[2023-09-23 18:34:02.427] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-23 18:34:02.427] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-23 18:34:02.427] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-23 18:34:02.427] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-23 18:34:02.427] [jointLog] [info] parsing read library format
[2023-09-23 18:34:02.427] [jointLog] [info] There is 1 library.
[2023-09-23 18:34:02.427] [jointLog] [info] Loading pufferfish index
[2023-09-23 18:34:02.427] [jointLog] [info] Loading dense pufferfish index.
[2023-09-23 18:35:27.254] [jointLog] [info] done
[2023-09-23 18:35:27.423] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-23 18:36:07.810] [jointLog] [info] Number of decoys : 194
[2023-09-23 18:36:07.810] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-23 18:36:09.796] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-23 18:36:10.755] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-23 18:36:41.343] [jointLog] [info] Thread saw mini-batch with a maximum of 4.16% zero probability fragments
[2023-09-23 18:36:41.437] [jointLog] [info] Thread saw mini-batch with a maximum of 4.46% zero probability fragments
[2023-09-23 18:36:41.498] [jointLog] [info] Thread saw mini-batch with a maximum of 4.40% zero probability fragments
[2023-09-23 18:36:41.503] [jointLog] [info] Thread saw mini-batch with a maximum of 4.32% zero probability fragments
[2023-09-23 18:36:41.638] [jointLog] [info] Thread saw mini-batch with a maximum of 4.22% zero probability fragments
[2023-09-23 18:36:41.722] [jointLog] [info] Thread saw mini-batch with a maximum of 4.46% zero probability fragments
[2023-09-23 18:36:41.845] [jointLog] [info] Thread saw mini-batch with a maximum of 4.48% zero probability fragments
[2023-09-23 18:36:41.926] [jointLog] [info] Thread saw mini-batch with a maximum of 4.92% zero probability fragments
[2023-09-23 18:36:42.171] [jointLog] [info] Computed 65,784 rich equivalence classes for further processing
[2023-09-23 18:36:42.171] [jointLog] [info] Counted 1,443,672 total reads in the equivalence classes 
[2023-09-23 18:36:42.194] [jointLog] [info] Number of mappings discarded because of alignment score : 24,131,639
[2023-09-23 18:36:42.194] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 144,368
[2023-09-23 18:36:42.194] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 51,278
[2023-09-23 18:36:42.194] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-23 18:36:42.172] [fileLog] [info] 
At end of round 0
==================
Observed 1944983 total fragments (1944983 in most recent round)

[2023-09-23 18:36:43.626] [jointLog] [warning] Only 1443672 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-23 18:36:43.626] [jointLog] [info] Mapping rate = 74.2254%

[2023-09-23 18:36:43.626] [jointLog] [info] finished quantifyLibrary()
[2023-09-23 18:36:43.626] [jointLog] [info] Starting optimizer
[2023-09-23 18:36:48.772] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-23 18:36:49.116] [jointLog] [info] iteration = 0 | max rel diff. = 31.5062
[2023-09-23 18:36:52.623] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-23 18:37:47.792] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-23 18:37:47.793] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-23 18:37:52.865] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-23 18:37:58.173] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-23 18:38:03.648] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-23 18:38:08.980] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-23 18:38:14.379] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-23 18:38:19.936] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-23 18:38:25.186] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-23 18:38:31.371] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-23 18:38:37.441] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-23 18:38:43.108] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-23 18:39:16.026] [jointLog] [info] iteration = 100 | max rel diff. = 1.2897
[2023-09-23 18:39:52.617] [jointLog] [info] iteration = 200 | max rel diff. = 3.97252
[2023-09-23 18:40:29.319] [jointLog] [info] iteration = 300 | max rel diff. = 11.7868
[2023-09-23 18:41:05.449] [jointLog] [info] iteration = 400 | max rel diff. = 0.106323
[2023-09-23 18:41:41.799] [jointLog] [info] iteration = 500 | max rel diff. = 0.0128509
[2023-09-23 18:42:18.470] [jointLog] [info] iteration = 600 | max rel diff. = 1.19666
[2023-09-23 18:42:54.314] [jointLog] [info] iteration = 700 | max rel diff. = 0.132928
[2023-09-23 18:42:57.640] [jointLog] [info] iteration = 710 | max rel diff. = 0.0072541
[2023-09-23 18:43:00.114] [jointLog] [info] Finished optimizer
[2023-09-23 18:43:00.114] [jointLog] [info] writing output