile-to-json.pl <http://flatfile-to-json.pl/> --bed 
>> refGene.bed --tracklabel refGene
>> Segmentation fault
>>
>> With a fuller set of parameters I'm getting an additional error message:
>>
>> bin/flatfile-to-json.pl <http://flatfile-to-json.pl/> --bed 
>> all_mrna.bed --tracklabel all_mrna --key "Drosophila mRNAs" 
>> --cssClass transcript --subfeatureClasses '{"CDS": "transcript-CDS", 
>> "UTR": "transcript-UTR"}' --arrowheadClass transcript-arrowhead 
>> --getLabel --autoComplete label --getSubs
>>
>> Can't store CODE items at ../../lib/Storable.pm (autosplit into 
>> ../../lib/auto/Storable/_store_fd.al <http://store_fd.al/>) line 304, 
>> <GEN1> line 33158, at 
>> /Users/gregg/projects/webapollo/jbrowse/bin/../lib/ExternalSorter.pm 
>> line 92
>> Segmentation fault
>>
>> I tried whittling down the bed file to simplify, but even with a one 
>> line bed file I still get the seg fault.   I've attached the one-line 
>> bed file, can someone try to reproduce this problem to see if it's 
>> specific to my setup or not?
>>
>> These are standard bed files dowloaded from UCSC.  I'm using a fresh 
>> install of BioPerl, so to verify that the problem is specific to the 
>> new JBrowse release I went back to an earlier version of JBrowse 
>> (from September 2010) and tried processing the same bed files.  The 
>> earlier version worked.
>>
>> When processing normal-sized bed files there's a significant delay 
>> (proportional to the size of the bed file) before the seg fault.  
>> During the delay memory usage climbs linearly, and is 10x to 20x 
>> greater than the earlier JBrowse version.  I'm not hitting my overall 
>> memory limits, but wondering if something is causing a recursion that 
>> leads to exceeding my stack size limits?
>>
>> Gregg
>> <tiny.bed>------------------------------------------------------------------------------
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