[2023-09-24 09:07:47.756] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-24 09:07:47.756] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-24 09:07:47.756] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-24 09:07:47.756] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-24 09:07:47.756] [jointLog] [info] parsing read library format
[2023-09-24 09:07:47.756] [jointLog] [info] There is 1 library.
[2023-09-24 09:07:47.757] [jointLog] [info] Loading pufferfish index
[2023-09-24 09:07:47.757] [jointLog] [info] Loading dense pufferfish index.
[2023-09-24 09:09:06.433] [jointLog] [info] done
[2023-09-24 09:09:06.600] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-24 09:09:46.995] [jointLog] [info] Number of decoys : 194
[2023-09-24 09:09:46.995] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-24 09:09:49.186] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-24 09:09:49.804] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-24 09:10:35.345] [jointLog] [info] Thread saw mini-batch with a maximum of 3.48% zero probability fragments
[2023-09-24 09:10:35.368] [jointLog] [info] Thread saw mini-batch with a maximum of 3.82% zero probability fragments
[2023-09-24 09:10:35.438] [jointLog] [info] Thread saw mini-batch with a maximum of 3.38% zero probability fragments
[2023-09-24 09:10:35.685] [jointLog] [info] Thread saw mini-batch with a maximum of 3.60% zero probability fragments
[2023-09-24 09:10:35.762] [jointLog] [info] Thread saw mini-batch with a maximum of 3.36% zero probability fragments
[2023-09-24 09:10:35.795] [jointLog] [info] Thread saw mini-batch with a maximum of 3.32% zero probability fragments
[2023-09-24 09:10:35.811] [jointLog] [info] Thread saw mini-batch with a maximum of 3.68% zero probability fragments
[2023-09-24 09:10:35.946] [jointLog] [info] Thread saw mini-batch with a maximum of 3.56% zero probability fragments
[2023-09-24 09:10:36.142] [jointLog] [info] Computed 80,503 rich equivalence classes for further processing
[2023-09-24 09:10:36.142] [jointLog] [info] Counted 2,895,270 total reads in the equivalence classes 
[2023-09-24 09:10:36.152] [jointLog] [info] Number of mappings discarded because of alignment score : 51,507,745
[2023-09-24 09:10:36.152] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 374,550
[2023-09-24 09:10:36.152] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 85,166
[2023-09-24 09:10:36.152] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-24 09:10:36.143] [fileLog] [info] 
At end of round 0
==================
Observed 3714541 total fragments (3714541 in most recent round)

[2023-09-24 09:10:37.355] [jointLog] [warning] Only 2895270 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-24 09:10:37.355] [jointLog] [info] Mapping rate = 77.9442%

[2023-09-24 09:10:37.355] [jointLog] [info] finished quantifyLibrary()
[2023-09-24 09:10:37.356] [jointLog] [info] Starting optimizer
[2023-09-24 09:10:41.826] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-24 09:10:42.168] [jointLog] [info] iteration = 0 | max rel diff. = 64.0596
[2023-09-24 09:10:45.589] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-24 09:11:37.534] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-24 09:11:37.534] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-24 09:11:41.959] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-24 09:11:46.720] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-24 09:11:51.850] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-24 09:11:56.826] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-24 09:12:01.228] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-24 09:12:05.813] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-24 09:12:10.430] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-24 09:12:15.339] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-24 09:12:20.115] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-24 09:12:24.863] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-24 09:12:58.489] [jointLog] [info] iteration = 100 | max rel diff. = 12.1444
[2023-09-24 09:13:34.363] [jointLog] [info] iteration = 200 | max rel diff. = 20.1864
[2023-09-24 09:14:06.114] [jointLog] [info] iteration = 300 | max rel diff. = 5.80181
[2023-09-24 09:14:37.851] [jointLog] [info] iteration = 400 | max rel diff. = 0.0924468
[2023-09-24 09:15:09.868] [jointLog] [info] iteration = 500 | max rel diff. = 0.121744
[2023-09-24 09:15:42.428] [jointLog] [info] iteration = 600 | max rel diff. = 0.211947
[2023-09-24 09:16:16.508] [jointLog] [info] iteration = 700 | max rel diff. = 0.0239449
[2023-09-24 09:16:50.080] [jointLog] [info] iteration = 800 | max rel diff. = 0.031257
[2023-09-24 09:17:21.532] [jointLog] [info] iteration = 900 | max rel diff. = 0.169001
[2023-09-24 09:17:53.174] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.269288
[2023-09-24 09:17:54.708] [jointLog] [info] iteration = 1,006 | max rel diff. = 0.00483339
[2023-09-24 09:17:56.736] [jointLog] [info] Finished optimizer
[2023-09-24 09:17:56.736] [jointLog] [info] writing output