[2023-08-28 16:16:58.500] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-08-28 16:16:58.500] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-08-28 16:16:58.500] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-08-28 16:16:58.500] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-08-28 16:16:58.500] [jointLog] [info] parsing read library format
[2023-08-28 16:16:58.500] [jointLog] [info] There is 1 library.
[2023-08-28 16:16:58.500] [jointLog] [info] Loading pufferfish index
[2023-08-28 16:16:58.501] [jointLog] [info] Loading dense pufferfish index.
[2023-08-28 16:18:23.294] [jointLog] [info] done
[2023-08-28 16:18:23.459] [jointLog] [info] Index contained 5,382,683 targets
[2023-08-28 16:19:02.001] [jointLog] [info] Number of decoys : 194
[2023-08-28 16:19:02.001] [jointLog] [info] First decoy index : 5,185,409 
[2023-08-28 16:19:05.284] [jointLog] [info] Automatically detected most likely library type as ISR

[2023-08-28 16:36:54.065] [jointLog] [info] Thread saw mini-batch with a maximum of 1.36% zero probability fragments
[2023-08-28 16:36:54.109] [jointLog] [info] Thread saw mini-batch with a maximum of 1.34% zero probability fragments
[2023-08-28 16:36:54.151] [jointLog] [info] Thread saw mini-batch with a maximum of 1.34% zero probability fragments
[2023-08-28 16:36:54.236] [jointLog] [info] Thread saw mini-batch with a maximum of 1.32% zero probability fragments
[2023-08-28 16:36:54.259] [jointLog] [info] Thread saw mini-batch with a maximum of 1.44% zero probability fragments
[2023-08-28 16:36:54.489] [jointLog] [info] Thread saw mini-batch with a maximum of 1.38% zero probability fragments
[2023-08-28 16:36:54.504] [jointLog] [info] Thread saw mini-batch with a maximum of 1.38% zero probability fragments
[2023-08-28 16:36:54.537] [jointLog] [info] Thread saw mini-batch with a maximum of 1.32% zero probability fragments
[2023-08-28 16:36:54.986] [jointLog] [info] Computed 210,595 rich equivalence classes for further processing
[2023-08-28 16:36:54.986] [jointLog] [info] Counted 28,946,175 total reads in the equivalence classes 
[2023-08-28 16:36:54.995] [jointLog] [info] Number of mappings discarded because of alignment score : 22,222,334
[2023-08-28 16:36:54.995] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 1,921,846
[2023-08-28 16:36:54.995] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 763,961
[2023-08-28 16:36:54.995] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 4,397,154
[2023-08-28 16:36:54.995] [jointLog] [info] Mapping rate = 39.7525%

[2023-08-28 16:36:54.995] [jointLog] [info] finished quantifyLibrary()
[2023-08-28 16:36:54.996] [jointLog] [info] Starting optimizer
[2023-08-28 16:36:54.987] [fileLog] [info] 
At end of round 0
==================
Observed 72816053 total fragments (72816053 in most recent round)

[2023-08-28 16:36:59.912] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-08-28 16:37:00.262] [jointLog] [info] iteration = 0 | max rel diff. = 296.469
[2023-08-28 16:37:03.807] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-08-28 16:40:01.710] [jointLog] [info] Computed expected counts (for bias correction)
[2023-08-28 16:40:01.710] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-08-28 16:40:16.116] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-08-28 16:40:31.059] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-08-28 16:40:46.404] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-08-28 16:41:01.995] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-08-28 16:41:17.692] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-08-28 16:41:50.366] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-08-28 16:42:23.181] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-08-28 16:42:54.124] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-08-28 16:43:26.432] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-08-28 16:44:01.279] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-28 16:44:52.991] [jointLog] [info] iteration = 100 | max rel diff. = 19.9221
[2023-08-28 16:45:47.411] [jointLog] [info] iteration = 200 | max rel diff. = 2.32537
[2023-08-28 16:46:39.751] [jointLog] [info] iteration = 300 | max rel diff. = 0.407702
[2023-08-28 16:47:31.777] [jointLog] [info] iteration = 400 | max rel diff. = 0.781274
[2023-08-28 16:48:25.203] [jointLog] [info] iteration = 500 | max rel diff. = 0.832454
[2023-08-28 16:49:18.098] [jointLog] [info] iteration = 600 | max rel diff. = 1.80636
[2023-08-28 16:50:10.352] [jointLog] [info] iteration = 700 | max rel diff. = 0.177672
[2023-08-28 16:51:02.746] [jointLog] [info] iteration = 800 | max rel diff. = 0.640056
[2023-08-28 16:51:59.329] [jointLog] [info] iteration = 900 | max rel diff. = 0.0281393
[2023-08-28 16:52:24.820] [jointLog] [info] iteration = 940 | max rel diff. = 0.00972021
[2023-08-28 16:52:27.652] [jointLog] [info] Finished optimizer
[2023-08-28 16:52:27.652] [jointLog] [info] writing output