Won't load track details from previous session xml file

[ohmstead]

I have an issue loading a previous session from a session xml file.

In a previous session, I changed the track height and set track colors to correspond to their conditions. However, when I reload the session from file, it loads in the tracks in the grey color and default height.

In the xml file, it specifies their custom height and color changes. I'm a little bit at a loss for why IGV doesn't incorporate these details.

I'm on macOS Sonoma 14.5. Plotting RNA-seq data. Below is my session session file in full text, since GitHub won't allow an XML file upload.

Thanks!

<?xml version="1.0" encoding="UTF-8" standalone="no"?> <Session genome="mm39" hasGeneTrack="true" hasSequenceTrack="true" locus="chr19:5034541-5037701" nextAutoscaleGroup="5" path="/Volumes/jack/seq/analysis_May2024/sublibrary1/process/igv_only_coverage.xml" version="8"> <Resources> <Resource path="/Volumes/jack/seq/analysis_May2024/sublibrary1/process/sample_bams/dSE3.bam"/> <Resource path="/Volumes/jack/seq/analysis_May2024/sublibrary1/process/sample_bams/d30m1.bam"/> <Resource path="/Volumes/jack/seq/analysis_May2024/sublibrary1/process/sample_bams/d30m2.bam"/> <Resource path="/Volumes/jack/seq/analysis_May2024/sublibrary1/process/sample_bams/d6h2.bam"/> <Resource path="/Volumes/jack/seq/analysis_May2024/sublibrary1/process/sample_bams/KA2.bam"/> <Resource path="/Volumes/jack/seq/analysis_May2024/sublibrary1/process/sample_bams/d6h1.bam"/> <Resource path="/Volumes/jack/seq/analysis_May2024/sublibrary1/process/sample_bams/KA1.bam"/> <Resource path="/Volumes/jack/seq/analysis_May2024/sublibrary1/process/sample_bams/dSE2.bam"/> <Resource path="/Volumes/jack/seq/analysis_May2024/sublibrary1/process/sample_bams/dSE1.bam"/> <Resource path="/Volumes/jack/seq/analysis_May2024/sublibrary1/process/sample_bams/KA3.bam"/> <Resource path="/Volumes/jack/seq/analysis_May2024/sublibrary1/process/sample_bams/d30m3.bam"/> <Resource path="/Volumes/jack/seq/analysis_May2024/sublibrary1/process/sample_bams/d6h3.bam"/> </Resources> <Panel height="900" name="DataPanel" width="2543"> <Track autoScale="true" clazz="org.broad.igv.sam.CoverageTrack" color="30,136,229" colorScale="ContinuousColorScale;0.0;19.0;255,255,255;175,175,175" fontSize="15" height="75" id="/Volumes/jack/seq/analysis_May2024/sublibrary1/process/sample_bams/dSE1.bam_coverage" name="dSE1.bam Coverage" snpThreshold="0.2" visible="true"> <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="19.0" minimum="0.0" type="LINEAR"/> </Track> <Track autoScale="true" clazz="org.broad.igv.sam.CoverageTrack" color="30,136,229" colorScale="ContinuousColorScale;0.0;15.0;255,255,255;175,175,175" fontSize="15" height="75" id="/Volumes/jack/seq/analysis_May2024/sublibrary1/process/sample_bams/dSE2.bam_coverage" name="dSE2.bam Coverage" snpThreshold="0.2" visible="true"> <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="15.0" minimum="0.0" type="LINEAR"/> </Track> <Track autoScale="true" clazz="org.broad.igv.sam.CoverageTrack" color="30,136,229" colorScale="ContinuousColorScale;0.0;30.0;255,255,255;175,175,175" fontSize="15" height="75" id="/Volumes/jack/seq/analysis_May2024/sublibrary1/process/sample_bams/dSE3.bam_coverage" name="dSE3.bam Coverage" snpThreshold="0.2" visible="true"> <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="30.0" minimum="0.0" type="LINEAR"/> </Track> <Track autoScale="true" clazz="org.broad.igv.sam.CoverageTrack" color="216,27,96" colorScale="ContinuousColorScale;0.0;24.0;255,255,255;175,175,175" fontSize="15" height="75" id="/Volumes/jack/seq/analysis_May2024/sublibrary1/process/sample_bams/d30m1.bam_coverage" name="d30m1.bam Coverage" snpThreshold="0.2" visible="true"> <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="24.0" minimum="0.0" type="LINEAR"/> </Track> <Track autoScale="true" clazz="org.broad.igv.sam.CoverageTrack" color="216,27,96" colorScale="ContinuousColorScale;0.0;57.0;255,255,255;175,175,175" fontSize="15" height="75" id="/Volumes/jack/seq/analysis_May2024/sublibrary1/process/sample_bams/d30m2.bam_coverage" name="d30m2.bam Coverage" snpThreshold="0.2" visible="true"> <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="57.0" minimum="0.0" type="LINEAR"/> </Track> <Track