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

Thu Mar 25 11:54:23 EDT 2010

Hey Scott, Dave:

I posted this on the gbrowse forums but have had not bites.  I'm really 
stuck on this and have no idea where or how to start debugging this.  
Any ideas?

Jeff

On 23/03/2010 2:17 PM, Jeff Bowes 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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