[2023-10-02 19:23:15.891] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-02 19:23:15.891] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-02 19:23:15.891] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-02 19:23:15.891] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-02 19:23:15.891] [jointLog] [info] parsing read library format
[2023-10-02 19:23:15.891] [jointLog] [info] There is 1 library.
[2023-10-02 19:23:15.891] [jointLog] [info] Loading pufferfish index
[2023-10-02 19:23:15.891] [jointLog] [info] Loading dense pufferfish index.
[2023-10-02 19:24:36.162] [jointLog] [info] done
[2023-10-02 19:24:36.318] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-02 19:25:17.700] [jointLog] [info] Number of decoys : 194
[2023-10-02 19:25:17.700] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-02 19:25:19.621] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-02 19:25:21.037] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-02 19:25:56.759] [jointLog] [info] Thread saw mini-batch with a maximum of 3.10% zero probability fragments
[2023-10-02 19:25:56.804] [jointLog] [info] Thread saw mini-batch with a maximum of 3.12% zero probability fragments
[2023-10-02 19:25:56.915] [jointLog] [info] Thread saw mini-batch with a maximum of 2.94% zero probability fragments
[2023-10-02 19:25:56.936] [jointLog] [info] Thread saw mini-batch with a maximum of 3.52% zero probability fragments
[2023-10-02 19:25:56.946] [jointLog] [info] Thread saw mini-batch with a maximum of 3.34% zero probability fragments
[2023-10-02 19:25:56.988] [jointLog] [info] Thread saw mini-batch with a maximum of 2.98% zero probability fragments
[2023-10-02 19:25:57.016] [jointLog] [info] Thread saw mini-batch with a maximum of 3.50% zero probability fragments
[2023-10-02 19:25:57.163] [jointLog] [info] Thread saw mini-batch with a maximum of 3.08% zero probability fragments
[2023-10-02 19:25:57.319] [jointLog] [info] Computed 77,292 rich equivalence classes for further processing
[2023-10-02 19:25:57.319] [jointLog] [info] Counted 1,683,136 total reads in the equivalence classes 
[2023-10-02 19:25:57.327] [jointLog] [info] Number of mappings discarded because of alignment score : 36,233,135
[2023-10-02 19:25:57.327] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 198,227
[2023-10-02 19:25:57.327] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 47,447
[2023-10-02 19:25:57.327] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-02 19:25:57.320] [fileLog] [info] 
At end of round 0
==================
Observed 2167961 total fragments (2167961 in most recent round)

[2023-10-02 19:25:58.681] [jointLog] [warning] Only 1683136 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-10-02 19:25:58.681] [jointLog] [info] Mapping rate = 77.6368%

[2023-10-02 19:25:58.681] [jointLog] [info] finished quantifyLibrary()
[2023-10-02 19:25:58.682] [jointLog] [info] Starting optimizer
[2023-10-02 19:26:03.469] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-02 19:26:03.796] [jointLog] [info] iteration = 0 | max rel diff. = 43.242
[2023-10-02 19:26:07.079] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-02 19:26:59.329] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-02 19:26:59.329] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-02 19:27:03.985] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-02 19:27:09.238] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-02 19:27:14.075] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-02 19:27:19.187] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-02 19:27:24.441] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-02 19:27:29.984] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-02 19:27:35.581] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-02 19:27:40.427] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-02 19:27:45.456] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-02 19:27:50.487] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-02 19:28:23.994] [jointLog] [info] iteration = 100 | max rel diff. = 20.8458
[2023-10-02 19:29:02.506] [jointLog] [info] iteration = 200 | max rel diff. = 3.64947
[2023-10-02 19:29:39.820] [jointLog] [info] iteration = 300 | max rel diff. = 0.151608
[2023-10-02 19:30:17.338] [jointLog] [info] iteration = 400 | max rel diff. = 0.120613
[2023-10-02 19:30:55.025] [jointLog] [info] iteration = 500 | max rel diff. = 0.117795
[2023-10-02 19:31:32.238] [jointLog] [info] iteration = 600 | max rel diff. = 0.0232818
[2023-10-02 19:32:08.942] [jointLog] [info] iteration = 700 | max rel diff. = 0.0530457
[2023-10-02 19:32:45.469] [jointLog] [info] iteration = 800 | max rel diff. = 0.0873321
[2023-10-02 19:33:21.495] [jointLog] [info] iteration = 900 | max rel diff. = 0.300453
[2023-10-02 19:33:57.411] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0810626
[2023-10-02 19:34:18.370] [jointLog] [info] iteration = 1,059 | max rel diff. = 0.00134239
[2023-10-02 19:34:21.219] [jointLog] [info] Finished optimizer
[2023-10-02 19:34:21.219] [jointLog] [info] writing output