autoScale="true" clazz="org.broad.igv.sam.CoverageTrack" color="216,27,96" colorScale="ContinuousColorScale;0.0;32.0;255,255,255;175,175,175" fontSize="15" height="75" id="/Volumes/jack/seq/analysis_May2024/sublibrary1/process/sample_bams/d30m3.bam_coverage" name="d30m3.bam Coverage" snpThreshold="0.2" visible="true"> <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="32.0" minimum="0.0" type="LINEAR"/> </Track> <Track autoScale="true" clazz="org.broad.igv.sam.CoverageTrack" color="255,193,7" colorScale="ContinuousColorScale;0.0;19.0;255,255,255;175,175,175" fontSize="15" height="75" id="/Volumes/jack/seq/analysis_May2024/sublibrary1/process/sample_bams/d6h1.bam_coverage" name="d6h1.bam Coverage" snpThreshold="0.2" visible="true"> <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="19.0" minimum="0.0" type="LINEAR"/> </Track> <Track autoScale="true" clazz="org.broad.igv.sam.CoverageTrack" color="255,193,7" colorScale="ContinuousColorScale;0.0;23.0;255,255,255;175,175,175" fontSize="15" height="75" id="/Volumes/jack/seq/analysis_May2024/sublibrary1/process/sample_bams/d6h2.bam_coverage" name="d6h2.bam Coverage" snpThreshold="0.2" visible="true"> <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="23.0" minimum="0.0" type="LINEAR"/> </Track> <Track autoScale="true" clazz="org.broad.igv.sam.CoverageTrack" color="255,193,7" colorScale="ContinuousColorScale;0.0;29.0;255,255,255;175,175,175" fontSize="15" height="75" id="/Volumes/jack/seq/analysis_May2024/sublibrary1/process/sample_bams/d6h3.bam_coverage" name="d6h3.bam Coverage" snpThreshold="0.2" visible="true"> <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="29.0" minimum="0.0" type="LINEAR"/> </Track> <Track autoScale="true" clazz="org.broad.igv.sam.CoverageTrack" color="9,129,84" colorScale="ContinuousColorScale;0.0;807.0;255,255,255;175,175,175" fontSize="15" height="75" id="/Volumes/jack/seq/analysis_May2024/sublibrary1/process/sample_bams/KA1.bam_coverage" name="KA1.bam Coverage" snpThreshold="0.2" visible="true"> <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="807.0" minimum="0.0" type="LINEAR"/> </Track> <Track autoScale="true" clazz="org.broad.igv.sam.CoverageTrack" color="9,129,84" colorScale="ContinuousColorScale;0.0;1295.0;255,255,255;175,175,175" fontSize="15" height="75" id="/Volumes/jack/seq/analysis_May2024/sublibrary1/process/sample_bams/KA2.bam_coverage" name="KA2.bam Coverage" snpThreshold="0.2" visible="true"> <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="1295.0" minimum="0.0" type="LINEAR"/> </Track> <Track autoScale="true" clazz="org.broad.igv.sam.CoverageTrack" color="9,129,84" colorScale="ContinuousColorScale;0.0;2392.0;255,255,255;175,175,175" fontSize="15" height="75" id="/Volumes/jack/seq/analysis_May2024/sublibrary1/process/sample_bams/KA3.bam_coverage" name="KA3.bam Coverage" snpThreshold="0.2" visible="true"> <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="2392.0" minimum="0.0" type="LINEAR"/> </Track> </Panel> <Panel height="285" name="FeaturePanel" width="2543"> <Track clazz="org.broad.igv.track.SequenceTrack" fontSize="10" height="72" id="Reference sequence" name="Reference sequence" visible="true"/> <Track altColor="0,0,178" clazz="org.broad.igv.track.FeatureTrack" color="0,0,178" colorScale="ContinuousColorScale;0.0;474.0;255,255,255;0,0,178" displayMode="EXPANDED" fontSize="10" height="73" id="mm39_genes" name="Gene" visible="true"/> </Panel> <PanelLayout dividerFractions="0.7544453852667231"/> <HiddenAttributes> <Attribute name="DATA FILE"/> <Attribute name="DATA TYPE"/> <Attribute name="NAME"/> </HiddenAttributes> </Session>

[jrobinso]

I can't really debug this visually, and could not load it even if you uploaded as it references local files. If you can diff the
before and after hand-edit and post the changes here we might be able to pinpoint something.

BTW you can zip the XML file, or any other type, and upload the zipped file

[ohmstead]

Here's a link to an example bam.

Also attached a zipped xml. I didn't hand-edit it at all. igv_only_coverage.xml.zip

Appreciate your help!

[jrobinso]

I can't load your example BAM, it has non-standard sequence names (mm39_1, etc).

[jrobinso]

Attached is a session with a blue coverage track (see screenshot). I created this with IGV 2.18.4. You should be able to load it, after unzipping, it uses a public bam file. If you can recreate your issue starting with this session please zip and post it here, along with the exact steps you took to reproduce it.

igv_session.xml.zip