[2023-08-28 16:33:11.695] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-08-28 16:33:11.695] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-08-28 16:33:11.695] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-08-28 16:33:11.695] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-08-28 16:33:11.695] [jointLog] [info] parsing read library format
[2023-08-28 16:33:11.695] [jointLog] [info] There is 1 library.
[2023-08-28 16:33:11.695] [jointLog] [info] Loading pufferfish index
[2023-08-28 16:33:11.695] [jointLog] [info] Loading dense pufferfish index.
[2023-08-28 16:34:38.384] [jointLog] [info] done
[2023-08-28 16:34:38.532] [jointLog] [info] Index contained 5,382,683 targets
[2023-08-28 16:35:18.499] [jointLog] [info] Number of decoys : 194
[2023-08-28 16:35:18.499] [jointLog] [info] First decoy index : 5,185,409 
[2023-08-28 16:35:20.456] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-08-28 16:35:20.893] [jointLog] [info] Automatically detected most likely library type as SR

[2023-08-28 16:37:38.165] [jointLog] [info] Thread saw mini-batch with a maximum of 2.84% zero probability fragments
[2023-08-28 16:37:38.183] [jointLog] [info] Thread saw mini-batch with a maximum of 2.82% zero probability fragments
[2023-08-28 16:37:38.199] [jointLog] [info] Thread saw mini-batch with a maximum of 2.90% zero probability fragments
[2023-08-28 16:37:38.204] [jointLog] [info] Thread saw mini-batch with a maximum of 2.82% zero probability fragments
[2023-08-28 16:37:38.234] [jointLog] [info] Thread saw mini-batch with a maximum of 2.82% zero probability fragments
[2023-08-28 16:37:38.259] [jointLog] [info] Thread saw mini-batch with a maximum of 2.90% zero probability fragments
[2023-08-28 16:37:38.326] [jointLog] [info] Thread saw mini-batch with a maximum of 3.00% zero probability fragments
[2023-08-28 16:37:38.335] [jointLog] [info] Thread saw mini-batch with a maximum of 2.92% zero probability fragments
[2023-08-28 16:37:38.641] [fileLog] [info] 
At end of round 0
==================
Observed 21929457 total fragments (21929457 in most recent round)

[2023-08-28 16:37:38.640] [jointLog] [info] Computed 235,984 rich equivalence classes for further processing
[2023-08-28 16:37:38.640] [jointLog] [info] Counted 20,538,089 total reads in the equivalence classes 
[2023-08-28 16:37:38.647] [jointLog] [info] Number of mappings discarded because of alignment score : 22,692,191
[2023-08-28 16:37:38.647] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 335,108
[2023-08-28 16:37:38.647] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 211,547
[2023-08-28 16:37:38.647] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-08-28 16:37:38.647] [jointLog] [info] Mapping rate = 93.6553%

[2023-08-28 16:37:38.647] [jointLog] [info] finished quantifyLibrary()
[2023-08-28 16:37:38.649] [jointLog] [info] Starting optimizer
[2023-08-28 16:37:42.216] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-08-28 16:37:42.566] [jointLog] [info] iteration = 0 | max rel diff. = 287.819
[2023-08-28 16:37:46.037] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-08-28 16:39:09.142] [jointLog] [info] Computed expected counts (for bias correction)
[2023-08-28 16:39:09.143] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-08-28 16:39:17.342] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-08-28 16:39:24.726] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-08-28 16:39:32.344] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-08-28 16:39:39.736] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-08-28 16:39:46.827] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-08-28 16:39:54.350] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-08-28 16:40:01.290] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-08-28 16:40:08.010] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-08-28 16:40:14.804] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-08-28 16:40:22.061] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-28 16:40:22.063] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-28 16:40:53.230] [jointLog] [info] iteration = 100 | max rel diff. = 15.4007
[2023-08-28 16:41:37.684] [jointLog] [info] iteration = 200 | max rel diff. = 14.0417
[2023-08-28 16:42:38.568] [jointLog] [info] iteration = 300 | max rel diff. = 5.62693
[2023-08-28 16:43:35.530] [jointLog] [info] iteration = 400 | max rel diff. = 2.70335
[2023-08-28 16:44:35.163] [jointLog] [info] iteration = 500 | max rel diff. = 0.323602
[2023-08-28 16:45:31.117] [jointLog] [info] iteration = 600 | max rel diff. = 7.23254
[2023-08-28 16:46:24.332] [jointLog] [info] iteration = 700 | max rel diff. = 0.116781
[2023-08-28 16:47:15.747] [jointLog] [info] iteration = 800 | max rel diff. = 0.998398
[2023-08-28 16:48:08.894] [jointLog] [info] iteration = 900 | max rel diff. = 0.354923
[2023-08-28 16:49:02.052] [jointLog] [info] iteration = 1,000 | max rel diff. = 1.07879
[2023-08-28 16:49:54.281] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.150716
[2023-08-28 16:50:42.422] [jointLog] [info] iteration = 1,193 | max rel diff. = 0.00809021
[2023-08-28 16:50:45.019] [jointLog] [info] Finished optimizer
[2023-08-28 16:50:45.019] [jointLog] [info] writing output