[2021-08-02 18:11:30.351] [jointLog] [info] setting maxHashResizeThreads to 8
[2021-08-02 18:11:30.351] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2021-08-02 18:11:30.351] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2021-08-02 18:11:30.351] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2021-08-02 18:11:30.351] [jointLog] [info] parsing read library format
[2021-08-02 18:11:30.351] [jointLog] [info] There is 1 library.
[2021-08-02 18:11:30.431] [jointLog] [info] Loading pufferfish index
[2021-08-02 18:11:30.431] [jointLog] [info] Loading dense pufferfish index.
[2021-08-02 18:12:58.860] [jointLog] [info] done
[2021-08-02 18:12:58.860] [jointLog] [info] Index contained 5,382,683 targets
[2021-08-02 18:13:39.544] [jointLog] [info] Number of decoys : 194
[2021-08-02 18:13:39.544] [jointLog] [info] First decoy index : 5,185,409 
[2021-08-02 18:13:40.238] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2021-08-02 18:13:40.543] [jointLog] [info] Automatically detected most likely library type as SR
[2021-08-02 18:13:57.088] [jointLog] [info] Thread saw mini-batch with a maximum of 3.00% zero probability fragments
[2021-08-02 18:13:57.117] [jointLog] [info] Thread saw mini-batch with a maximum of 3.80% zero probability fragments
[2021-08-02 18:13:57.124] [jointLog] [info] Thread saw mini-batch with a maximum of 3.28% zero probability fragments
[2021-08-02 18:13:57.134] [jointLog] [info] Thread saw mini-batch with a maximum of 3.30% zero probability fragments
[2021-08-02 18:13:57.179] [jointLog] [info] Thread saw mini-batch with a maximum of 3.34% zero probability fragments
[2021-08-02 18:13:57.193] [jointLog] [info] Thread saw mini-batch with a maximum of 2.96% zero probability fragments
[2021-08-02 18:13:57.194] [jointLog] [info] Thread saw mini-batch with a maximum of 3.06% zero probability fragments
[2021-08-02 18:13:57.219] [jointLog] [info] Thread saw mini-batch with a maximum of 3.18% zero probability fragments
[2021-08-02 18:13:57.333] [jointLog] [info] Computed 125,574 rich equivalence classes for further processing
[2021-08-02 18:13:57.333] [jointLog] [info] Counted 3,910,494 total reads in the equivalence classes 
[2021-08-02 18:13:57.345] [jointLog] [info] Number of mappings discarded because of alignment score : 5,191,284
[2021-08-02 18:13:57.345] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 28,424
[2021-08-02 18:13:57.345] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 20,425
[2021-08-02 18:13:57.345] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2021-08-02 18:13:57.334] [fileLog] [info] 
At end of round 0
==================
Observed 4180868 total fragments (4180868 in most recent round)

[2021-08-02 18:13:58.382] [jointLog] [warning] Only 3910494 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2021-08-02 18:13:58.382] [jointLog] [info] Mapping rate = 93.5331%

[2021-08-02 18:13:58.382] [jointLog] [info] finished quantifyLibrary()
[2021-08-02 18:13:58.382] [jointLog] [info] Starting optimizer
[2021-08-02 18:14:00.847] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2021-08-02 18:14:01.197] [jointLog] [info] iteration = 0 | max rel diff. = 93.3807
[2021-08-02 18:14:04.659] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2021-08-02 18:14:50.650] [jointLog] [info] Computed expected counts (for bias correction)
[2021-08-02 18:14:50.653] [jointLog] [info] processed bias for 0.0% of the transcripts
[2021-08-02 18:14:54.885] [jointLog] [info] processed bias for 10.0% of the transcripts
[2021-08-02 18:14:59.270] [jointLog] [info] processed bias for 20.0% of the transcripts
[2021-08-02 18:15:03.573] [jointLog] [info] processed bias for 30.0% of the transcripts
[2021-08-02 18:15:08.103] [jointLog] [info] processed bias for 40.0% of the transcripts
[2021-08-02 18:15:12.518] [jointLog] [info] processed bias for 50.0% of the transcripts
[2021-08-02 18:15:16.858] [jointLog] [info] processed bias for 60.0% of the transcripts
[2021-08-02 18:15:21.062] [jointLog] [info] processed bias for 70.0% of the transcripts
[2021-08-02 18:15:25.229] [jointLog] [info] processed bias for 80.0% of the transcripts
[2021-08-02 18:15:29.665] [jointLog] [info] processed bias for 90.0% of the transcripts
[2021-08-02 18:15:34.152] [jointLog] [info] processed bias for 100.0% of the transcripts
[2021-08-02 18:16:05.396] [jointLog] [info] iteration = 100 | max rel diff. = 19.5504
[2021-08-02 18:16:39.903] [jointLog] [info] iteration = 200 | max rel diff. = 17.4455
[2021-08-02 18:17:14.466] [jointLog] [info] iteration = 300 | max rel diff. = 16.1947
[2021-08-02 18:17:49.212] [jointLog] [info] iteration = 400 | max rel diff. = 1.82227
[2021-08-02 18:18:23.805] [jointLog] [info] iteration = 500 | max rel diff. = 13.7788
[2021-08-02 18:18:58.335] [jointLog] [info] iteration = 600 | max rel diff. = 0.127387
[2021-08-02 18:19:32.885] [jointLog] [info] iteration = 700 | max rel diff. = 5.00536
[2021-08-02 18:20:07.555] [jointLog] [info] iteration = 800 | max rel diff. = 0.165171
[2021-08-02 18:20:42.240] [jointLog] [info] iteration = 900 | max rel diff. = 2.04046
[2021-08-02 18:21:16.992] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.196691
[2021-08-02 18:21:24.639] [jointLog] [info] iteration = 1,023 | max rel diff. = 0.00956847
[2021-08-02 18:21:26.050] [jointLog] [info] Finished optimizer
[2021-08-02 18:21:26.050] [jointLog] [info] writing output