[2021-08-01 11:44:19.809] [jointLog] [info] setting maxHashResizeThreads to 8
[2021-08-01 11:44:19.809] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2021-08-01 11:44:19.809] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2021-08-01 11:44:19.809] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2021-08-01 11:44:19.809] [jointLog] [info] parsing read library format
[2021-08-01 11:44:19.809] [jointLog] [info] There is 1 library.
[2021-08-01 11:44:19.939] [jointLog] [info] Loading pufferfish index
[2021-08-01 11:44:19.939] [jointLog] [info] Loading dense pufferfish index.
[2021-08-01 11:46:04.722] [jointLog] [info] done
[2021-08-01 11:46:04.722] [jointLog] [info] Index contained 5,382,683 targets
[2021-08-01 11:47:01.391] [jointLog] [info] Number of decoys : 194
[2021-08-01 11:47:01.391] [jointLog] [info] First decoy index : 5,185,409 
[2021-08-01 11:47:02.808] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2021-08-01 11:47:03.512] [jointLog] [info] Automatically detected most likely library type as SR
[2021-08-01 11:47:20.567] [jointLog] [info] Thread saw mini-batch with a maximum of 3.74% zero probability fragments
[2021-08-01 11:47:20.604] [jointLog] [info] Thread saw mini-batch with a maximum of 3.66% zero probability fragments
[2021-08-01 11:47:20.620] [jointLog] [info] Thread saw mini-batch with a maximum of 3.52% zero probability fragments
[2021-08-01 11:47:20.628] [jointLog] [info] Thread saw mini-batch with a maximum of 3.78% zero probability fragments
[2021-08-01 11:47:20.632] [jointLog] [info] Thread saw mini-batch with a maximum of 3.52% zero probability fragments
[2021-08-01 11:47:20.669] [jointLog] [info] Thread saw mini-batch with a maximum of 3.66% zero probability fragments
[2021-08-01 11:47:20.690] [jointLog] [info] Thread saw mini-batch with a maximum of 3.68% zero probability fragments
[2021-08-01 11:47:20.701] [jointLog] [info] Thread saw mini-batch with a maximum of 3.62% zero probability fragments
[2021-08-01 11:47:20.838] [jointLog] [info] Computed 115,785 rich equivalence classes for further processing
[2021-08-01 11:47:20.838] [jointLog] [info] Counted 3,105,396 total reads in the equivalence classes 
[2021-08-01 11:47:20.851] [jointLog] [info] Number of mappings discarded because of alignment score : 4,360,335
[2021-08-01 11:47:20.851] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 23,198
[2021-08-01 11:47:20.851] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 17,326
[2021-08-01 11:47:20.851] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2021-08-01 11:47:20.839] [fileLog] [info] 
At end of round 0
==================
Observed 3316958 total fragments (3316958 in most recent round)

[2021-08-01 11:47:22.712] [jointLog] [warning] Only 3105396 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 11:47:22.712] [jointLog] [info] Mapping rate = 93.6218%

[2021-08-01 11:47:22.712] [jointLog] [info] finished quantifyLibrary()
[2021-08-01 11:47:22.712] [jointLog] [info] Starting optimizer
[2021-08-01 11:48:11.258] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2021-08-01 11:48:11.618] [jointLog] [info] iteration = 0 | max rel diff. = 57.1546
[2021-08-01 11:48:15.051] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2021-08-01 11:48:59.887] [jointLog] [info] Computed expected counts (for bias correction)
[2021-08-01 11:48:59.888] [jointLog] [info] processed bias for 0.0% of the transcripts
[2021-08-01 11:49:04.250] [jointLog] [info] processed bias for 10.0% of the transcripts
[2021-08-01 11:49:08.476] [jointLog] [info] processed bias for 20.0% of the transcripts
[2021-08-01 11:49:12.615] [jointLog] [info] processed bias for 30.0% of the transcripts
[2021-08-01 11:49:17.039] [jointLog] [info] processed bias for 40.0% of the transcripts
[2021-08-01 11:49:21.342] [jointLog] [info] processed bias for 50.0% of the transcripts
[2021-08-01 11:49:25.416] [jointLog] [info] processed bias for 60.0% of the transcripts
[2021-08-01 11:49:29.494] [jointLog] [info] processed bias for 70.0% of the transcripts
[2021-08-01 11:49:33.609] [jointLog] [info] processed bias for 80.0% of the transcripts
[2021-08-01 11:49:38.131] [jointLog] [info] processed bias for 90.0% of the transcripts
[2021-08-01 11:49:42.303] [jointLog] [info] processed bias for 100.0% of the transcripts
[2021-08-01 11:49:42.306] [jointLog] [info] processed bias for 100.0% of the transcripts
[2021-08-01 11:50:15.369] [jointLog] [info] iteration = 100 | max rel diff. = 14.081
[2021-08-01 11:50:51.965] [jointLog] [info] iteration = 200 | max rel diff. = 7.84472
[2021-08-01 11:51:28.167] [jointLog] [info] iteration = 300 | max rel diff. = 1.39769
[2021-08-01 11:52:03.169] [jointLog] [info] iteration = 400 | max rel diff. = 0.257714
[2021-08-01 11:52:37.283] [jointLog] [info] iteration = 500 | max rel diff. = 0.67563
[2021-08-01 11:53:11.629] [jointLog] [info] iteration = 600 | max rel diff. = 0.29646
[2021-08-01 11:53:45.636] [jointLog] [info] iteration = 700 | max rel diff. = 0.0879538
[2021-08-01 11:54:20.435] [jointLog] [info] iteration = 800 | max rel diff. = 0.0137762
[2021-08-01 11:54:54.723] [jointLog] [info] iteration = 900 | max rel diff. = 0.173348
[2021-08-01 11:55:28.086] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.079918
[2021-08-01 11:56:00.832] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.103195
[2021-08-01 11:56:04.483] [jointLog] [info] iteration = 1,112 | max rel diff. = 0.0095508
[2021-08-01 11:56:06.502] [jointLog] [info] Finished optimizer
[2021-08-01 11:56:06.502] [jointLog] [info] writing output