[2023-10-03 19:14:31.591] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-03 19:14:31.591] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-03 19:14:31.591] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-03 19:14:31.591] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-03 19:14:31.591] [jointLog] [info] parsing read library format
[2023-10-03 19:14:31.592] [jointLog] [info] There is 1 library.
[2023-10-03 19:14:31.592] [jointLog] [info] Loading pufferfish index
[2023-10-03 19:14:31.592] [jointLog] [info] Loading dense pufferfish index.
[2023-10-03 19:15:44.439] [jointLog] [info] done
[2023-10-03 19:15:44.560] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-03 19:16:19.343] [jointLog] [info] Number of decoys : 194
[2023-10-03 19:16:19.343] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-03 19:16:20.424] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-03 19:16:21.457] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-03 19:16:59.317] [jointLog] [info] Thread saw mini-batch with a maximum of 4.26% zero probability fragments
[2023-10-03 19:16:59.446] [jointLog] [info] Thread saw mini-batch with a maximum of 4.04% zero probability fragments
[2023-10-03 19:16:59.484] [jointLog] [info] Thread saw mini-batch with a maximum of 4.08% zero probability fragments
[2023-10-03 19:16:59.550] [jointLog] [info] Thread saw mini-batch with a maximum of 4.10% zero probability fragments
[2023-10-03 19:16:59.556] [jointLog] [info] Thread saw mini-batch with a maximum of 3.86% zero probability fragments
[2023-10-03 19:16:59.633] [jointLog] [info] Thread saw mini-batch with a maximum of 4.22% zero probability fragments
[2023-10-03 19:16:59.712] [jointLog] [info] Thread saw mini-batch with a maximum of 4.08% zero probability fragments
[2023-10-03 19:17:00.113] [fileLog] [info] 
At end of round 0
==================
Observed 2088017 total fragments (2088017 in most recent round)

[2023-10-03 19:16:59.968] [jointLog] [info] Thread saw mini-batch with a maximum of 4.20% zero probability fragments
[2023-10-03 19:17:00.112] [jointLog] [info] Computed 72,400 rich equivalence classes for further processing
[2023-10-03 19:17:00.112] [jointLog] [info] Counted 1,478,428 total reads in the equivalence classes 
[2023-10-03 19:17:00.119] [jointLog] [info] Number of mappings discarded because of alignment score : 52,404,342
[2023-10-03 19:17:00.119] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 189,013
[2023-10-03 19:17:00.119] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 54,456
[2023-10-03 19:17:00.119] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-03 19:17:01.270] [jointLog] [warning] Only 1478428 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-10-03 19:17:01.270] [jointLog] [info] Mapping rate = 70.8054%

[2023-10-03 19:17:01.270] [jointLog] [info] finished quantifyLibrary()
[2023-10-03 19:17:01.271] [jointLog] [info] Starting optimizer
[2023-10-03 19:17:04.762] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-03 19:17:05.083] [jointLog] [info] iteration = 0 | max rel diff. = 36.17
[2023-10-03 19:17:08.291] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-03 19:18:01.453] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-03 19:18:01.454] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-03 19:18:06.048] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-03 19:18:10.788] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-03 19:18:15.795] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-03 19:18:20.745] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-03 19:18:25.244] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-03 19:18:29.897] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-03 19:18:35.126] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-03 19:18:39.695] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-03 19:18:44.458] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-03 19:18:49.459] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-03 19:19:18.201] [jointLog] [info] iteration = 100 | max rel diff. = 20.6368
[2023-10-03 19:19:49.664] [jointLog] [info] iteration = 200 | max rel diff. = 0.19546
[2023-10-03 19:20:20.979] [jointLog] [info] iteration = 300 | max rel diff. = 0.384228
[2023-10-03 19:20:52.285] [jointLog] [info] iteration = 400 | max rel diff. = 0.670965
[2023-10-03 19:21:23.648] [jointLog] [info] iteration = 500 | max rel diff. = 0.483898
[2023-10-03 19:21:55.887] [jointLog] [info] iteration = 600 | max rel diff. = 0.596933
[2023-10-03 19:22:20.710] [jointLog] [info] iteration = 678 | max rel diff. = 0.00206381
[2023-10-03 19:22:22.648] [jointLog] [info] Finished optimizer
[2023-10-03 19:22:22.648] [jointLog] [info] writing output