[AbstractTrack.java:1189] Unrecognized DataRange

[Kyle Williams]

Hello,

I received the above error when attempting to launch and igv session via xml. I am using a user defined genome. I am not positive, but I believe the error is the result of the following lines in the xml:

<Track attributeKey="Reference sequence" clazz="org.broad.igv.track.SequenceTrack" fontSize="10" id="Reference sequence" name="Reference sequence" visible="true"/>

        <Track altColor="0,0,178" attributeKey="RefSeq Genes" clazz="org.broad.igv.track.FeatureTrack" color="0,0,178" colorScale="ContinuousColorScale;0.0;373.0;255,255,255;0,0,178" fontSize="10" height="35" id="hg19_genes" name="RefSeq Genes" visible="true"/>

The session is using the following:
genome="hg19"

I have attached my preferences file, igv.log, proprty.txt, and genomes.txt files. 

Thank you for your time,

Kyle

[Kyle Williams]

The files can be found here:

https://drive.google.com/drive/folders/1JlW6EzLBxFrmncKXaMYwyRDR7xyXVdvT?usp=sharing

[James Robinson]

Thanks for the files.    How was the ".genome" file created, and has it every worked?   Could you share the ".genome" file?

Also, you are using an out-of-date IGV.   Could you try the latest version?

[Kyle Williams]

The genome file was created by zipping the property.txt, cytoband, refgene, and alias file. I have attached the .genome file. Essentially what I did was use the same hg19 ID, so existing sessions that used the default Human hg19 could be compatible with the updated reference, namely the inclusion of the Cambridge mitochondrial sequence. 

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[James Robinson]

Using the same ID as an IGV hosted genome is likely to cause unpredictable behavior.     Secondly, by specifying.  genome="hg19",  in your session you are triggering a download of hg19 from our server, most likely, but again I can't really predict the behavior.   When referencing a custom genome you should use the full path to the ".genome" file in your session,  not an ID.

The only comment about the .genome file is the fasta reference is just a filename,  not a full path or URL.   I don't honestly know what path this is going to resolve to, and its probably OS dependent.

[Kyle Williams]

Thank you, that was very helpful. Out of curiosity, if I used my own Ref Seq file, how would that affect the id="hg19_genes" name="XYZ RefSeq Genes" portion of the xml? Since the _genes part is not one of the input resources within the xml file, how is that generated as well as if that ID needs to be consistent with the others in the .genome file. 

Thank you for your time,

Kyle

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/182f38b6-e163-4490-ad44-250475616f9fn%40googlegroups.com.

[James Robinson]

If you are generating session XML yourself I suggest you just specify the resources section, and not try to generate. the "panels" entries you are referring to.    If you do want to generate panels don't use a ".genome" file,  or leave the gene annotations out (they are optional), and just load them as you would any annotation track.