[2022-11-09 12:47:29.571] [jointLog] [info] setting maxHashResizeThreads to 8
[2022-11-09 12:47:29.571] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2022-11-09 12:47:29.571] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2022-11-09 12:47:29.572] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2022-11-09 12:47:29.572] [jointLog] [info] parsing read library format
[2022-11-09 12:47:29.572] [jointLog] [info] There is 1 library.
[2022-11-09 12:47:29.572] [jointLog] [info] Loading pufferfish index
[2022-11-09 12:47:29.573] [jointLog] [info] Loading dense pufferfish index.
[2022-11-09 12:48:03.745] [jointLog] [info] done
[2022-11-09 12:48:03.808] [jointLog] [info] Index contained 177,651 targets
[2022-11-09 12:48:04.174] [jointLog] [info] Number of decoys : 195
[2022-11-09 12:48:04.174] [jointLog] [info] First decoy index : 177,412 
[2022-11-09 12:48:08.120] [jointLog] [info] Automatically detected most likely library type as ISR

[2022-11-09 12:54:22.610] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2022-11-09 12:54:22.687] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments
[2022-11-09 12:54:22.788] [jointLog] [info] Thread saw mini-batch with a maximum of 0.06% zero probability fragments
[2022-11-09 12:54:23.002] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments
[2022-11-09 12:54:23.093] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2022-11-09 12:54:23.093] [jointLog] [info] Thread saw mini-batch with a maximum of 0.06% zero probability fragments
[2022-11-09 12:54:23.253] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2022-11-09 12:54:23.264] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments
[2022-11-09 12:54:23.374] [jointLog] [info] Computed 96,851 rich equivalence classes for further processing
[2022-11-09 12:54:23.374] [jointLog] [info] Counted 2,794,796 total reads in the equivalence classes 
[2022-11-09 12:54:23.377] [jointLog] [info] Number of mappings discarded because of alignment score : 36,880,861
[2022-11-09 12:54:23.377] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 3,114,737
[2022-11-09 12:54:23.377] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 72,304
[2022-11-09 12:54:23.377] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 1,517,491
[2022-11-09 12:54:23.393] [jointLog] [warning] Only 2794796 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2022-11-09 12:54:23.393] [jointLog] [info] Mapping rate = 15.4703%

[2022-11-09 12:54:23.393] [jointLog] [info] finished quantifyLibrary()
[2022-11-09 12:54:23.393] [jointLog] [info] Starting optimizer
[2022-11-09 12:54:23.459] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2022-11-09 12:54:23.472] [jointLog] [info] iteration = 0 | max rel diff. = 1453.33
[2022-11-09 12:54:23.580] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2022-11-09 12:54:23.375] [fileLog] [info] 
At end of round 0
==================
Observed 18065581 total fragments (18065581 in most recent round)

[2022-11-09 12:54:24.038] [jointLog] [info] Computed expected counts (for bias correction)
[2022-11-09 12:54:24.039] [jointLog] [info] processed bias for 0.2% of the transcripts
[2022-11-09 12:54:24.338] [jointLog] [info] processed bias for 10.0% of the transcripts
[2022-11-09 12:54:24.647] [jointLog] [info] processed bias for 20.0% of the transcripts
[2022-11-09 12:54:24.931] [jointLog] [info] processed bias for 30.0% of the transcripts
[2022-11-09 12:54:25.199] [jointLog] [info] processed bias for 40.0% of the transcripts
[2022-11-09 12:54:25.358] [jointLog] [info] processed bias for 50.0% of the transcripts
[2022-11-09 12:54:25.541] [jointLog] [info] processed bias for 60.0% of the transcripts
[2022-11-09 12:54:25.820] [jointLog] [info] processed bias for 70.0% of the transcripts
[2022-11-09 12:54:26.087] [jointLog] [info] processed bias for 80.0% of the transcripts
[2022-11-09 12:54:26.360] [jointLog] [info] processed bias for 90.0% of the transcripts
[2022-11-09 12:54:26.642] [jointLog] [info] processed bias for 100.0% of the transcripts
[2022-11-09 12:54:26.642] [jointLog] [info] processed bias for 100.0% of the transcripts
[2022-11-09 12:54:27.632] [jointLog] [info] iteration = 100 | max rel diff. = 20.5422
[2022-11-09 12:54:28.682] [jointLog] [info] iteration = 200 | max rel diff. = 14.5091
[2022-11-09 12:54:29.740] [jointLog] [info] iteration = 300 | max rel diff. = 2.33094
[2022-11-09 12:54:30.818] [jointLog] [info] iteration = 400 | max rel diff. = 0.578134
[2022-11-09 12:54:32.046] [jointLog] [info] iteration = 500 | max rel diff. = 1.01912
[2022-11-09 12:54:33.195] [jointLog] [info] iteration = 600 | max rel diff. = 0.196223
[2022-11-09 12:54:34.353] [jointLog] [info] iteration = 700 | max rel diff. = 0.0631765
[2022-11-09 12:54:35.536] [jointLog] [info] iteration = 800 | max rel diff. = 0.089374
[2022-11-09 12:54:36.680] [jointLog] [info] iteration = 900 | max rel diff. = 0.0760544
[2022-11-09 12:54:37.826] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0893242
[2022-11-09 12:54:39.021] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.976415
[2022-11-09 12:54:39.044] [jointLog] [info] iteration = 1,103 | max rel diff. = 0.00442963
[2022-11-09 12:54:39.069] [jointLog] [info] Finished optimizer
[2022-11-09 12:54:39.069] [jointLog] [info] writing output