[2023-08-27 15:51:10.429] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-08-27 15:51:10.429] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-08-27 15:51:10.429] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-08-27 15:51:10.429] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-08-27 15:51:10.429] [jointLog] [info] parsing read library format
[2023-08-27 15:51:10.429] [jointLog] [info] There is 1 library.
[2023-08-27 15:51:10.429] [jointLog] [info] Loading pufferfish index
[2023-08-27 15:51:10.429] [jointLog] [info] Loading dense pufferfish index.
[2023-08-27 15:52:29.307] [jointLog] [info] done
[2023-08-27 15:52:29.456] [jointLog] [info] Index contained 5,382,683 targets
[2023-08-27 15:53:08.568] [jointLog] [info] Number of decoys : 194
[2023-08-27 15:53:08.568] [jointLog] [info] First decoy index : 5,185,409 
[2023-08-27 15:53:10.450] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-08-27 15:53:11.454] [jointLog] [info] Automatically detected most likely library type as SF

[2023-08-27 16:00:28.379] [jointLog] [info] Thread saw mini-batch with a maximum of 2.48% zero probability fragments
[2023-08-27 16:00:28.611] [jointLog] [info] Thread saw mini-batch with a maximum of 2.74% zero probability fragments
[2023-08-27 16:00:28.677] [jointLog] [info] Thread saw mini-batch with a maximum of 2.52% zero probability fragments
[2023-08-27 16:00:28.724] [jointLog] [info] Thread saw mini-batch with a maximum of 2.62% zero probability fragments
[2023-08-27 16:00:28.985] [jointLog] [info] Thread saw mini-batch with a maximum of 2.58% zero probability fragments
[2023-08-27 16:00:29.036] [jointLog] [info] Thread saw mini-batch with a maximum of 2.64% zero probability fragments
[2023-08-27 16:00:29.080] [jointLog] [info] Thread saw mini-batch with a maximum of 2.52% zero probability fragments
[2023-08-27 16:00:29.271] [jointLog] [info] Thread saw mini-batch with a maximum of 2.66% zero probability fragments
[2023-08-27 16:00:29.564] [jointLog] [info] Computed 200,919 rich equivalence classes for further processing
[2023-08-27 16:00:29.564] [jointLog] [info] Counted 9,957,925 total reads in the equivalence classes 
[2023-08-27 16:00:29.571] [jointLog] [info] Number of mappings discarded because of alignment score : 581,169,028
[2023-08-27 16:00:29.571] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 6,256,853
[2023-08-27 16:00:29.571] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 436,383
[2023-08-27 16:00:29.571] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-08-27 16:00:29.571] [jointLog] [info] Mapping rate = 52.7658%

[2023-08-27 16:00:29.571] [jointLog] [info] finished quantifyLibrary()
[2023-08-27 16:00:29.572] [jointLog] [info] Starting optimizer
[2023-08-27 16:00:29.565] [fileLog] [info] 
At end of round 0
==================
Observed 18871924 total fragments (18871924 in most recent round)

[2023-08-27 16:00:33.968] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-08-27 16:00:34.309] [jointLog] [info] iteration = 0 | max rel diff. = 182.374
[2023-08-27 16:00:37.753] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-08-27 16:02:08.157] [jointLog] [info] Computed expected counts (for bias correction)
[2023-08-27 16:02:08.157] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-08-27 16:02:16.154] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-08-27 16:02:24.542] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-08-27 16:02:33.027] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-08-27 16:02:41.228] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-08-27 16:02:49.274] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-08-27 16:02:57.828] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-08-27 16:03:05.592] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-08-27 16:03:13.449] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-08-27 16:03:21.691] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-08-27 16:03:30.102] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-27 16:03:30.114] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-27 16:04:00.568] [jointLog] [info] iteration = 100 | max rel diff. = 15.8653
[2023-08-27 16:04:33.341] [jointLog] [info] iteration = 200 | max rel diff. = 2.42819
[2023-08-27 16:05:05.540] [jointLog] [info] iteration = 300 | max rel diff. = 3.99534
[2023-08-27 16:05:37.841] [jointLog] [info] iteration = 400 | max rel diff. = 0.0417089
[2023-08-27 16:06:10.642] [jointLog] [info] iteration = 500 | max rel diff. = 0.0283381
[2023-08-27 16:06:43.477] [jointLog] [info] iteration = 600 | max rel diff. = 0.766814
[2023-08-27 16:07:16.070] [jointLog] [info] iteration = 700 | max rel diff. = 0.375339
[2023-08-27 16:07:48.640] [jointLog] [info] iteration = 800 | max rel diff. = 0.0231399
[2023-08-27 16:07:55.571] [jointLog] [info] iteration = 822 | max rel diff. = 0.00533166
[2023-08-27 16:07:57.618] [jointLog] [info] Finished optimizer
[2023-08-27 16:07:57.618] [jointLog] [info] writing output