[2021-03-08 11:37:52.668] [jointLog] [info] setting maxHashResizeThreads to 8
[2021-03-08 11:37:52.668] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2021-03-08 11:37:52.668] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2021-03-08 11:37:52.668] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2021-03-08 11:37:52.668] [jointLog] [info] parsing read library format
[2021-03-08 11:37:52.669] [jointLog] [info] There is 1 library.
[2021-03-08 11:37:52.739] [jointLog] [info] Loading pufferfish index
[2021-03-08 11:37:52.739] [jointLog] [info] Loading dense pufferfish index.
[2021-03-08 11:39:27.670] [jointLog] [info] done
[2021-03-08 11:39:27.670] [jointLog] [info] Index contained 5,382,683 targets
[2021-03-08 11:40:18.833] [jointLog] [info] Number of decoys : 194
[2021-03-08 11:40:18.834] [jointLog] [info] First decoy index : 5,185,409 
[2021-03-08 11:40:20.585] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2021-03-08 11:40:21.085] [jointLog] [info] Automatically detected most likely library type as SR
[2021-03-08 11:43:12.432] [jointLog] [info] Thread saw mini-batch with a maximum of 12.44% zero probability fragments
[2021-03-08 11:43:12.446] [jointLog] [info] Thread saw mini-batch with a maximum of 13.20% zero probability fragments
[2021-03-08 11:43:12.461] [jointLog] [info] Thread saw mini-batch with a maximum of 13.58% zero probability fragments
[2021-03-08 11:43:12.484] [jointLog] [info] Thread saw mini-batch with a maximum of 12.34% zero probability fragments
[2021-03-08 11:43:12.577] [jointLog] [info] Thread saw mini-batch with a maximum of 12.74% zero probability fragments
[2021-03-08 11:43:12.604] [jointLog] [info] Thread saw mini-batch with a maximum of 12.78% zero probability fragments
[2021-03-08 11:43:12.618] [jointLog] [info] Thread saw mini-batch with a maximum of 12.72% zero probability fragments
[2021-03-08 11:43:12.664] [jointLog] [info] Thread saw mini-batch with a maximum of 13.10% zero probability fragments
[2021-03-08 11:43:13.006] [jointLog] [info] Computed 342,324 rich equivalence classes for further processing
[2021-03-08 11:43:13.006] [jointLog] [info] Counted 19,415,231 total reads in the equivalence classes 
[2021-03-08 11:43:13.015] [jointLog] [info] Number of mappings discarded because of alignment score : 93,321,774
[2021-03-08 11:43:13.015] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 1,218,818
[2021-03-08 11:43:13.015] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 246,058
[2021-03-08 11:43:13.015] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2021-03-08 11:43:13.015] [jointLog] [info] Mapping rate = 68.7707%

[2021-03-08 11:43:13.015] [jointLog] [info] finished quantifyLibrary()
[2021-03-08 11:43:13.016] [jointLog] [info] Starting optimizer
[2021-03-08 11:43:13.007] [fileLog] [info] 
At end of round 0
==================
Observed 28231848 total fragments (28231848 in most recent round)

[2021-03-08 11:43:17.449] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2021-03-08 11:43:17.779] [jointLog] [info] iteration = 0 | max rel diff. = 271.539
[2021-03-08 11:43:21.156] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2021-03-08 11:45:31.419] [jointLog] [info] Computed expected counts (for bias correction)
[2021-03-08 11:45:31.419] [jointLog] [info] processed bias for 0.0% of the transcripts
[2021-03-08 11:45:43.318] [jointLog] [info] processed bias for 10.0% of the transcripts
[2021-03-08 11:45:55.255] [jointLog] [info] processed bias for 20.0% of the transcripts
[2021-03-08 11:46:07.453] [jointLog] [info] processed bias for 30.0% of the transcripts
[2021-03-08 11:46:19.715] [jointLog] [info] processed bias for 40.0% of the transcripts
[2021-03-08 11:46:31.545] [jointLog] [info] processed bias for 50.0% of the transcripts
[2021-03-08 11:46:43.408] [jointLog] [info] processed bias for 60.0% of the transcripts
[2021-03-08 11:46:55.565] [jointLog] [info] processed bias for 70.0% of the transcripts
[2021-03-08 11:47:07.788] [jointLog] [info] processed bias for 80.0% of the transcripts
[2021-03-08 11:47:19.689] [jointLog] [info] processed bias for 90.0% of the transcripts
[2021-03-08 11:47:31.838] [jointLog] [info] processed bias for 100.0% of the transcripts
[2021-03-08 11:48:04.956] [jointLog] [info] iteration = 100 | max rel diff. = 17.5082
[2021-03-08 11:48:40.667] [jointLog] [info] iteration = 200 | max rel diff. = 11.2224
[2021-03-08 11:49:15.529] [jointLog] [info] iteration = 300 | max rel diff. = 6.89564
[2021-03-08 11:49:49.942] [jointLog] [info] iteration = 400 | max rel diff. = 3.94663
[2021-03-08 11:50:23.762] [jointLog] [info] iteration = 500 | max rel diff. = 1.04893
[2021-03-08 11:50:57.773] [jointLog] [info] iteration = 600 | max rel diff. = 1.55925
[2021-03-08 11:51:32.043] [jointLog] [info] iteration = 700 | max rel diff. = 12.225
[2021-03-08 11:52:06.867] [jointLog] [info] iteration = 800 | max rel diff. = 0.14175
[2021-03-08 11:52:41.197] [jointLog] [info] iteration = 900 | max rel diff. = 19.9614
[2021-03-08 11:53:16.240] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.086664
[2021-03-08 11:53:50.243] [jointLog] [info] iteration = 1,100 | max rel diff. = 1.07407
[2021-03-08 11:54:24.662] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.312248
[2021-03-08 11:55:00.210] [jointLog] [info] iteration = 1,300 | max rel diff. = 0.387464
[2021-03-08 11:55:34.689] [jointLog] [info] iteration = 1,400 | max rel diff. = 0.060064
[2021-03-08 11:56:09.538] [jointLog] [info] iteration = 1,500 | max rel diff. = 0.141506
[2021-03-08 11:56:14.329] [jointLog] [info] iteration = 1,515 | max rel diff. = 0.00799885
[2021-03-08 11:56:16.329] [jointLog] [info] Finished optimizer
[2021-03-08 11:56:16.329] [jointLog] [info] writing output