[2023-08-21 17:46:18.827] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-08-21 17:46:18.827] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-08-21 17:46:18.827] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-08-21 17:46:18.827] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-08-21 17:46:18.827] [jointLog] [info] parsing read library format
[2023-08-21 17:46:18.827] [jointLog] [info] There is 1 library.
[2023-08-21 17:46:18.828] [jointLog] [info] Loading pufferfish index
[2023-08-21 17:46:18.828] [jointLog] [info] Loading dense pufferfish index.
[2023-08-21 17:48:10.382] [jointLog] [info] done
[2023-08-21 17:48:10.565] [jointLog] [info] Index contained 5,382,683 targets
[2023-08-21 17:49:00.477] [jointLog] [info] Number of decoys : 194
[2023-08-21 17:49:00.477] [jointLog] [info] First decoy index : 5,185,409 
[2023-08-21 17:49:04.478] [jointLog] [info] Automatically detected most likely library type as ISR

[2023-08-21 17:50:28.308] [jointLog] [info] Thread saw mini-batch with a maximum of 3.68% zero probability fragments
[2023-08-21 17:50:28.547] [jointLog] [info] Thread saw mini-batch with a maximum of 3.78% zero probability fragments
[2023-08-21 17:50:28.610] [jointLog] [info] Thread saw mini-batch with a maximum of 3.80% zero probability fragments
[2023-08-21 17:50:28.720] [jointLog] [info] Thread saw mini-batch with a maximum of 3.70% zero probability fragments
[2023-08-21 17:50:28.936] [jointLog] [info] Thread saw mini-batch with a maximum of 3.54% zero probability fragments
[2023-08-21 17:50:28.996] [jointLog] [info] Thread saw mini-batch with a maximum of 3.72% zero probability fragments
[2023-08-21 17:50:29.004] [jointLog] [info] Thread saw mini-batch with a maximum of 3.66% zero probability fragments
[2023-08-21 17:50:29.081] [jointLog] [info] Thread saw mini-batch with a maximum of 3.74% zero probability fragments
[2023-08-21 17:50:29.538] [jointLog] [info] Computed 115,509 rich equivalence classes for further processing
[2023-08-21 17:50:29.538] [jointLog] [info] Counted 3,288,205 total reads in the equivalence classes 
[2023-08-21 17:50:29.548] [jointLog] [info] Number of mappings discarded because of alignment score : 1,535,917
[2023-08-21 17:50:29.548] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 249,080
[2023-08-21 17:50:29.548] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 115,318
[2023-08-21 17:50:29.548] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 390,800
[2023-08-21 17:50:29.539] [fileLog] [info] 
At end of round 0
==================
Observed 3695247 total fragments (3695247 in most recent round)

[2023-08-21 17:50:31.395] [jointLog] [warning] Only 3288205 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-08-21 17:50:31.395] [jointLog] [info] Mapping rate = 88.9847%

[2023-08-21 17:50:31.395] [jointLog] [info] finished quantifyLibrary()
[2023-08-21 17:50:31.396] [jointLog] [info] Starting optimizer
[2023-08-21 17:50:36.159] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-08-21 17:50:36.603] [jointLog] [info] iteration = 0 | max rel diff. = 58.4605
[2023-08-21 17:50:42.289] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-08-21 17:54:36.735] [jointLog] [info] Computed expected counts (for bias correction)
[2023-08-21 17:54:36.736] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-08-21 17:54:58.882] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-08-21 17:55:20.280] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-08-21 17:55:40.863] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-08-21 17:56:05.297] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-08-21 17:56:32.406] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-08-21 17:57:01.019] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-08-21 17:57:25.579] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-08-21 17:57:48.163] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-08-21 17:58:10.134] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-08-21 17:58:34.318] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-21 17:58:34.326] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-08-21 17:59:16.029] [jointLog] [info] iteration = 100 | max rel diff. = 15.9538
[2023-08-21 18:00:00.110] [jointLog] [info] iteration = 200 | max rel diff. = 17.1441
[2023-08-21 18:00:45.206] [jointLog] [info] iteration = 300 | max rel diff. = 2.24368
[2023-08-21 18:01:32.761] [jointLog] [info] iteration = 400 | max rel diff. = 0.549252
[2023-08-21 18:02:20.032] [jointLog] [info] iteration = 500 | max rel diff. = 0.456727
[2023-08-21 18:03:07.177] [jointLog] [info] iteration = 600 | max rel diff. = 0.129264
[2023-08-21 18:03:52.224] [jointLog] [info] iteration = 700 | max rel diff. = 0.158785
[2023-08-21 18:04:36.057] [jointLog] [info] iteration = 800 | max rel diff. = 0.0333296
[2023-08-21 18:05:25.657] [jointLog] [info] iteration = 900 | max rel diff. = 0.0508142
[2023-08-21 18:06:13.495] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.683516
[2023-08-21 18:06:14.804] [jointLog] [info] iteration = 1,004 | max rel diff. = 0.00921527
[2023-08-21 18:06:17.061] [jointLog] [info] Finished optimizer
[2023-08-21 18:06:17.061] [jointLog] [info] writing output