Wow, that seems to have done the trick. After going to Genomes>Load From File, the genome loaded fine. I then tried to open my session and that worked as well. This is all after deleting the log file but I doubt that could have been it...? The non-snapshot of IGV is working properly now, too. The log is below. Thanks!!
INFO [2016-08-19 15:19:50,751] [Main.java:135] Startup IGV Version Snapshot (690 (690))08/19/2016 03:26 PM
INFO [2016-08-19 15:19:50,752] [Main.java:136] Java 1.8.0_101
INFO [2016-08-19 15:19:50,752] [DirectoryManager.java:72] Fetching user directory...
INFO [2016-08-19 15:19:51,254] [Main.java:137] Default User Directory: /Users/Dan
INFO [2016-08-19 15:19:51,254] [Main.java:138] OS: Mac OS X
INFO [2016-08-19 15:19:56,016] [GenomeManager.java:145] Loading genome: /Users/Dan/Documents/Genome/From_genometools_rev765/S_cerevisiae_r64.genome
INFO [2016-08-19 15:19:57,145] [GenomeManager.java:192] Genome loaded. id= S. cerevisiae r64
INFO [2016-08-19 15:19:57,241] [CommandListener.java:106] Listening on port 60151
INFO [2016-08-19 15:20:50,894] [IGV.java:641] Loading genome:
file.name=SK1 rebuild.genome file.path=/Volumes/dsantos/igv/genomes/SK1 rebuild.genome file.absolutePath=/Volumes/dsantos/igv/genomes/SK1 rebuild.genome
INFO [2016-08-19 15:20:51,289] [GenomeManager.java:145] Loading genome: /Volumes/dsantos/igv/genomes/SK1 rebuild.genome
INFO [2016-08-19 15:20:51,574] [GenomeManager.java:192] Genome loaded. id= SK1 rebuild
INFO [2016-08-19 15:21:16,669] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_04_rpf_rc.tdf
INFO [2016-08-19 15:21:16,675] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_07_rpf_rc.tdf
INFO [2016-08-19 15:21:16,675] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_01_rna_rc.tdf
INFO [2016-08-19 15:21:16,675] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_09_rpf_fw.tdf
INFO [2016-08-19 15:21:16,675] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_08_rpf_rc.tdf
INFO [2016-08-19 15:21:16,675] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_02_rna_rc.tdf
INFO [2016-08-19 15:21:16,675] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_05_rna_fw.tdf
INFO [2016-08-19 15:21:16,675] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_10_rna_rc.tdf
INFO [2016-08-19 15:21:16,675] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_01_rna_fw.tdf
INFO [2016-08-19 15:21:16,674] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_04_rna_fw.tdf
INFO [2016-08-19 15:21:16,674] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_02_rna_fw.tdf
INFO [2016-08-19 15:21:16,674] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_03_rna_fw.tdf
INFO [2016-08-19 15:21:16,674] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_07_rna_fw.tdf
INFO [2016-08-19 15:21:16,674] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_05_rna_rc.tdf
INFO [2016-08-19 15:21:16,674] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_04_rna_rc.tdf
INFO [2016-08-19 15:21:16,674] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_08_rna_fw.tdf
INFO [2016-08-19 15:21:16,674] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_06_rna_fw.tdf
INFO [2016-08-19 15:21:16,674] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_09_rna_fw.tdf
INFO [2016-08-19 15:21:16,669] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_08_rpf_fw.tdf
INFO [2016-08-19 15:21:16,669] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_06_rpf_rc.tdf
INFO [2016-08-19 15:21:16,674] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_07_rna_rc.tdf
INFO [2016-08-19 15:21:16,673] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_03_rna_rc.tdf
INFO [2016-08-19 15:21:16,673] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_06_rna_rc.tdf
INFO [2016-08-19 15:21:16,673] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_09_rna_rc.tdf
INFO [2016-08-19 15:21:16,673] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_01_rpf_fw.tdf
INFO [2016-08-19 15:21:16,673] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_10_rpf_rc.tdf
INFO [2016-08-19 15:21:16,673] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_08_rna_rc.tdf
INFO [2016-08-19 15:21:16,673] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_01_rpf_rc.tdf
INFO [2016-08-19 15:21:16,673] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_10_rpf_fw.tdf
INFO [2016-08-19 15:21:16,672] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_04_rpf_fw.tdf
INFO [2016-08-19 15:21:16,672] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_03_rpf_fw.tdf
INFO [2016-08-19 15:21:16,672] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_02_rpf_fw.tdf
INFO [2016-08-19 15:21:16,672] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/libraries/SK1_sanger/SK1_sanger_26_2_crossmap.bed
INFO [2016-08-19 15:21:16,672] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_03_rpf_rc.tdf
INFO [2016-08-19 15:21:16,671] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_10_rna_fw.tdf
INFO [2016-08-19 15:21:16,671] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_05_rpf_fw.tdf
INFO [2016-08-19 15:21:16,670] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_02_rpf_rc.tdf
INFO [2016-08-19 15:21:16,670] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_07_rpf_fw.tdf
INFO [2016-08-19 15:21:16,670] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_06_rpf_fw.tdf
INFO [2016-08-19 15:21:16,670] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_09_rpf_rc.tdf
INFO [2016-08-19 15:21:16,670] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_05_rpf_rc.tdf
INFO [2016-08-19 15:23:04,835] [Main.java:133] Startup IGV Version 2.3.80 (119)08/04/2016 05:06 PM
INFO [2016-08-19 15:23:04,861] [Main.java:134] Java 1.8.0_101
INFO [2016-08-19 15:23:04,861] [DirectoryManager.java:72] Fetching user directory...
