[2021-08-01 16:24:52.108] [jointLog] [info] setting maxHashResizeThreads to 8
[2021-08-01 16:24:52.108] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2021-08-01 16:24:52.108] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2021-08-01 16:24:52.109] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2021-08-01 16:24:52.109] [jointLog] [info] parsing read library format
[2021-08-01 16:24:52.109] [jointLog] [info] There is 1 library.
[2021-08-01 16:24:52.184] [jointLog] [info] Loading pufferfish index
[2021-08-01 16:24:52.184] [jointLog] [info] Loading dense pufferfish index.
[2021-08-01 16:26:18.868] [jointLog] [info] done
[2021-08-01 16:26:18.868] [jointLog] [info] Index contained 5,382,683 targets
[2021-08-01 16:27:05.863] [jointLog] [info] Number of decoys : 194
[2021-08-01 16:27:05.863] [jointLog] [info] First decoy index : 5,185,409 
[2021-08-01 16:27:06.557] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2021-08-01 16:27:06.852] [jointLog] [info] Automatically detected most likely library type as SR
[2021-08-01 16:27:25.322] [jointLog] [info] Thread saw mini-batch with a maximum of 3.44% zero probability fragments
[2021-08-01 16:27:25.343] [jointLog] [info] Thread saw mini-batch with a maximum of 3.26% zero probability fragments
[2021-08-01 16:27:25.353] [jointLog] [info] Thread saw mini-batch with a maximum of 3.32% zero probability fragments
[2021-08-01 16:27:25.356] [jointLog] [info] Thread saw mini-batch with a maximum of 3.18% zero probability fragments
[2021-08-01 16:27:25.397] [jointLog] [info] Thread saw mini-batch with a maximum of 3.16% zero probability fragments
[2021-08-01 16:27:25.413] [jointLog] [info] Thread saw mini-batch with a maximum of 3.08% zero probability fragments
[2021-08-01 16:27:25.420] [jointLog] [info] Thread saw mini-batch with a maximum of 3.38% zero probability fragments
[2021-08-01 16:27:25.421] [jointLog] [info] Thread saw mini-batch with a maximum of 3.32% zero probability fragments
[2021-08-01 16:27:25.581] [jointLog] [info] Computed 131,841 rich equivalence classes for further processing
[2021-08-01 16:27:25.581] [jointLog] [info] Counted 4,422,924 total reads in the equivalence classes 
[2021-08-01 16:27:25.593] [jointLog] [info] Number of mappings discarded because of alignment score : 5,817,769
[2021-08-01 16:27:25.593] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 31,851
[2021-08-01 16:27:25.593] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 23,147
[2021-08-01 16:27:25.593] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2021-08-01 16:27:25.582] [fileLog] [info] 
At end of round 0
==================
Observed 4697498 total fragments (4697498 in most recent round)

[2021-08-01 16:27:26.605] [jointLog] [warning] Only 4422924 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2021-08-01 16:27:26.605] [jointLog] [info] Mapping rate = 94.1549%

[2021-08-01 16:27:26.605] [jointLog] [info] finished quantifyLibrary()
[2021-08-01 16:27:26.606] [jointLog] [info] Starting optimizer
[2021-08-01 16:27:29.040] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2021-08-01 16:27:29.380] [jointLog] [info] iteration = 0 | max rel diff. = 89.4998
[2021-08-01 16:27:32.849] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2021-08-01 16:28:20.566] [jointLog] [info] Computed expected counts (for bias correction)
[2021-08-01 16:28:20.567] [jointLog] [info] processed bias for 0.0% of the transcripts
[2021-08-01 16:28:25.281] [jointLog] [info] processed bias for 10.0% of the transcripts
[2021-08-01 16:28:29.778] [jointLog] [info] processed bias for 20.0% of the transcripts
[2021-08-01 16:28:34.134] [jointLog] [info] processed bias for 30.0% of the transcripts
[2021-08-01 16:28:38.756] [jointLog] [info] processed bias for 40.0% of the transcripts
[2021-08-01 16:28:43.419] [jointLog] [info] processed bias for 50.0% of the transcripts
[2021-08-01 16:28:47.904] [jointLog] [info] processed bias for 60.0% of the transcripts
[2021-08-01 16:28:52.428] [jointLog] [info] processed bias for 70.0% of the transcripts
[2021-08-01 16:28:57.122] [jointLog] [info] processed bias for 80.0% of the transcripts
[2021-08-01 16:29:01.827] [jointLog] [info] processed bias for 90.0% of the transcripts
[2021-08-01 16:29:06.147] [jointLog] [info] processed bias for 100.0% of the transcripts
[2021-08-01 16:29:06.150] [jointLog] [info] processed bias for 100.0% of the transcripts
[2021-08-01 16:29:36.485] [jointLog] [info] iteration = 100 | max rel diff. = 15.9591
[2021-08-01 16:30:09.872] [jointLog] [info] iteration = 200 | max rel diff. = 1.91492
[2021-08-01 16:30:44.252] [jointLog] [info] iteration = 300 | max rel diff. = 1.08714
[2021-08-01 16:31:18.730] [jointLog] [info] iteration = 400 | max rel diff. = 7.68327
[2021-08-01 16:31:52.161] [jointLog] [info] iteration = 500 | max rel diff. = 1.03144
[2021-08-01 16:32:26.035] [jointLog] [info] iteration = 600 | max rel diff. = 0.248303
[2021-08-01 16:33:00.469] [jointLog] [info] iteration = 700 | max rel diff. = 5.81654
[2021-08-01 16:33:34.754] [jointLog] [info] iteration = 800 | max rel diff. = 0.215677
[2021-08-01 16:34:08.816] [jointLog] [info] iteration = 900 | max rel diff. = 0.0452369
[2021-08-01 16:34:42.832] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.122624
[2021-08-01 16:35:16.889] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.0994737
[2021-08-01 16:35:51.028] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.0548643
[2021-08-01 16:36:25.449] [jointLog] [info] iteration = 1,300 | max rel diff. = 0.609757
[2021-08-01 16:36:26.488] [jointLog] [info] iteration = 1,304 | max rel diff. = 0.002778
[2021-08-01 16:36:27.770] [jointLog] [info] Finished optimizer
[2021-08-01 16:36:27.770] [jointLog] [info] writing output