[2023-10-03 18:30:58.082] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-03 18:30:58.082] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-03 18:30:58.082] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-03 18:30:58.082] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-03 18:30:58.082] [jointLog] [info] parsing read library format
[2023-10-03 18:30:58.082] [jointLog] [info] There is 1 library.
[2023-10-03 18:30:58.082] [jointLog] [info] Loading pufferfish index
[2023-10-03 18:30:58.082] [jointLog] [info] Loading dense pufferfish index.
[2023-10-03 18:32:22.358] [jointLog] [info] done
[2023-10-03 18:32:22.479] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-03 18:32:57.376] [jointLog] [info] Number of decoys : 194
[2023-10-03 18:32:57.376] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-03 18:32:58.715] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-03 18:32:59.810] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-03 18:33:50.352] [jointLog] [info] Thread saw mini-batch with a maximum of 3.00% zero probability fragments
[2023-10-03 18:33:50.376] [jointLog] [info] Thread saw mini-batch with a maximum of 3.10% zero probability fragments
[2023-10-03 18:33:50.405] [jointLog] [info] Thread saw mini-batch with a maximum of 3.26% zero probability fragments
[2023-10-03 18:33:50.486] [jointLog] [info] Thread saw mini-batch with a maximum of 3.42% zero probability fragments
[2023-10-03 18:33:50.525] [jointLog] [info] Thread saw mini-batch with a maximum of 3.26% zero probability fragments
[2023-10-03 18:33:50.578] [jointLog] [info] Thread saw mini-batch with a maximum of 3.22% zero probability fragments
[2023-10-03 18:33:50.669] [jointLog] [info] Thread saw mini-batch with a maximum of 3.08% zero probability fragments
[2023-10-03 18:33:50.714] [jointLog] [info] Thread saw mini-batch with a maximum of 3.26% zero probability fragments
[2023-10-03 18:33:50.837] [jointLog] [info] Computed 79,081 rich equivalence classes for further processing
[2023-10-03 18:33:50.837] [jointLog] [info] Counted 2,970,958 total reads in the equivalence classes 
[2023-10-03 18:33:50.844] [jointLog] [info] Number of mappings discarded because of alignment score : 63,746,552
[2023-10-03 18:33:50.844] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 400,249
[2023-10-03 18:33:50.844] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 91,132
[2023-10-03 18:33:50.844] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-03 18:33:50.838] [fileLog] [info] 
At end of round 0
==================
Observed 4067309 total fragments (4067309 in most recent round)

[2023-10-03 18:33:51.669] [jointLog] [warning] Only 2970958 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-10-03 18:33:51.669] [jointLog] [info] Mapping rate = 73.0448%

[2023-10-03 18:33:51.669] [jointLog] [info] finished quantifyLibrary()
[2023-10-03 18:33:51.669] [jointLog] [info] Starting optimizer
[2023-10-03 18:33:55.341] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-03 18:33:55.689] [jointLog] [info] iteration = 0 | max rel diff. = 73.2146
[2023-10-03 18:33:58.973] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-03 18:34:52.023] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-03 18:34:52.024] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-03 18:34:56.480] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-03 18:35:01.199] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-03 18:35:06.323] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-03 18:35:11.169] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-03 18:35:15.994] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-03 18:35:20.974] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-03 18:35:25.909] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-03 18:35:30.435] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-03 18:35:35.167] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-03 18:35:40.092] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-03 18:36:08.949] [jointLog] [info] iteration = 100 | max rel diff. = 9.46563
[2023-10-03 18:36:41.556] [jointLog] [info] iteration = 200 | max rel diff. = 5.00757
[2023-10-03 18:37:14.148] [jointLog] [info] iteration = 300 | max rel diff. = 0.241507
[2023-10-03 18:37:46.827] [jointLog] [info] iteration = 400 | max rel diff. = 0.179345
[2023-10-03 18:38:19.579] [jointLog] [info] iteration = 500 | max rel diff. = 0.0725469
[2023-10-03 18:38:52.755] [jointLog] [info] iteration = 600 | max rel diff. = 0.160071
[2023-10-03 18:39:25.852] [jointLog] [info] iteration = 700 | max rel diff. = 0.042771
[2023-10-03 18:39:35.837] [jointLog] [info] iteration = 731 | max rel diff. = 0.00783571
[2023-10-03 18:39:37.615] [jointLog] [info] Finished optimizer
[2023-10-03 18:39:37.615] [jointLog] [info] writing output