[2022-12-20 23:52:16.188] [jointLog] [info] setting maxHashResizeThreads to 8
[2022-12-20 23:52:16.188] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2022-12-20 23:52:16.188] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2022-12-20 23:52:16.188] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2022-12-20 23:52:16.188] [jointLog] [info] parsing read library format
[2022-12-20 23:52:16.188] [jointLog] [info] There is 1 library.
[2022-12-20 23:52:16.188] [jointLog] [info] Loading pufferfish index
[2022-12-20 23:52:16.189] [jointLog] [info] Loading dense pufferfish index.
[2022-12-20 23:52:40.182] [jointLog] [info] done
[2022-12-20 23:52:40.235] [jointLog] [info] Index contained 147,889 targets
[2022-12-20 23:52:40.731] [jointLog] [info] Number of decoys : 61
[2022-12-20 23:52:40.731] [jointLog] [info] First decoy index : 147,789 
[2022-12-20 23:52:41.518] [jointLog] [info] Automatically detected most likely library type as ISR

[2022-12-20 23:55:41.401] [jointLog] [info] Thread saw mini-batch with a maximum of 0.26% zero probability fragments
[2022-12-20 23:55:41.407] [jointLog] [info] Thread saw mini-batch with a maximum of 0.24% zero probability fragments
[2022-12-20 23:55:41.429] [jointLog] [info] Thread saw mini-batch with a maximum of 0.28% zero probability fragments
[2022-12-20 23:55:41.491] [jointLog] [info] Thread saw mini-batch with a maximum of 0.26% zero probability fragments
[2022-12-20 23:55:41.565] [jointLog] [info] Thread saw mini-batch with a maximum of 0.26% zero probability fragments
[2022-12-20 23:55:41.575] [jointLog] [info] Thread saw mini-batch with a maximum of 0.22% zero probability fragments
[2022-12-20 23:55:41.601] [jointLog] [info] Thread saw mini-batch with a maximum of 0.28% zero probability fragments
[2022-12-20 23:55:41.770] [jointLog] [info] Thread saw mini-batch with a maximum of 0.24% zero probability fragments
[2022-12-20 23:55:42.001] [fileLog] [info] 
At end of round 0
==================
Observed 14987267 total fragments (14987267 in most recent round)

[2022-12-20 23:55:42.001] [jointLog] [info] Computed 250,681 rich equivalence classes for further processing
[2022-12-20 23:55:42.001] [jointLog] [info] Counted 12,000,229 total reads in the equivalence classes 
[2022-12-20 23:55:42.006] [jointLog] [info] Number of mappings discarded because of alignment score : 22,593,726
[2022-12-20 23:55:42.006] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 2,537,189
[2022-12-20 23:55:42.006] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 304,465
[2022-12-20 23:55:42.006] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 4,461,189
[2022-12-20 23:55:42.007] [jointLog] [info] Mapping rate = 80.0695%

[2022-12-20 23:55:42.007] [jointLog] [info] finished quantifyLibrary()
[2022-12-20 23:55:42.007] [jointLog] [info] Starting optimizer
[2022-12-20 23:55:42.097] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2022-12-20 23:55:42.111] [jointLog] [info] iteration = 0 | max rel diff. = 5921.2
[2022-12-20 23:55:42.256] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2022-12-20 23:55:43.592] [jointLog] [info] Computed expected counts (for bias correction)
[2022-12-20 23:55:43.592] [jointLog] [info] processed bias for 0.0% of the transcripts
[2022-12-20 23:55:44.477] [jointLog] [info] processed bias for 10.0% of the transcripts
[2022-12-20 23:55:45.419] [jointLog] [info] processed bias for 20.0% of the transcripts
[2022-12-20 23:55:46.275] [jointLog] [info] processed bias for 30.0% of the transcripts
[2022-12-20 23:55:47.081] [jointLog] [info] processed bias for 40.0% of the transcripts
[2022-12-20 23:55:47.592] [jointLog] [info] processed bias for 50.0% of the transcripts
[2022-12-20 23:55:48.363] [jointLog] [info] processed bias for 60.0% of the transcripts
[2022-12-20 23:55:49.233] [jointLog] [info] processed bias for 70.0% of the transcripts
[2022-12-20 23:55:50.098] [jointLog] [info] processed bias for 80.1% of the transcripts
[2022-12-20 23:55:50.925] [jointLog] [info] processed bias for 90.0% of the transcripts
[2022-12-20 23:55:51.744] [jointLog] [info] processed bias for 100.0% of the transcripts
[2022-12-20 23:55:51.746] [jointLog] [info] processed bias for 100.0% of the transcripts
[2022-12-20 23:55:53.002] [jointLog] [info] iteration = 100 | max rel diff. = 15.6118
[2022-12-20 23:55:54.485] [jointLog] [info] iteration = 200 | max rel diff. = 13.2333
[2022-12-20 23:55:55.922] [jointLog] [info] iteration = 300 | max rel diff. = 2.51776
[2022-12-20 23:55:57.059] [jointLog] [info] iteration = 400 | max rel diff. = 0.67957
[2022-12-20 23:55:58.258] [jointLog] [info] iteration = 500 | max rel diff. = 0.468013
[2022-12-20 23:55:59.388] [jointLog] [info] iteration = 600 | max rel diff. = 0.274696
[2022-12-20 23:56:00.533] [jointLog] [info] iteration = 700 | max rel diff. = 0.126156
[2022-12-20 23:56:01.650] [jointLog] [info] iteration = 800 | max rel diff. = 0.0250969
[2022-12-20 23:56:02.798] [jointLog] [info] iteration = 900 | max rel diff. = 0.38295
[2022-12-20 23:56:03.935] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.122027
[2022-12-20 23:56:05.092] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.127669
[2022-12-20 23:56:06.219] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.0403974
[2022-12-20 23:56:06.718] [jointLog] [info] iteration = 1,245 | max rel diff. = 0.0094379
[2022-12-20 23:56:06.736] [jointLog] [info] Finished optimizer
[2022-12-20 23:56:06.736] [jointLog] [info] writing output