[Gmod-help] Re: [Gmod-gbrowse] Problems displaying a wiggle track for .wig data in gbrowse 2.01

Jeff Bowes bowes at ucalgary.ca
Thu Mar 25 17:43:22 EDT 2010 

Hi Dave,

That did not help.  Are hyphens also problematic in the SO feature  
names in the GFF3 for gbrowse? 

Thanks,


Jeff




Dave Clements, GMOD Help Desk wrote:
> Hi Jeff,
>
> GBrowse does not like hyphens in track names.  From the GBrowse Admin
> Tutorial:
>
> This is a "stanza" that describes one of the tracks displayed by GBrowse.
> The track has an internal name of "ExampleFeatures" which you can use in the
> URL to turn the track on. The internal name is enclosed by square brackets.
> Names can be any combination of printable characters and whitespace, but can
> not contain the hyphen ("-") character (you can use the underscore "_"
> character instead).
>
> Try that and let the list know if that helps.  If not, we'll look for other
> problems.
>
> Dave C
>
> On Tue, Mar 23, 2010 at 4:17 PM, Jeff Bowes <bowes at ucalgary.ca> wrote:
>
>   
>>  Hi,
>>
>> We have received som Chip-seq methylation data in .wig format and we are
>> currently having trouble displaying this data.  No glyphs appear under the
>> wiggle track.  I am not sure what I might be doing wrong. We are using
>> Gbrowse 2.01.
>>
>> The .wig file I received open as follows.
>>
>> browser position scaffold_163:520000-690000
>> track type=wiggle_0 name=H3K27me3_animal_ChIP-seq_st10-12
>> maxHeightPixels=64:64:11 color=254,196,79 visibility=full
>> fixedStep chrom=scaffold_1 start=321 step=10 span=10
>> 1
>> 1
>> 1
>>
>> The scores range from 1 to 198,
>>
>> I created gff3 for this file with wiggle2gff3.  The binaries were all
>> created in a directory that is readable by apache.  All the .wib files are
>> readable by apache.  The gff3 file reads
>>
>> ##gff-version 3
>>
>> scaffold_1      H3K27me3_animal_ChIP-seq_st10-12_xenTro2
>> Chip-seq        321     7792370 .       .       .
>> Name=H3K27me3_animal_ChIP-seq_st10-12;wigfile=/data/gbrowse/wiggle_data/H3K27me3_animal_ChIP-seq_st10-12_xenTro2.wig/track_001.scaffold_1.1269301611.wib
>>
>> This wiggle file was loaded into mysql using the  bp_seqfeature_load.pl.
>> The load did not seem to produce any errors.
>>
>> The last track definition I tried in the config file was:
>>
>> [H3K27me3_animal_ChIP-seq_st10-12_xenTro2 WIG]
>> feature = H3K27me3_animal_ChIP-seq_st10-12_xenTro2
>> glyph   = wiggle_xyplot
>> min_score = 1
>> max_score = 198
>> key     = H3K27 animal ChiP-seq_Xenopus Tropicalis stages 10 to 12
>>
>> The key appears but no glyphs appear under the key on that track.
>>
>> Here is a error_log output from an attempt to view a section that should
>> have had wiggle data.  There was an "uninitialized value in concatenation
>> (.) or string"  error but nothing specific to the wiggle track that I can
>> see:   That error and the line retrieving the methylation wiggle track are
>> bolded.
>>
>> Thanks,
>>
>> Jeff
>>
>> error_log output follows:
>>
>> [Tue Mar 23 13:50:25 2010] [error] [client 136.159.4.22] [2538] RUN():
>> POST:
>> http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/force_submit=0;plugin_find=0;name=scaffold_165%3A82942..88271;Search=Search
>> at
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm
>> line 160., referer:
>> http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database
>> [Tue Mar 23 13:50:25 2010] [error] [client 136.159.4.22] [2538]
>> add_user_tracks() at
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm
>> line 167., referer:
>> http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database
>> [Tue Mar 23 13:50:25 2010] [error] [client 136.159.4.22] [2538] testing for
>> asynchronous event() at
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm
>> line 178., referer:
>> http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database
>> [Tue Mar 23 13:50:25 2010] [error] [client 136.159.4.22] [2538] init() at
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm
>> line 185., referer:
>> http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database
>> [Tue Mar 23 13:50:25 2010] [error] [client 136.159.4.22] [2538]
>> update_state() at
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm
>> line 188., referer:
>> http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database
>> [Tue Mar 23 13:50:25 2010] [error] [client 136.159.4.22] [2538] render() at
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm
>> line 195., referer:
>> http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database
>> [Tue Mar 23 13:50:25 2010] [error] [client 136.159.4.22] *Use of
>> uninitialized value in concatenation (.) or string at
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm
>> line 139.*, referer:
>> http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database
>> [Tue Mar 23 13:50:26 2010] [error] [client 136.159.4.22] [2538] cleanup at
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm
>> line 199., referer:
