[2022-02-21 13:24:32.505] [jointLog] [info] setting maxHashResizeThreads to 12
[2022-02-21 13:24:32.505] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2022-02-21 13:24:32.513] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2022-02-21 13:24:32.513] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2022-02-21 13:24:32.513] [jointLog] [info] parsing read library format
[2022-02-21 13:24:32.513] [jointLog] [info] There is 1 library.
[2022-02-21 13:24:32.702] [jointLog] [info] Loading pufferfish index
[2022-02-21 13:24:32.708] [jointLog] [info] Loading dense pufferfish index.
[2022-02-21 13:26:18.575] [jointLog] [info] done
[2022-02-21 13:26:18.575] [jointLog] [info] Index contained 5,382,683 targets
[2022-02-21 13:27:11.029] [jointLog] [info] Number of decoys : 194
[2022-02-21 13:27:11.030] [jointLog] [info] First decoy index : 5,185,409 
[2022-02-21 13:27:13.729] [jointLog] [info] Automatically detected most likely library type as ISR
[2022-02-21 13:36:16.005] [jointLog] [info] Thread saw mini-batch with a maximum of 98.12% zero probability fragments
[2022-02-21 13:36:16.025] [jointLog] [info] Thread saw mini-batch with a maximum of 97.32% zero probability fragments
[2022-02-21 13:36:16.096] [jointLog] [info] Thread saw mini-batch with a maximum of 99.00% zero probability fragments
[2022-02-21 13:36:16.107] [jointLog] [info] Thread saw mini-batch with a maximum of 98.08% zero probability fragments
[2022-02-21 13:36:16.142] [jointLog] [info] Thread saw mini-batch with a maximum of 98.32% zero probability fragments
[2022-02-21 13:36:16.143] [jointLog] [info] Thread saw mini-batch with a maximum of 97.68% zero probability fragments
[2022-02-21 13:36:16.255] [jointLog] [info] Thread saw mini-batch with a maximum of 98.06% zero probability fragments
[2022-02-21 13:36:16.285] [jointLog] [info] Thread saw mini-batch with a maximum of 97.58% zero probability fragments
[2022-02-21 13:36:16.453] [jointLog] [info] Thread saw mini-batch with a maximum of 97.94% zero probability fragments
[2022-02-21 13:36:16.624] [jointLog] [info] Thread saw mini-batch with a maximum of 97.50% zero probability fragments
[2022-02-21 13:36:16.624] [jointLog] [info] Thread saw mini-batch with a maximum of 98.38% zero probability fragments
[2022-02-21 13:36:17.091] [jointLog] [info] Thread saw mini-batch with a maximum of 98.82% zero probability fragments
[2022-02-21 13:36:17.667] [fileLog] [info] 
At end of round 0
==================
Observed 64461618 total fragments (64461618 in most recent round)

[2022-02-21 13:36:17.666] [jointLog] [info] Computed 612,742 rich equivalence classes for further processing
[2022-02-21 13:36:17.666] [jointLog] [info] Counted 52,402,956 total reads in the equivalence classes 
[2022-02-21 13:36:17.677] [jointLog] [info] Number of mappings discarded because of alignment score : 22,663,091
[2022-02-21 13:36:17.677] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 3,755,480
[2022-02-21 13:36:17.677] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 2,687,210
[2022-02-21 13:36:17.677] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 1,485,277
[2022-02-21 13:36:17.677] [jointLog] [info] Mapping rate = 81.2933%

[2022-02-21 13:36:17.677] [jointLog] [info] finished quantifyLibrary()
[2022-02-21 13:36:17.720] [jointLog] [info] Starting optimizer
[2022-02-21 13:36:22.758] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2022-02-21 13:36:23.075] [jointLog] [info] iteration = 0 | max rel diff. = 189.684
[2022-02-21 13:36:26.251] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2022-02-21 13:44:23.703] [jointLog] [info] Computed expected counts (for bias correction)
[2022-02-21 13:44:23.703] [jointLog] [info] processed bias for 0.0% of the transcripts
[2022-02-21 13:45:01.677] [jointLog] [info] processed bias for 10.0% of the transcripts
[2022-02-21 13:45:40.533] [jointLog] [info] processed bias for 20.0% of the transcripts
[2022-02-21 13:46:18.570] [jointLog] [info] processed bias for 30.0% of the transcripts
[2022-02-21 13:46:57.106] [jointLog] [info] processed bias for 40.0% of the transcripts
[2022-02-21 13:47:34.470] [jointLog] [info] processed bias for 50.0% of the transcripts
[2022-02-21 13:48:15.492] [jointLog] [info] processed bias for 60.0% of the transcripts
[2022-02-21 13:49:03.629] [jointLog] [info] processed bias for 70.0% of the transcripts
[2022-02-21 13:49:41.565] [jointLog] [info] processed bias for 80.0% of the transcripts
[2022-02-21 13:50:20.364] [jointLog] [info] processed bias for 90.0% of the transcripts
[2022-02-21 13:50:57.376] [jointLog] [info] processed bias for 100.0% of the transcripts
[2022-02-21 13:51:25.324] [jointLog] [info] iteration = 100 | max rel diff. = 6.92043
[2022-02-21 13:51:56.124] [jointLog] [info] iteration = 200 | max rel diff. = 1.31066
[2022-02-21 13:52:26.788] [jointLog] [info] iteration = 300 | max rel diff. = 0.84269
[2022-02-21 13:52:57.760] [jointLog] [info] iteration = 400 | max rel diff. = 0.311987
[2022-02-21 13:53:28.719] [jointLog] [info] iteration = 500 | max rel diff. = 0.383432
[2022-02-21 13:53:59.340] [jointLog] [info] iteration = 600 | max rel diff. = 14.809
[2022-02-21 13:54:30.574] [jointLog] [info] iteration = 700 | max rel diff. = 0.188848
[2022-02-21 13:55:02.554] [jointLog] [info] iteration = 800 | max rel diff. = 0.0279049
[2022-02-21 13:55:34.671] [jointLog] [info] iteration = 900 | max rel diff. = 0.0506517
[2022-02-21 13:55:47.050] [jointLog] [info] iteration = 940 | max rel diff. = 0.00451552
[2022-02-21 13:55:48.873] [jointLog] [info] Finished optimizer
[2022-02-21 13:55:48.873] [jointLog] [info] writing output