[2023-10-03 07:56:20.382] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-03 07:56:20.382] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-03 07:56:20.382] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-03 07:56:20.382] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-03 07:56:20.382] [jointLog] [info] parsing read library format
[2023-10-03 07:56:20.382] [jointLog] [info] There is 1 library.
[2023-10-03 07:56:20.383] [jointLog] [info] Loading pufferfish index
[2023-10-03 07:56:20.383] [jointLog] [info] Loading dense pufferfish index.
[2023-10-03 07:57:38.592] [jointLog] [info] done
[2023-10-03 07:57:38.763] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-03 07:58:20.466] [jointLog] [info] Number of decoys : 194
[2023-10-03 07:58:20.466] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-03 07:58:22.697] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-03 07:58:24.026] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-03 07:58:50.054] [jointLog] [info] Thread saw mini-batch with a maximum of 3.44% zero probability fragments
[2023-10-03 07:58:50.336] [jointLog] [info] Thread saw mini-batch with a maximum of 3.60% zero probability fragments
[2023-10-03 07:58:50.338] [jointLog] [info] Thread saw mini-batch with a maximum of 3.42% zero probability fragments
[2023-10-03 07:58:50.381] [jointLog] [info] Thread saw mini-batch with a maximum of 3.48% zero probability fragments
[2023-10-03 07:58:50.494] [jointLog] [info] Thread saw mini-batch with a maximum of 3.42% zero probability fragments
[2023-10-03 07:58:50.501] [jointLog] [info] Thread saw mini-batch with a maximum of 3.28% zero probability fragments
[2023-10-03 07:58:50.589] [jointLog] [info] Thread saw mini-batch with a maximum of 3.62% zero probability fragments
[2023-10-03 07:58:50.615] [jointLog] [info] Thread saw mini-batch with a maximum of 3.50% zero probability fragments
[2023-10-03 07:58:50.780] [jointLog] [info] Computed 62,465 rich equivalence classes for further processing
[2023-10-03 07:58:50.780] [jointLog] [info] Counted 1,013,582 total reads in the equivalence classes 
[2023-10-03 07:58:50.790] [jointLog] [info] Number of mappings discarded because of alignment score : 30,926,980
[2023-10-03 07:58:50.790] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 173,804
[2023-10-03 07:58:50.790] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 41,279
[2023-10-03 07:58:50.790] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-03 07:58:50.781] [fileLog] [info] 
At end of round 0
==================
Observed 1387840 total fragments (1387840 in most recent round)

[2023-10-03 07:58:52.016] [jointLog] [warning] Only 1013582 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 07:58:52.016] [jointLog] [info] Mapping rate = 73.0331%

[2023-10-03 07:58:52.016] [jointLog] [info] finished quantifyLibrary()
[2023-10-03 07:58:52.016] [jointLog] [info] Starting optimizer
[2023-10-03 07:58:57.585] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-03 07:58:57.925] [jointLog] [info] iteration = 0 | max rel diff. = 21.9444
[2023-10-03 07:59:01.302] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-03 07:59:45.729] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-03 07:59:45.730] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-03 07:59:49.500] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-03 07:59:53.380] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-03 07:59:57.638] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-03 08:00:01.829] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-03 08:00:06.173] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-03 08:00:10.185] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-03 08:00:14.346] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-03 08:00:18.658] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-03 08:00:22.732] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-03 08:00:26.801] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-03 08:00:56.585] [jointLog] [info] iteration = 100 | max rel diff. = 18.0756
[2023-10-03 08:01:29.442] [jointLog] [info] iteration = 200 | max rel diff. = 3.45487
[2023-10-03 08:02:02.819] [jointLog] [info] iteration = 300 | max rel diff. = 0.572335
[2023-10-03 08:02:36.235] [jointLog] [info] iteration = 400 | max rel diff. = 0.0636916
[2023-10-03 08:03:09.796] [jointLog] [info] iteration = 500 | max rel diff. = 0.26288
[2023-10-03 08:03:43.216] [jointLog] [info] iteration = 600 | max rel diff. = 0.241718
[2023-10-03 08:04:03.088] [jointLog] [info] iteration = 660 | max rel diff. = 0.00389009
[2023-10-03 08:04:05.664] [jointLog] [info] Finished optimizer
[2023-10-03 08:04:05.664] [jointLog] [info] writing output