Hi, Ross.
There's nothing wrong.
You just got impatient and bailed out on the page
before it was done.
We did insert a flush(stdout) after the long snp markers
fetch finished (over 15 million now) so that the browser would
not get impatient waiting for the rest of the thing
to finish. However you yourself still need to be patient :)
Data Upload Complete (62 bytes)
Loaded 15625346 elements from snp129 table for mapping.
Mapped 226064 of 228694 (98.8%) of markers
These data are now available in the drop-down menus on the main page for
graphing.
FYI in GG upload format
you should have a marker followed by 1 or more numeric values that
are graphs. Poor GG is trying to interpret every (numeric) column
in your input after the snpId as another graph.
That's why you will see that 10 graphs have loaded.
Several of the columns will contain useless data.
The ones that say "log..." are the columns that
would probably be of most use to you.
Perhaps there is a way in Galaxy to select
just the columns you actually want to graph.
-Galt
On Fri, 19 Jun 2009, Ross Lazarus wrote:
> It's back! Same problem that got fixed in February - after a successful
> upload to genome graphs, the 'data upload complete' page is missing any
> button to proceed to viewing the data!
> Looks like a fix got overwritten?
>
> Here's the source from today - even less at the end than the previous bug
> report (see below for that previous report please) - note that the last
> <FORM> element is not being closed - nor is there a </body></html>
>
> ================source of page 19 june
> 2009=======================================
>
> <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
> <HTML>
> <HEAD>
>
>
> <META HTTP-EQUIV="Content-Type" CONTENT="text/html;CHARSET=iso-8859-1">
> <META http-equiv="Content-Script-Type" content="text/javascript">
> <META HTTP-EQUIV="Pragma" CONTENT="no-cache">
> <META HTTP-EQUIV="Expires" CONTENT="-1">
> <TITLE>
> Data Upload Complete (67 bytes) </TITLE>
> <LINK REL="STYLESHEET" HREF="../style/HGStyle.css" TYPE="text/css">
>
> </HEAD>
> <BODY BGCOLOR="#FFF9D2" LINK="#0000CC" VLINK="#330066" ALINK="#6600FF">
> <style type='text/css'>
> .trDrag {background-color:#EEEEEE;} .pale {background-color:#F8F8F8;}
> .inputBox {border: 2px inset #CCCCCC;}
> .greenRoof {border-top: 3px groove #008800;}
> .greenBox {border: 5px outset #008800;}
> .blueBox {border: 4px inset #000088;}
> </style>
> <A NAME="TOP"></A>
>
> <TABLE BORDER=0 CELLPADDING=0 CELLSPACING=0 WIDTH="100%">
>
> <!-- +++++++++++++++++++++ HOTLINKS BAR +++++++++++++++++++ -->
> <TR><TD COLSPAN=3 HEIGHT=40 >
> <table bgcolor="#000000" cellpadding="1" cellspacing="1" width="100%%"
> height="27">
> <tr bgcolor="#2636D1"><td valign="middle">
> <table BORDER=0 CELLSPACING=0 CELLPADDING=0 bgcolor="#2636D1"
> height="24"><TR>
> <TD VALIGN="middle"><font color="#89A1DE">
>
> <A HREF="../index.html?org=Human&db=hg18&hgsid=135739082"
> class="topbar">
> Home</A>
> <A HREF="../cgi-bin/hgGateway?org=Human&db=hg18&hgsid=135739082"
> class="topbar">
> Genomes</A>
> <A
> HREF="../cgi-bin/hgBlat?command=start&org=Human&db=hg18&hgsid=135739082"
