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>------------------------------------------------------------------------------
>> The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE:
>> Pinpoint memory and threading errors before they happen.
>> Find and fix more than 250 security defects in the development cycle.
>> Locate bottlenecks in serial and parallel code that limit performance.
>> http://p.sf.net/sfu/intel-dev2devfeb_______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
|
