[2023-09-25 09:16:31.660] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-25 09:16:31.660] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-25 09:16:31.660] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-25 09:16:31.660] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-25 09:16:31.660] [jointLog] [info] parsing read library format
[2023-09-25 09:16:31.660] [jointLog] [info] There is 1 library.
[2023-09-25 09:16:31.660] [jointLog] [info] Loading pufferfish index
[2023-09-25 09:16:31.660] [jointLog] [info] Loading dense pufferfish index.
[2023-09-25 09:17:50.001] [jointLog] [info] done
[2023-09-25 09:17:50.120] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-25 09:18:25.230] [jointLog] [info] Number of decoys : 194
[2023-09-25 09:18:25.230] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-25 09:18:26.723] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-25 09:18:27.869] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-25 09:18:54.067] [jointLog] [info] Thread saw mini-batch with a maximum of 3.82% zero probability fragments
[2023-09-25 09:18:54.072] [jointLog] [info] Thread saw mini-batch with a maximum of 3.76% zero probability fragments
[2023-09-25 09:18:54.146] [jointLog] [info] Thread saw mini-batch with a maximum of 3.94% zero probability fragments
[2023-09-25 09:18:54.224] [jointLog] [info] Thread saw mini-batch with a maximum of 3.94% zero probability fragments
[2023-09-25 09:18:54.411] [jointLog] [info] Thread saw mini-batch with a maximum of 3.88% zero probability fragments
[2023-09-25 09:18:54.446] [jointLog] [info] Thread saw mini-batch with a maximum of 3.54% zero probability fragments
[2023-09-25 09:18:54.583] [jointLog] [info] Thread saw mini-batch with a maximum of 3.48% zero probability fragments
[2023-09-25 09:18:54.591] [jointLog] [info] Thread saw mini-batch with a maximum of 3.72% zero probability fragments
[2023-09-25 09:18:54.719] [jointLog] [info] Computed 65,314 rich equivalence classes for further processing
[2023-09-25 09:18:54.719] [jointLog] [info] Counted 1,505,819 total reads in the equivalence classes 
[2023-09-25 09:18:54.726] [jointLog] [info] Number of mappings discarded because of alignment score : 31,932,960
[2023-09-25 09:18:54.726] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 184,573
[2023-09-25 09:18:54.726] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 48,590
[2023-09-25 09:18:54.726] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-25 09:18:54.720] [fileLog] [info] 
At end of round 0
==================
Observed 1963414 total fragments (1963414 in most recent round)

[2023-09-25 09:18:55.555] [jointLog] [warning] Only 1505819 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-25 09:18:55.555] [jointLog] [info] Mapping rate = 76.6939%

[2023-09-25 09:18:55.555] [jointLog] [info] finished quantifyLibrary()
[2023-09-25 09:18:55.556] [jointLog] [info] Starting optimizer
[2023-09-25 09:18:59.952] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-25 09:19:00.329] [jointLog] [info] iteration = 0 | max rel diff. = 33.814
[2023-09-25 09:19:03.755] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-25 09:19:50.216] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-25 09:19:50.218] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-25 09:19:54.165] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-25 09:19:58.174] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-25 09:20:02.359] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-25 09:20:06.740] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-25 09:20:10.700] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-25 09:20:15.037] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-25 09:20:19.032] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-25 09:20:23.286] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-25 09:20:27.664] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-25 09:20:31.698] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-25 09:21:00.994] [jointLog] [info] iteration = 100 | max rel diff. = 10.8835
[2023-09-25 09:21:32.508] [jointLog] [info] iteration = 200 | max rel diff. = 1.3742
[2023-09-25 09:22:03.711] [jointLog] [info] iteration = 300 | max rel diff. = 0.10305
[2023-09-25 09:22:36.642] [jointLog] [info] iteration = 400 | max rel diff. = 0.0943769
[2023-09-25 09:23:09.992] [jointLog] [info] iteration = 500 | max rel diff. = 0.127623
[2023-09-25 09:23:33.887] [jointLog] [info] iteration = 573 | max rel diff. = 0.00809222
[2023-09-25 09:23:36.399] [jointLog] [info] Finished optimizer
[2023-09-25 09:23:36.399] [jointLog] [info] writing output