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Hey Scott, Dave:<br>
<br>
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?<br>
<br>
Jeff<br>
<br>
<br>
<br>
<br>
<br>
On 23/03/2010 2:17 PM, Jeff Bowes wrote:
<blockquote cite="mid:4BA921CA.8010006@ucalgary.ca" type="cite">Hi,<br>
<br>
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. <br>
<br>
The .wig file I received open as follows.<br>
<br>
<tt>browser position scaffold_163:520000-690000<br>
track type=wiggle_0 name=H3K27me3_animal_ChIP-seq_st10-12
maxHeightPixels=64:64:11 color=254,196,79 visibility=full<br>
fixedStep chrom=scaffold_1 start=321 step=10 span=10<br>
1<br>
1<br>
1</tt><br>
<br>
The scores range from 1 to 198,<br>
<br>
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 <br>
<tt><br>
##gff-version 3<br>
<br>
</tt><tt>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<br>
</tt><br>
This wiggle file was loaded into mysql using the
bp_seqfeature_load.pl. The load did not seem to produce any errors.<br>
<br>
The last track definition I tried in the config file was:<br>
<tt><br>
[H3K27me3_animal_ChIP-seq_st10-12_xenTro2 WIG]<br>
feature = H3K27me3_animal_ChIP-seq_st10-12_xenTro2<br>
glyph = wiggle_xyplot<br>
min_score = 1<br>
max_score = 198<br>
key = H3K27 animal ChiP-seq_Xenopus Tropicalis stages 10 to 12<br>
<br>
The key appears but no glyphs appear under the key on that track.<br>
</tt><br>
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.<br>
<br>
Thanks, <br>
<br>
Jeff<br>
<br>
error_log output follows:<br>
<br>
[Tue Mar 23 13:50:25 2010] [error] [client 136.159.4.22] [2538] RUN():
POST:
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/">http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/</a>
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:
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database">http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database</a><br>
[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:
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database">http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database</a><br>
[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:
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database">http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database</a><br>
[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:
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database">http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database</a><br>
[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:
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database">http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database</a><br>
[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:
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database">http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database</a><br>
[Tue Mar 23 13:50:25 2010] [error] [client 136.159.4.22] <b>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.</b>, referer:
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database">http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database</a><br>
[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:
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database">http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database</a><br>
[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:
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database">http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database</a><br>
[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:
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database">http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database</a><br>
[Tue Mar 23 13:50:31 2010] [error] [client 136.159.4.22] [2541] RUN():
POST:
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/">http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/</a>
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:
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database">http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database</a><br>
[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:
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database">http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database</a><br>
[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:
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database">http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database</a><br>
[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:
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database">http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database</a><br>
[Tue Mar 23 13:50:32 2010] [error] [client 136.159.4.22] [2549] RUN():
POST:
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/">http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/</a>
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:
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database">http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database</a><br>
[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:
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database">http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database</a><br>
[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:
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database">http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database</a><br>
[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:
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database">http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database</a><br>
<b>[Tue Mar 23 13:50:33 2010] [error] [client 136.159.4.22] [2550]
RUN(): POST:
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/">http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/</a>
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:
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database">http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database</a></b><br>
[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:
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database">http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database</a><br>
[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:
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database">http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database</a><br>
[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:
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database">http://xtropicalis.cpsc.ucalgary.ca/cgi-bin/gb2/gbrowse/Xenopus_tropicalis_4_1_mysql/?name=id:1198108;dbid=scaffolds:database</a><br>
<br>
<pre class="moz-signature" cols="72">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
</pre>
</blockquote>
<br>
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