[2023-09-25 08:35:22.162] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-25 08:35:22.162] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-25 08:35:22.162] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-25 08:35:22.162] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-25 08:35:22.162] [jointLog] [info] parsing read library format
[2023-09-25 08:35:22.162] [jointLog] [info] There is 1 library.
[2023-09-25 08:35:22.162] [jointLog] [info] Loading pufferfish index
[2023-09-25 08:35:22.162] [jointLog] [info] Loading dense pufferfish index.
[2023-09-25 08:36:36.815] [jointLog] [info] done
[2023-09-25 08:36:36.935] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-25 08:37:12.451] [jointLog] [info] Number of decoys : 194
[2023-09-25 08:37:12.451] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-25 08:37:14.152] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-25 08:37:15.164] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-25 08:37:59.368] [jointLog] [info] Thread saw mini-batch with a maximum of 3.80% zero probability fragments
[2023-09-25 08:37:59.373] [jointLog] [info] Thread saw mini-batch with a maximum of 3.80% zero probability fragments
[2023-09-25 08:37:59.403] [jointLog] [info] Thread saw mini-batch with a maximum of 3.60% zero probability fragments
[2023-09-25 08:37:59.404] [jointLog] [info] Thread saw mini-batch with a maximum of 3.46% zero probability fragments
[2023-09-25 08:37:59.456] [jointLog] [info] Thread saw mini-batch with a maximum of 3.70% zero probability fragments
[2023-09-25 08:37:59.467] [jointLog] [info] Thread saw mini-batch with a maximum of 3.68% zero probability fragments
[2023-09-25 08:37:59.724] [jointLog] [info] Thread saw mini-batch with a maximum of 3.80% zero probability fragments
[2023-09-25 08:37:59.756] [jointLog] [info] Thread saw mini-batch with a maximum of 3.86% zero probability fragments
[2023-09-25 08:37:59.923] [jointLog] [info] Computed 79,999 rich equivalence classes for further processing
[2023-09-25 08:37:59.923] [jointLog] [info] Counted 2,961,744 total reads in the equivalence classes 
[2023-09-25 08:37:59.930] [jointLog] [info] Number of mappings discarded because of alignment score : 53,819,973
[2023-09-25 08:37:59.930] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 347,075
[2023-09-25 08:37:59.930] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 104,235
[2023-09-25 08:37:59.930] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-25 08:37:59.924] [fileLog] [info] 
At end of round 0
==================
Observed 3944076 total fragments (3944076 in most recent round)

[2023-09-25 08:38:01.005] [jointLog] [warning] Only 2961744 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-25 08:38:01.005] [jointLog] [info] Mapping rate = 75.0935%

[2023-09-25 08:38:01.005] [jointLog] [info] finished quantifyLibrary()
[2023-09-25 08:38:01.005] [jointLog] [info] Starting optimizer
[2023-09-25 08:38:04.980] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-25 08:38:05.309] [jointLog] [info] iteration = 0 | max rel diff. = 82.5602
[2023-09-25 08:38:08.554] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-25 08:39:02.101] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-25 08:39:02.101] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-25 08:39:07.031] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-25 08:39:11.904] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-25 08:39:16.886] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-25 08:39:22.178] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-25 08:39:26.834] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-25 08:39:32.039] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-25 08:39:36.924] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-25 08:39:41.806] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-25 08:39:46.754] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-25 08:39:51.758] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-25 08:40:20.961] [jointLog] [info] iteration = 100 | max rel diff. = 1.99111
[2023-09-25 08:40:52.941] [jointLog] [info] iteration = 200 | max rel diff. = 0.303931
[2023-09-25 08:41:25.711] [jointLog] [info] iteration = 300 | max rel diff. = 4.42595
[2023-09-25 08:41:58.106] [jointLog] [info] iteration = 400 | max rel diff. = 0.824743
[2023-09-25 08:42:30.205] [jointLog] [info] iteration = 500 | max rel diff. = 0.0940926
[2023-09-25 08:43:02.170] [jointLog] [info] iteration = 600 | max rel diff. = 0.129631
[2023-09-25 08:43:33.369] [jointLog] [info] iteration = 700 | max rel diff. = 0.501598
[2023-09-25 08:43:53.887] [jointLog] [info] iteration = 764 | max rel diff. = 0.00911922
[2023-09-25 08:43:55.945] [jointLog] [info] Finished optimizer
[2023-09-25 08:43:55.945] [jointLog] [info] writing output