>> http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database
>> [Tue Mar 23 13:50:26 2010] [error] [client 136.159.4.22] [2538] session
>> flush at
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm
>> line 203., referer:
>> http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database
>> [Tue Mar 23 13:50:26 2010] [error] [client 136.159.4.22] [2538] synchronous
>> exit at
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm
>> line 205., referer:
>> http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database
>> [Tue Mar 23 13:50:31 2010] [error] [client 136.159.4.22] [2541] RUN():
>> POST:
>> http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/action=navigate;navigate=left%200 at
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm
>> line 160., referer:
>> http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database
>> [Tue Mar 23 13:50:31 2010] [error] [client 136.159.4.22] [2541]
>> add_user_tracks() at
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm
>> line 167., referer:
>> http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database
>> [Tue Mar 23 13:50:31 2010] [error] [client 136.159.4.22] [2541] testing for
>> asynchronous event() at
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm
>> line 178., referer:
>> http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database
>> [Tue Mar 23 13:50:31 2010] [error] [client 136.159.4.22] [2541]
>> asynchronous exit at
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm
>> line 180., referer:
>> http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database
>> [Tue Mar 23 13:50:32 2010] [error] [client 136.159.4.22] [2549] RUN():
>> POST:
>> http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/action=update_sections;section_names=page_title;section_names=span;section_names=galaxy_form;section_names=search_form_objects
>> at
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm
>> line 160., referer:
>> http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database
>> [Tue Mar 23 13:50:32 2010] [error] [client 136.159.4.22] [2549]
>> add_user_tracks() at
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm
>> line 167., referer:
>> http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database
>> [Tue Mar 23 13:50:32 2010] [error] [client 136.159.4.22] [2549] testing for
>> asynchronous event() at
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm
>> line 178., referer:
>> http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database
>> [Tue Mar 23 13:50:32 2010] [error] [client 136.159.4.22] [2549]
>> asynchronous exit at
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm
>> line 180., referer:
>> http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database
>> *[Tue Mar 23 13:50:33 2010] [error] [client 136.159.4.22] [2550] RUN():
>> POST:
>> http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/action=retrieve_multiple;track_ids=DNA%2FGC%20Content;track_ids=Xenbase_XT_Gene_4.1;track_ids=Jgi_XT_Gene_4.1;track_ids=Jgi_XT_Mrna_4.1;track_ids=Ensembl_XT_Gene_4.1;track_ids=Gurdon_xt7.1_est;track_ids=%20H3K27me3_animal_ChIP-seq_st10-12_xenTro2%20WIG;tk_DNA%2FGC%20Content=63cc431bb4a3ae7ef5e6b6d708ee71c1;tk_Xenbase_XT_Gene_4.1=012653797c6e2ddd07ce56cfef2d3884;tk_Jgi_XT_Gene_4.1=4e7b66bd0c6f1a1416073694fef6352f;tk_Jgi_XT_Mrna_4.1=95da4a70614a3b23606e182662b0e4c4;tk_Ensembl_XT_Gene_4.1=c3b31b5e53cd8773545a5a2f6c77ce0e;tk_Gurdon_xt7.1_est=d73f47066f8f6d4e868d20ffa3c59148;tk_%20H3K27me3_animal_ChIP-seq_st10-12_xenTro2%20WIG=2a2bafb7bfe61a0489ccef1d400aeee0
>> at
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm
>> line 160., referer:
>> http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database
>> *
>> [Tue Mar 23 13:50:33 2010] [error] [client 136.159.4.22] [2550]
>> add_user_tracks() at
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm
>> line 167., referer:
>> http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database
>> [Tue Mar 23 13:50:33 2010] [error] [client 136.159.4.22] [2550] testing for
>> asynchronous event() at
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm
>> line 178., referer:
>> http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database
>> [Tue Mar 23 13:50:34 2010] [error] [client 136.159.4.22] [2550]
>> asynchronous exit at
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm
>> line 180., referer:
>> http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database
>>
>> Jeff Bowes M.Sc.
>> Technical Director, Xenbase
>> Department of Biological Sciences
>> University of Calgary
>> Calgary, Alberta T2N 1N4
>> CANADA
>> Tel: (403) 220-2824
>> Fax: (403) 284-4707
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
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>>
>>     
>
>
>   

-- 
Jeff Bowes M.Sc.
Technical Director, Xenbase
Department of Biological Sciences
University of Calgary
Calgary, Alberta T2N 1N4
CANADA
Tel: (403) 220-2824 
Fax: (403) 284-4707

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