[2023-10-05 04:42:32.573] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-05 04:42:32.573] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-05 04:42:32.573] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-05 04:42:32.573] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-05 04:42:32.573] [jointLog] [info] parsing read library format
[2023-10-05 04:42:32.573] [jointLog] [info] There is 1 library.
[2023-10-05 04:42:32.573] [jointLog] [info] Loading pufferfish index
[2023-10-05 04:42:32.573] [jointLog] [info] Loading dense pufferfish index.
[2023-10-05 04:43:50.113] [jointLog] [info] done
[2023-10-05 04:43:50.238] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-05 04:44:29.059] [jointLog] [info] Number of decoys : 194
[2023-10-05 04:44:29.059] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-05 04:44:30.763] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-05 04:44:31.581] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-05 04:44:53.510] [jointLog] [info] Thread saw mini-batch with a maximum of 2.86% zero probability fragments
[2023-10-05 04:44:53.540] [jointLog] [info] Thread saw mini-batch with a maximum of 2.88% zero probability fragments
[2023-10-05 04:44:53.543] [jointLog] [info] Thread saw mini-batch with a maximum of 3.08% zero probability fragments
[2023-10-05 04:44:53.552] [jointLog] [info] Thread saw mini-batch with a maximum of 3.10% zero probability fragments
[2023-10-05 04:44:53.603] [jointLog] [info] Thread saw mini-batch with a maximum of 2.88% zero probability fragments
[2023-10-05 04:44:53.724] [jointLog] [info] Thread saw mini-batch with a maximum of 3.10% zero probability fragments
[2023-10-05 04:44:53.729] [jointLog] [info] Thread saw mini-batch with a maximum of 2.98% zero probability fragments
[2023-10-05 04:44:53.743] [jointLog] [info] Thread saw mini-batch with a maximum of 3.18% zero probability fragments
[2023-10-05 04:44:53.897] [jointLog] [info] Computed 57,267 rich equivalence classes for further processing
[2023-10-05 04:44:53.897] [jointLog] [info] Counted 1,189,789 total reads in the equivalence classes 
[2023-10-05 04:44:53.905] [jointLog] [info] Number of mappings discarded because of alignment score : 25,337,094
[2023-10-05 04:44:53.905] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 135,903
[2023-10-05 04:44:53.905] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 41,331
[2023-10-05 04:44:53.905] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-05 04:44:53.898] [fileLog] [info] 
At end of round 0
==================
Observed 1607502 total fragments (1607502 in most recent round)

[2023-10-05 04:44:54.930] [jointLog] [warning] Only 1189789 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-10-05 04:44:54.930] [jointLog] [info] Mapping rate = 74.0148%

[2023-10-05 04:44:54.930] [jointLog] [info] finished quantifyLibrary()
[2023-10-05 04:44:54.931] [jointLog] [info] Starting optimizer
[2023-10-05 04:44:59.372] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-05 04:44:59.707] [jointLog] [info] iteration = 0 | max rel diff. = 27.0134
[2023-10-05 04:45:03.100] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-05 04:45:42.340] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-05 04:45:42.340] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-05 04:45:45.912] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-05 04:45:49.406] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-05 04:45:52.943] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-05 04:45:56.472] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-05 04:46:00.082] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-05 04:46:03.593] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-05 04:46:07.078] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-05 04:46:10.595] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-05 04:46:14.078] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-05 04:46:17.922] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-05 04:46:48.372] [jointLog] [info] iteration = 100 | max rel diff. = 1.40926
[2023-10-05 04:47:21.969] [jointLog] [info] iteration = 200 | max rel diff. = 0.96301
[2023-10-05 04:47:56.048] [jointLog] [info] iteration = 300 | max rel diff. = 0.26203
[2023-10-05 04:48:29.951] [jointLog] [info] iteration = 400 | max rel diff. = 0.0827458
[2023-10-05 04:49:03.288] [jointLog] [info] iteration = 500 | max rel diff. = 0.231158
[2023-10-05 04:49:36.667] [jointLog] [info] iteration = 600 | max rel diff. = 0.189193
[2023-10-05 04:49:59.679] [jointLog] [info] iteration = 670 | max rel diff. = 0.00996374
[2023-10-05 04:50:01.774] [jointLog] [info] Finished optimizer
[2023-10-05 04:50:01.774] [jointLog] [info] writing output