[Gmod-ajax] Fwd: Fwd: Jbrowse question

[Ian H. <ihh...@gm...>]

Terry, please see Seth's suggestion below. The problem may lie in JSON::XS.
Please let us know how you get on.
Thanks, Ian

---------- Forwarded message ----------
From: Seth Carbon <sjc...@lb...>
Date: Mon, Sep 12, 2011 at 7:54 PM
Subject: Re: [Gmod-ajax] Fwd: Jbrowse question

> From: Terry Camerlengo <ter...@gm...>
> Date: Mon, Sep 12, 2011 at 5:58 PM
> Subject: RE: Jbrowse question
>
>
> To the JBrowse team:
>
> I have been trying to get JBrowse included as part of our groups core NGS image.
> We are using Solid/Lifescope to generate bam files and so I am working
> with the bam-to-json.pl script. I am running Centos 5.6 and the
> tutorial works for me (except the bam file part of course). If I run
> the bam-to-json script with no params I am getting the help display.
> (I assume this means I have all of the library prerequisites.) Then I
> run the following...
>
>>> bin/bam-to-json.pl --bam /data/fragmentMapping-1-1.bam (The index file is in the same directory with the same base name)
>
> and I get  the following message:
>
> "Use of uninitialized value in concatenation (.) or string at
> bin/bam-to-json.pl line 91."
>
> followed by a Segmentation Fault.
>
> Then I run the following thinking it has something to do with a
> missing parameter..
>
>>> bin/bam-to-json.pl --bam /data/fragmentMapping-1-1.bam  --tracklabel bam_simulated --key "Simulated next-gen reads" --cssClass basic --clientConfig '{"featureCss": "background-color: #66F; height: 8px", "histCss": "background-color: #88F"}'
>
> And I just get the Segmentation Fault.

Ian,

This is somewhat similar to a JSON module problem I had with perl a
while ago--it turned out that the JSON::XS module had issues with really
big ints and would segfault. Since the JSON module will automatically
use JSON::XS if available, and fall back to JSON::PP if it's not, you
can test for this by forcing the choice and removing JSON::XS from your
system.

I thought it sounded familiar and might be worth a try.

Cheers,

-Seth


> An online search provided nothing useful and I am not sure what the
> problem could be. This is a general .bam file used for testing and is
> valid. Is there anyway to trouble shoot this? Does JBrowse log error
> info someplace? Is there a verbose setting for bam-to-json? Am I
> messing up the command line?
>
> Thanks.
>
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