INFO [2016-08-19 15:23:05,384] [Main.java:135] Default User Directory: /Users/Dan
INFO [2016-08-19 15:23:05,385] [Main.java:136] OS: Mac OS X
INFO [2016-08-19 15:23:12,614] [GenomeManager.java:145] Loading genome: /Volumes/dsantos/igv/genomes/SK1 rebuild.genome
INFO [2016-08-19 15:23:13,368] [GenomeManager.java:192] Genome loaded. id= SK1 rebuild
ERROR [2016-08-19 15:23:13,379] [ReferenceFrame.java:682] Null chromosome:
ERROR [2016-08-19 15:23:13,519] [CommandListener.java:124] java.net.BindException: Address already in use
INFO [2016-08-19 15:23:26,270] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_04_rpf_rc.tdf
INFO [2016-08-19 15:23:26,277] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_07_rpf_rc.tdf
INFO [2016-08-19 15:23:26,276] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_01_rna_rc.tdf
INFO [2016-08-19 15:23:26,276] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_09_rpf_fw.tdf
INFO [2016-08-19 15:23:26,276] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_08_rpf_rc.tdf
INFO [2016-08-19 15:23:26,276] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_02_rna_rc.tdf
INFO [2016-08-19 15:23:26,276] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_05_rna_fw.tdf
INFO [2016-08-19 15:23:26,276] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_10_rna_rc.tdf
INFO [2016-08-19 15:23:26,276] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_01_rna_fw.tdf
INFO [2016-08-19 15:23:26,276] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_04_rna_fw.tdf
INFO [2016-08-19 15:23:26,276] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_02_rna_fw.tdf
INFO [2016-08-19 15:23:26,276] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_03_rna_fw.tdf
INFO [2016-08-19 15:23:26,275] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_07_rna_fw.tdf
INFO [2016-08-19 15:23:26,275] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_05_rna_rc.tdf
INFO [2016-08-19 15:23:26,275] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_04_rna_rc.tdf
INFO [2016-08-19 15:23:26,275] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_08_rna_fw.tdf
INFO [2016-08-19 15:23:26,275] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_06_rna_fw.tdf
INFO [2016-08-19 15:23:26,275] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_09_rna_fw.tdf
INFO [2016-08-19 15:23:26,275] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_07_rna_rc.tdf
INFO [2016-08-19 15:23:26,275] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_03_rna_rc.tdf
INFO [2016-08-19 15:23:26,274] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_06_rna_rc.tdf
INFO [2016-08-19 15:23:26,274] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_09_rna_rc.tdf
INFO [2016-08-19 15:23:26,274] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_01_rpf_fw.tdf
INFO [2016-08-19 15:23:26,274] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_10_rpf_rc.tdf
INFO [2016-08-19 15:23:26,274] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_08_rna_rc.tdf
INFO [2016-08-19 15:23:26,274] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_01_rpf_rc.tdf
INFO [2016-08-19 15:23:26,274] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_10_rpf_fw.tdf
INFO [2016-08-19 15:23:26,273] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/libraries/SK1_sanger/SK1_sanger_26_2_crossmap.bed
INFO [2016-08-19 15:23:26,273] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_03_rpf_rc.tdf
INFO [2016-08-19 15:23:26,274] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_04_rpf_fw.tdf
INFO [2016-08-19 15:23:26,272] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/mrna/igv/meiosis_10_rna_fw.tdf
INFO [2016-08-19 15:23:26,272] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_05_rpf_fw.tdf
INFO [2016-08-19 15:23:26,272] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_02_rpf_rc.tdf
INFO [2016-08-19 15:23:26,272] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_07_rpf_fw.tdf
INFO [2016-08-19 15:23:26,273] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_03_rpf_fw.tdf
INFO [2016-08-19 15:23:26,272] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_06_rpf_fw.tdf
INFO [2016-08-19 15:23:26,271] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_09_rpf_rc.tdf
INFO [2016-08-19 15:23:26,271] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_05_rpf_rc.tdf
INFO [2016-08-19 15:23:26,271] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_08_rpf_fw.tdf
INFO [2016-08-19 15:23:26,273] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_02_rpf_fw.tdf
INFO [2016-08-19 15:23:26,271] [TrackLoader.java:120] Loading resource, path /Volumes/dsantos/meiosis/rpf/igv/meiosis_06_rpf_rc.tdf