> class="topbar"> Blat</A>
>
> <A
> HREF="../cgi-bin/hgTables?org=Human&db=hg18&hgsid=135739082&hgta_doMainPage=1"
> class="topbar">
> Tables</A>
> <A HREF="../cgi-bin/hgNear?org=Human&db=hg18&hgsid=135739082"
> class="topbar">
> Gene Sorter</A>
> <A HREF="../cgi-bin/hgPcr?org=Human&db=hg18&hgsid=135739082"
> class="topbar">
> PCR</A>
>
> <A
> HREF="../cgi-bin/hgGenome?org=Human&db=hg18&hgsid=135739082&hgGenome_doPsOutput=on"
> class="topbar">
> PDF/PS</A>
> <A
> HREF="../cgi-bin/hgSession?org=Human&db=hg18&hgsid=135739082&hgS_doMainPage=1"
> class="topbar">Session</A>
> <A HREF="../FAQ/" class="topbar">
> FAQ</A>
>
> <A HREF="../goldenPath/help/hgGenomeHelp.html"
> class="topbar">
>
> Help</A>
> </font></TD>
> </TR></TABLE>
> </TD></TR></TABLE>
> </TD></TR>
>
>
> <!-- +++++++++++++++++++++ CONTENT TABLES +++++++++++++++++++ -->
> <TR><TD COLSPAN=3>
> <!--outer table is for border purposes-->
> <TABLE WIDTH="100%" BGCOLOR="#888888" BORDER="0" CELLSPACING="0"
> CELLPADDING="1"><TR><TD>
> <TABLE BGCOLOR="#FFFEE8" WIDTH="100%" BORDER="0" CELLSPACING="0"
> CELLPADDING="0"><TR><TD>
> <TABLE BGCOLOR="#D9E4F8" BACKGROUND="../images/hr.gif"
> WIDTH="100%"><TR><TD>
> <FONT SIZE="4"><b>
>
> Data Upload Complete (67 bytes)</b></FONT></TD></TR></TABLE>
> <TABLE BGCOLOR="#FFFEE8" WIDTH="100%" CELLPADDING=0><TR><TH
> HEIGHT=10></TH></TR>
> <TR><TD WIDTH=10> </TD><TD>
>
>
> <FORM ACTION="../cgi-bin/hgGenome"><INPUT TYPE=HIDDEN NAME="hgsid"
> VALUE="135739082">Loaded 15625346 elements from snp129 table for
> mapping.<BR>
>
> ====================source ends here ============================
>>
>>
>
>
>
>
>
> On Sun, Feb 8, 2009 at 12:06 PM, Ross Lazarus <
> [email protected]> wrote:
>
>> Help please! I've been using GG from Galaxy for about 2 years but today,
>> when I went to make some nice pictures for my grant renewal (!), there
>> appears to be a new problem.
>>
>> Using a Galaxy constructed url like this:
>>
>> http://genome.ucsc.edu/cgi-bin/hgGenome?db=hg18&hgGenome_dataSetName=Plink%20sample%20wga%20data%20case%20control%20_CaCo_gg.track&hgGenome_dataSetDescription=GalaxyGG_data&hgGenome_formatType=best%20guess&hgGenome_markerType=best%20guess&hgGenome_columnLabels=first%20row&hgGenome_maxVal=&hgGenome_labelVals=&hgGenome_maxGapToFill=25000000&hgGenome_uploadFile=http%3A%2F%2Fgalaxy.esphealth.org%2Fdisplay_as%3Fid%3D477%26display_app%3Ducsc&hgGenome_doSubmitUpload=submit
>>
>> the data appear to upload fine, but the page that tells me how many snp and
>> where they mapped does not show the usual button to proceed to view the
>> karyotype, and when I view the page source, it is clearly truncated in the
>> middle of the form that usually shows that button - here's the source for
>> the UCSC page I'm getting after uploading (apparently successfully!) - note
>> where it ends - and no closing body or html tags:
>>
>>
>> ====================source=========================================================
>> <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
>> <HTML>
>> <HEAD>
>>
>>
>> <META HTTP-EQUIV="Content-Type"
>> CONTENT="text/html;CHARSET=iso-8859-1">
