There are two instances of the "a href=" problem on this page: http://igbquickload.org/D_discoideum_Ax4_May_2009/

There is an instance of the "a href=" problem here: http://igbquickload.org/D_melanogaster_Jul_2014/

There is no date for the release indicated in the title of this page: http://igbquickload.org/O_sativa_japonica_Oct_2011/

(All other genome assemblies included a date in the title)

There are two instances of the "a href=" problem on this page: http://igbquickload.org/P_patens_Jan_2008/

There is an instance of the "a href=" problem here: http://igbquickload.org/P_trichocarpa_Aug_2012/

There is no title indicating the genome on this page and there are two instances of the "a href=" problem: http://igbquickload.org/T_parvula_May_2012/

There is no header on this page: http://igbquickload.org/Y_lipolytica_CLIB122_Jul_2004/

There is no header on this page: http://igbquickload.org/Y_lipolytica_PO1f_May_2014/

There is no header on this page: http://igbquickload.org/Y_lipolytica_WSH-Z06_Mar_2014/

We should also examine the synonyms.txt, species.txt, and especially the chromosomes.txt files that are listed at the bottom of the Parent Directory. These files seemed like they may belong elsewhere.

Since you were able to find another instance of invalid html links, I applied some regular expressions to locate others.... documenting here so I will fix them.

./A_thaliana_Jun_2009/LFYAtTile1R/HEADER.md:10:href="http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28063">GSE28063</a>.
./A_thaliana_Jun_2009/LFYAtTile1R/HEADER.md:31:href="http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL10977">GPL10977</a>)
./A_thaliana_Jun_2009/cold_stress/HEADER.md:26:href="http://www.lorainelab.org">Loraine Lab</a> at <a
./A_thaliana_Jun_2009/cold_stress/HEADER.md:27:href="http://www.uncc.edu">UNC-Charlotte</a> in which we investigated
./D_discoideum_Ax4_May_2009/HEADER.md:11:href="http://www.transvar.org">Loraine Lab</a>) created all the files
./D_discoideum_Ax4_May_2009/HEADER.md:13:href="http://www.dictybase.org/Downloads/"> dictyBase file Download
./P_trichocarpa_Aug_2012/HEADER.md:21:href="http://samtools.sourceforge.net">samtools.sourceforge.net</a>
./D_melanogaster_Jul_2014/HEADER.md:11:href="ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r6.03_FB2014_06/gtf">ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r6.03_FB2014_06
./S_lycopersicum_May_2012/HEADER.md:12:href="http://samtools.sourceforge.net">samtools.sourceforge.net</a>
./P_patens_Jan_2008/HEADER.md:11:href="https://www.cosmoss.org/physcome_project/wiki/Downloads">Cossmoss.org
./P_patens_Jan_2008/HEADER.md:17:href="http://www.cosmoss.org">CossMoss</a>.
./T_parvula_May_2012/HEADER.md:7:href="http://www.bioviz.org/igb">BioViz.org</a>.
./T_parvula_May_2012/HEADER.md:30:href="http://samtools.sourceforge.net">samtools.sourceforge.net</a>

Applied fix
find -name HEADER.md -exec sed -i "s/^href/ href/" {} \;

Sending A_thaliana_Jun_2009/LFYAtTile1R/HEADER.md
Transmitting file data .
Committed revision 1145.
Sending A_thaliana_Jun_2009/cold_stress/HEADER.md
Transmitting file data .
Committed revision 1146.
Sending D_discoideum_Ax4_May_2009/HEADER.md
Transmitting file data .
Committed revision 1147.
Sending P_trichocarpa_Aug_2012/HEADER.md
Transmitting file data .
Committed revision 1148.
Sending D_melanogaster_Jul_2014/HEADER.md
Transmitting file data .
Committed revision 1149.
Sending S_lycopersicum_May_2012/HEADER.md
Transmitting file data .
Committed revision 1150.
Sending P_patens_Jan_2008/HEADER.md
Transmitting file data .
Committed revision 1151.
Sending T_parvula_May_2012/HEADER.md
Transmitting file data .
Committed revision 1152.

All instances of the "a href=" problem have been fixed. New stories IGBF-557 and IGBF-558 have been created to track the other issues with the Quickload Sites found while testing this story.

Since this story is resolved it will now be closed.