[2023-10-05 08:21:27.641] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-05 08:21:27.641] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-05 08:21:27.641] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-05 08:21:27.641] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-05 08:21:27.641] [jointLog] [info] parsing read library format
[2023-10-05 08:21:27.641] [jointLog] [info] There is 1 library.
[2023-10-05 08:21:27.641] [jointLog] [info] Loading pufferfish index
[2023-10-05 08:21:27.641] [jointLog] [info] Loading dense pufferfish index.
[2023-10-05 08:22:45.787] [jointLog] [info] done
[2023-10-05 08:22:45.943] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-05 08:23:25.988] [jointLog] [info] Number of decoys : 194
[2023-10-05 08:23:25.988] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-05 08:23:27.625] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-05 08:23:28.539] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-05 08:24:25.392] [jointLog] [info] Thread saw mini-batch with a maximum of 3.24% zero probability fragments
[2023-10-05 08:24:25.393] [jointLog] [info] Thread saw mini-batch with a maximum of 3.30% zero probability fragments
[2023-10-05 08:24:25.461] [jointLog] [info] Thread saw mini-batch with a maximum of 3.22% zero probability fragments
[2023-10-05 08:24:25.474] [jointLog] [info] Thread saw mini-batch with a maximum of 3.42% zero probability fragments
[2023-10-05 08:24:25.608] [jointLog] [info] Thread saw mini-batch with a maximum of 3.40% zero probability fragments
[2023-10-05 08:24:25.654] [jointLog] [info] Thread saw mini-batch with a maximum of 3.26% zero probability fragments
[2023-10-05 08:24:25.657] [jointLog] [info] Thread saw mini-batch with a maximum of 3.38% zero probability fragments
[2023-10-05 08:24:25.683] [jointLog] [info] Thread saw mini-batch with a maximum of 3.34% zero probability fragments
[2023-10-05 08:24:25.904] [jointLog] [info] Computed 94,029 rich equivalence classes for further processing
[2023-10-05 08:24:25.904] [jointLog] [info] Counted 3,498,971 total reads in the equivalence classes 
[2023-10-05 08:24:25.913] [jointLog] [info] Number of mappings discarded because of alignment score : 57,964,755
[2023-10-05 08:24:25.913] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 317,718
[2023-10-05 08:24:25.913] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 92,903
[2023-10-05 08:24:25.913] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-05 08:24:25.905] [fileLog] [info] 
At end of round 0
==================
Observed 4807129 total fragments (4807129 in most recent round)

[2023-10-05 08:24:27.698] [jointLog] [warning] Only 3498971 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-10-05 08:24:27.698] [jointLog] [info] Mapping rate = 72.7871%

[2023-10-05 08:24:27.698] [jointLog] [info] finished quantifyLibrary()
[2023-10-05 08:24:27.699] [jointLog] [info] Starting optimizer
[2023-10-05 08:24:33.368] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-05 08:24:33.731] [jointLog] [info] iteration = 0 | max rel diff. = 69.6184
[2023-10-05 08:24:37.415] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-05 08:25:42.400] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-05 08:25:42.400] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-05 08:25:47.884] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-05 08:25:53.646] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-05 08:25:59.304] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-05 08:26:04.914] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-05 08:26:10.412] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-05 08:26:16.213] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-05 08:26:21.759] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-05 08:26:27.534] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-05 08:26:33.271] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-05 08:26:38.618] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-05 08:27:08.131] [jointLog] [info] iteration = 100 | max rel diff. = 8.60079
[2023-10-05 08:27:40.684] [jointLog] [info] iteration = 200 | max rel diff. = 9.01129
[2023-10-05 08:28:13.120] [jointLog] [info] iteration = 300 | max rel diff. = 0.357614
[2023-10-05 08:28:45.502] [jointLog] [info] iteration = 400 | max rel diff. = 0.640507
[2023-10-05 08:29:17.947] [jointLog] [info] iteration = 500 | max rel diff. = 0.431601
[2023-10-05 08:29:52.839] [jointLog] [info] iteration = 600 | max rel diff. = 0.167277
[2023-10-05 08:30:24.606] [jointLog] [info] iteration = 700 | max rel diff. = 0.15526
[2023-10-05 08:30:56.176] [jointLog] [info] iteration = 800 | max rel diff. = 0.0313428
[2023-10-05 08:31:27.766] [jointLog] [info] iteration = 900 | max rel diff. = 0.0629067
[2023-10-05 08:31:59.517] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.132617
[2023-10-05 08:32:15.133] [jointLog] [info] iteration = 1,050 | max rel diff. = 0.00398065
[2023-10-05 08:32:17.073] [jointLog] [info] Finished optimizer
[2023-10-05 08:32:17.073] [jointLog] [info] writing output