>> <META http-equiv="Content-Script-Type" content="text/javascript">
>> <META HTTP-EQUIV="Pragma" CONTENT="no-cache">
>> <META HTTP-EQUIV="Expires" CONTENT="-1">
>> <TITLE>
>> Data Upload Complete (62 bytes) </TITLE>
>> <LINK REL="STYLESHEET" HREF="../style/HGStyle.css" TYPE="text/css">
>>
>> </HEAD>
>> <BODY BGCOLOR="#FFF9D2" LINK="#0000CC" VLINK="#330066" ALINK="#6600FF"><A
>> NAME="TOP"></A>
>>
>> <TABLE BORDER=0 CELLPADDING=0 CELLSPACING=0 WIDTH="100%">
>>
>> <!-- +++++++++++++++++++++ HOTLINKS BAR +++++++++++++++++++ -->
>> <TR><TD COLSPAN=3 HEIGHT=40 >
>> <table bgcolor="#000000" cellpadding="1" cellspacing="1" width="100%%"
>> height="27">
>> <tr bgcolor="#2636D1"><td valign="middle">
>> <table BORDER=0 CELLSPACING=0 CELLPADDING=0 bgcolor="#2636D1"
>> height="24"><TR>
>> <TD VALIGN="middle"><font color="#89A1DE">
>>
>> <A HREF="../index.html?org=Human&db=hg18&hgsid=1605988"
>> class="topbar">
>> Home</A>
>> <A HREF="../cgi-bin/hgGateway?org=Human&db=hg18&hgsid=1605988"
>> class="topbar">
>> Genomes</A>
>> <A
>> HREF="../cgi-bin/hgBlat?command=start&org=Human&db=hg18&hgsid=1605988"
>> class="topbar"> Blat</A>
>> <A
>> HREF="../cgi-bin/hgTables?org=Human&db=hg18&hgsid=1605988&hgta_doMainPage=1"
>> class="topbar">
>> Tables</A>
>> <A HREF="../cgi-bin/hgNear?org=Human&db=hg18&hgsid=1605988"
>> class="topbar">
>> Gene Sorter</A>
>> <A HREF="../cgi-bin/hgPcr?org=Human&db=hg18&hgsid=1605988"
>> class="topbar">
>> PCR</A>
>> <A
>> HREF="../cgi-bin/hgGenome?org=Human&db=hg18&hgsid=1605988&hgGenome_doPsOutput=on"
>> class="topbar">
>> PDF/PS</A>
>> <A
>> HREF="../cgi-bin/hgSession?org=Human&db=hg18&hgsid=1605988&hgS_doMainPage=1"
>> class="topbar">Session</A>
>> <A HREF="../FAQ/" class="topbar">
>> FAQ</A>
>>
>> <A HREF="../goldenPath/help/hgGenomeHelp.html"
>> class="topbar">
>> Help</A>
>> </font></TD>
>> </TR></TABLE>
>> </TD></TR></TABLE>
>> </TD></TR>
>>
>>
>> <!-- +++++++++++++++++++++ CONTENT TABLES +++++++++++++++++++ -->
>> <TR><TD COLSPAN=3>
>> <!--outer table is for border purposes-->
>> <TABLE WIDTH="100%" BGCOLOR="#888888" BORDER="0" CELLSPACING="0"
>> CELLPADDING="1"><TR><TD>
>> <TABLE BGCOLOR="#FFFEE8" WIDTH="100%" BORDER="0" CELLSPACING="0"
>> CELLPADDING="0"><TR><TD>
>> <TABLE BGCOLOR="#D9E4F8" BACKGROUND="../images/hr.gif"
>> WIDTH="100%"><TR><TD>
>> <FONT SIZE="4"><b>
>> Data Upload Complete (62 bytes)</b></FONT></TD></TR></TABLE>
>> <TABLE BGCOLOR="#FFFEE8" WIDTH="100%" CELLPADDING=0><TR><TH
>> HEIGHT=10></TH></TR>
>> <TR><TD WIDTH=10> </TD><TD>
>>
>>
>> <FORM ACTION="../cgi-bin/hgGenome"><INPUT TYPE=HIDDEN NAME="hgsid"
>> VALUE="1605988">Loaded 15625346 elements from snp129 table for mapping.<BR>
>> Mapped 226064 of 228694 (98.8%) of markers<BR>
>>
>> ====================source ends here ===================================
>>
>>
>> -
>
>
>
>
> --
> Ross Lazarus MBBS MPH
> Associate Professor, Department of Population Medicine; Director of
> Bioinformatics, Channing Laboratory
> 181 Longwood Ave., Boston MA 02115, USA.
> Tel: +617 525 2730 Fax: +617 525 0958
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
>
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
