Re: [Gmod-ajax] out of memory error

[Bernd J. <ber...@pa...>]

Hi Ian,
Thanks for your help!!!
could you please remind me on how to use git?

I am following the instructions on http://gmod.org/wiki/JBrowse_Tutorial
The following two lines produce error messages:

$ git branch --track lazyfeatures origin/lazyfeatures
$ git checkout lazyfeatures

fatal: Not a valid object name: 'origin/lazyfeatures'.

and I don't know how to update using git..

I believe there are some instructions missing (I just created a 
directory called origin...)

I also don't know what these lazyfeatures are and why I need them...

Then I believe I am not on the latest git branch but the release 
branch... How would I get access to the development branch?

Well sorry for these many questions, but I already have loaded the fasta 
file and some annotations and it looks very promising...

Kind regards and congratulations on your nice work,

Bernd


On 1/19/2011 6:21 PM, Ian Holmes wrote:
> Hi Bernd, yes this is a known issue, should be fixed on the latest git branch or in the next release (which is imminent)
>
> -Ian (by phone)
>
> On Jan 19, 2011, at 7:27 AM, Bernd Jagla<ber...@pa...>  wrote:
>
>> Hi,
>>
>> I am running into an out of memory error when reading/converting bam
>> files...
>>
>> Any suggestions?
>>
>> zoppel:jbrowse bernd$ bin/flatfile-to-json.pl --bam
>> data/annotation/HNB8/101217/L1.HPB8.bowtie.sam.bam --cssclass exon
>> --tracklabel L1 --key "Lane 1 data"
>>
>> working on seq HNB8
>> perl(6233) malloc: *** mmap(size=16777216) failed (error code=12)
>> *** error: can't allocate region
>> *** set a breakpoint in malloc_error_break to debug
>> Out of memory!
>>
>>
>> I have another machine with more memory, but I am not sure if I can
>> install everything on that one as I am not the sys admin.
>> and if I would have installed it could I use it to create whatever is
>> being created and then copy that to the web server?
>>
>> Thanks,
>>
>> Bernd
>>
>>
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