[2023-10-03 08:16:29.383] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-03 08:16:29.383] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-03 08:16:29.383] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-03 08:16:29.383] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-03 08:16:29.383] [jointLog] [info] parsing read library format
[2023-10-03 08:16:29.383] [jointLog] [info] There is 1 library.
[2023-10-03 08:16:29.384] [jointLog] [info] Loading pufferfish index
[2023-10-03 08:16:29.384] [jointLog] [info] Loading dense pufferfish index.
[2023-10-03 08:17:45.978] [jointLog] [info] done
[2023-10-03 08:17:46.097] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-03 08:18:26.153] [jointLog] [info] Number of decoys : 194
[2023-10-03 08:18:26.153] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-03 08:18:27.863] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-03 08:18:28.970] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-03 08:19:08.121] [jointLog] [info] Thread saw mini-batch with a maximum of 3.53% zero probability fragments
[2023-10-03 08:19:08.211] [jointLog] [info] Thread saw mini-batch with a maximum of 3.34% zero probability fragments
[2023-10-03 08:19:08.223] [jointLog] [info] Thread saw mini-batch with a maximum of 3.30% zero probability fragments
[2023-10-03 08:19:08.468] [jointLog] [info] Thread saw mini-batch with a maximum of 3.28% zero probability fragments
[2023-10-03 08:19:08.486] [jointLog] [info] Thread saw mini-batch with a maximum of 3.44% zero probability fragments
[2023-10-03 08:19:08.517] [jointLog] [info] Thread saw mini-batch with a maximum of 3.28% zero probability fragments
[2023-10-03 08:19:08.630] [jointLog] [info] Thread saw mini-batch with a maximum of 3.24% zero probability fragments
[2023-10-03 08:19:08.648] [jointLog] [info] Thread saw mini-batch with a maximum of 3.24% zero probability fragments
[2023-10-03 08:19:08.842] [jointLog] [info] Computed 91,806 rich equivalence classes for further processing
[2023-10-03 08:19:08.842] [jointLog] [info] Counted 1,909,521 total reads in the equivalence classes 
[2023-10-03 08:19:08.850] [jointLog] [info] Number of mappings discarded because of alignment score : 48,459,908
[2023-10-03 08:19:08.850] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 252,193
[2023-10-03 08:19:08.850] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 57,626
[2023-10-03 08:19:08.850] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-03 08:19:08.843] [fileLog] [info] 
At end of round 0
==================
Observed 2560085 total fragments (2560085 in most recent round)

[2023-10-03 08:19:10.002] [jointLog] [warning] Only 1909521 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 08:19:10.002] [jointLog] [info] Mapping rate = 74.5882%

[2023-10-03 08:19:10.002] [jointLog] [info] finished quantifyLibrary()
[2023-10-03 08:19:10.003] [jointLog] [info] Starting optimizer
[2023-10-03 08:19:15.240] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-03 08:19:15.576] [jointLog] [info] iteration = 0 | max rel diff. = 36.1506
[2023-10-03 08:19:18.917] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-03 08:20:17.132] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-03 08:20:17.133] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-03 08:20:22.500] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-03 08:20:27.899] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-03 08:20:33.340] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-03 08:20:38.726] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-03 08:20:44.268] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-03 08:20:49.748] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-03 08:20:54.877] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-03 08:21:00.039] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-03 08:21:05.486] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-03 08:21:10.827] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-03 08:21:39.951] [jointLog] [info] iteration = 100 | max rel diff. = 7.88892
[2023-10-03 08:22:11.641] [jointLog] [info] iteration = 200 | max rel diff. = 1.76546
[2023-10-03 08:22:43.287] [jointLog] [info] iteration = 300 | max rel diff. = 0.441752
[2023-10-03 08:23:14.501] [jointLog] [info] iteration = 400 | max rel diff. = 16.4145
[2023-10-03 08:23:45.950] [jointLog] [info] iteration = 500 | max rel diff. = 0.189071
[2023-10-03 08:23:48.735] [jointLog] [info] iteration = 510 | max rel diff. = 0.00763967
[2023-10-03 08:23:50.925] [jointLog] [info] Finished optimizer
[2023-10-03 08:23:50.925] [jointLog] [info] writing output