[2023-08-25 13:24:39.433] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-08-25 13:24:39.433] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-08-25 13:24:39.433] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-08-25 13:24:39.433] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-08-25 13:24:39.433] [jointLog] [info] parsing read library format
[2023-08-25 13:24:39.433] [jointLog] [info] There is 1 library.
[2023-08-25 13:24:39.433] [jointLog] [info] Loading pufferfish index
[2023-08-25 13:24:39.433] [jointLog] [info] Loading dense pufferfish index.
[2023-08-25 13:25:55.709] [jointLog] [info] done
[2023-08-25 13:25:55.836] [jointLog] [info] Index contained 5,382,683 targets
[2023-08-25 13:26:31.912] [jointLog] [info] Number of decoys : 194
[2023-08-25 13:26:31.912] [jointLog] [info] First decoy index : 5,185,409 
[2023-08-25 13:26:32.996] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-08-25 13:26:34.906] [jointLog] [info] Automatically detected most likely library type as SF

[2023-08-25 13:34:32.286] [jointLog] [info] Thread saw mini-batch with a maximum of 4.34% zero probability fragments
[2023-08-25 13:34:32.306] [jointLog] [info] Thread saw mini-batch with a maximum of 5.58% zero probability fragments
[2023-08-25 13:34:32.566] [jointLog] [info] Thread saw mini-batch with a maximum of 4.26% zero probability fragments
[2023-08-25 13:34:32.660] [jointLog] [info] Thread saw mini-batch with a maximum of 4.20% zero probability fragments
[2023-08-25 13:34:32.707] [jointLog] [info] Thread saw mini-batch with a maximum of 4.26% zero probability fragments
[2023-08-25 13:34:32.858] [jointLog] [info] Thread saw mini-batch with a maximum of 4.32% zero probability fragments
[2023-08-25 13:34:32.960] [jointLog] [info] Thread saw mini-batch with a maximum of 4.34% zero probability fragments
[2023-08-25 13:34:33.091] [jointLog] [info] Thread saw mini-batch with a maximum of 4.20% zero probability fragments
[2023-08-25 13:34:33.672] [fileLog] [info] 
At end of round 0
==================
Observed 18475251 total fragments (18475251 in most recent round)

[2023-08-25 13:34:33.670] [jointLog] [info] Computed 377,709 rich equivalence classes for further processing
[2023-08-25 13:34:33.670] [jointLog] [info] Counted 14,175,195 total reads in the equivalence classes 
[2023-08-25 13:34:33.682] [jointLog] [info] Number of mappings discarded because of alignment score : 316,427,770
[2023-08-25 13:34:33.682] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 2,842,058
[2023-08-25 13:34:33.682] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 720,253
[2023-08-25 13:34:33.682] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-08-25 13:34:33.682] [jointLog] [info] Mapping rate = 76.7253%

[2023-08-25 13:34:33.682] [jointLog] [info] finished quantifyLibrary()
[2023-08-25 13:34:33.683] [jointLog] [info] Starting optimizer
[2023-08-25 13:36:34.037] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-08-25 13:36:34.389] [jointLog] [info] iteration = 0 | max rel diff. = 330.837
[2023-08-25 13:36:37.896] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-08-25 13:39:00.772] [jointLog] [info] Computed expected counts (for bias correction)
[2023-08-25 13:39:00.773] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-08-25 13:39:13.751] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-08-25 13:39:27.090] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-08-25 13:39:40.550] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-08-25 13:39:53.781] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-08-25 13:40:06.668] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-08-25 13:40:19.726] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-08-25 13:40:32.455] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-08-25 13:40:45.238] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-08-25 13:40:57.702] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-08-25 13:41:10.400] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-25 13:41:41.758] [jointLog] [info] iteration = 100 | max rel diff. = 6.32805
[2023-08-25 13:42:17.722] [jointLog] [info] iteration = 200 | max rel diff. = 2.89678
[2023-08-25 13:42:53.386] [jointLog] [info] iteration = 300 | max rel diff. = 0.418131
[2023-08-25 13:43:28.782] [jointLog] [info] iteration = 400 | max rel diff. = 0.250877
[2023-08-25 13:44:04.176] [jointLog] [info] iteration = 500 | max rel diff. = 0.635976
[2023-08-25 13:44:39.532] [jointLog] [info] iteration = 600 | max rel diff. = 1.55818
[2023-08-25 13:45:15.058] [jointLog] [info] iteration = 700 | max rel diff. = 0.0317969
[2023-08-25 13:45:49.700] [jointLog] [info] iteration = 800 | max rel diff. = 0.0305639
[2023-08-25 13:46:23.779] [jointLog] [info] iteration = 900 | max rel diff. = 0.10778
[2023-08-25 13:46:57.637] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0608054
[2023-08-25 13:47:31.200] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.0457758
[2023-08-25 13:48:04.859] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.466467
[2023-08-25 13:48:38.493] [jointLog] [info] iteration = 1,300 | max rel diff. = 0.0184351
[2023-08-25 13:48:56.429] [jointLog] [info] iteration = 1,354 | max rel diff. = 0.0060818
[2023-08-25 13:48:58.185] [jointLog] [info] Finished optimizer
[2023-08-25 13:48:58.185] [jointLog] [info] writing output