[2023-10-04 19:00:19.557] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-04 19:00:19.557] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-04 19:00:19.557] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-04 19:00:19.557] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-04 19:00:19.557] [jointLog] [info] parsing read library format
[2023-10-04 19:00:19.557] [jointLog] [info] There is 1 library.
[2023-10-04 19:00:19.557] [jointLog] [info] Loading pufferfish index
[2023-10-04 19:00:19.557] [jointLog] [info] Loading dense pufferfish index.
[2023-10-04 19:01:39.936] [jointLog] [info] done
[2023-10-04 19:01:40.101] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-04 19:02:21.702] [jointLog] [info] Number of decoys : 194
[2023-10-04 19:02:21.702] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-04 19:02:23.267] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-04 19:02:24.698] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-04 19:03:37.745] [jointLog] [info] Thread saw mini-batch with a maximum of 3.72% zero probability fragments
[2023-10-04 19:03:37.749] [jointLog] [info] Thread saw mini-batch with a maximum of 3.80% zero probability fragments
[2023-10-04 19:03:37.977] [jointLog] [info] Thread saw mini-batch with a maximum of 3.94% zero probability fragments
[2023-10-04 19:03:37.989] [jointLog] [info] Thread saw mini-batch with a maximum of 3.88% zero probability fragments
[2023-10-04 19:03:37.999] [jointLog] [info] Thread saw mini-batch with a maximum of 3.74% zero probability fragments
[2023-10-04 19:03:38.011] [jointLog] [info] Thread saw mini-batch with a maximum of 3.78% zero probability fragments
[2023-10-04 19:03:38.059] [jointLog] [info] Thread saw mini-batch with a maximum of 3.94% zero probability fragments
[2023-10-04 19:03:38.288] [jointLog] [info] Thread saw mini-batch with a maximum of 3.66% zero probability fragments
[2023-10-04 19:03:38.489] [jointLog] [info] Computed 88,819 rich equivalence classes for further processing
[2023-10-04 19:03:38.489] [jointLog] [info] Counted 3,469,535 total reads in the equivalence classes 
[2023-10-04 19:03:38.496] [jointLog] [info] Number of mappings discarded because of alignment score : 62,793,338
[2023-10-04 19:03:38.496] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 344,726
[2023-10-04 19:03:38.496] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 99,531
[2023-10-04 19:03:38.496] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-04 19:03:38.489] [fileLog] [info] 
At end of round 0
==================
Observed 4569605 total fragments (4569605 in most recent round)

[2023-10-04 19:03:39.473] [jointLog] [warning] Only 3469535 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-10-04 19:03:39.473] [jointLog] [info] Mapping rate = 75.9264%

[2023-10-04 19:03:39.473] [jointLog] [info] finished quantifyLibrary()
[2023-10-04 19:03:39.474] [jointLog] [info] Starting optimizer
[2023-10-04 19:03:43.717] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-04 19:03:44.060] [jointLog] [info] iteration = 0 | max rel diff. = 74.2379
[2023-10-04 19:03:47.531] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-04 19:04:57.290] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-04 19:04:57.290] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-04 19:05:03.576] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-04 19:05:10.462] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-04 19:05:17.234] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-04 19:05:24.431] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-04 19:05:31.359] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-04 19:05:37.866] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-04 19:05:43.538] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-04 19:05:49.541] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-04 19:05:55.961] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-04 19:06:03.177] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-04 19:06:34.432] [jointLog] [info] iteration = 100 | max rel diff. = 7.98695
[2023-10-04 19:07:09.655] [jointLog] [info] iteration = 200 | max rel diff. = 3.86433
[2023-10-04 19:07:45.286] [jointLog] [info] iteration = 300 | max rel diff. = 16.7342
[2023-10-04 19:08:20.983] [jointLog] [info] iteration = 400 | max rel diff. = 3.2802
[2023-10-04 19:08:56.573] [jointLog] [info] iteration = 500 | max rel diff. = 0.124106
[2023-10-04 19:09:31.514] [jointLog] [info] iteration = 600 | max rel diff. = 0.0413664
[2023-10-04 19:10:06.102] [jointLog] [info] iteration = 700 | max rel diff. = 0.316419
[2023-10-04 19:10:41.296] [jointLog] [info] iteration = 800 | max rel diff. = 0.0170543
[2023-10-04 19:11:16.545] [jointLog] [info] iteration = 900 | max rel diff. = 0.0417534
[2023-10-04 19:11:50.340] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.056401
[2023-10-04 19:11:56.724] [jointLog] [info] iteration = 1,020 | max rel diff. = 0.00592225
[2023-10-04 19:11:58.623] [jointLog] [info] Finished optimizer
[2023-10-04 19:11:58.623] [jointLog] [info] writing output