[2023-10-03 05:44:50.812] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-03 05:44:50.812] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-03 05:44:50.812] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-03 05:44:50.812] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-03 05:44:50.812] [jointLog] [info] parsing read library format
[2023-10-03 05:44:50.812] [jointLog] [info] There is 1 library.
[2023-10-03 05:44:50.812] [jointLog] [info] Loading pufferfish index
[2023-10-03 05:44:50.813] [jointLog] [info] Loading dense pufferfish index.
[2023-10-03 05:46:03.770] [jointLog] [info] done
[2023-10-03 05:46:03.893] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-03 05:46:43.104] [jointLog] [info] Number of decoys : 194
[2023-10-03 05:46:43.104] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-03 05:46:45.026] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-03 05:46:45.846] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-03 05:47:21.179] [jointLog] [info] Thread saw mini-batch with a maximum of 3.18% zero probability fragments
[2023-10-03 05:47:21.239] [jointLog] [info] Thread saw mini-batch with a maximum of 3.16% zero probability fragments
[2023-10-03 05:47:21.325] [jointLog] [info] Thread saw mini-batch with a maximum of 3.40% zero probability fragments
[2023-10-03 05:47:21.374] [jointLog] [info] Thread saw mini-batch with a maximum of 3.44% zero probability fragments
[2023-10-03 05:47:21.397] [jointLog] [info] Thread saw mini-batch with a maximum of 3.40% zero probability fragments
[2023-10-03 05:47:21.410] [jointLog] [info] Thread saw mini-batch with a maximum of 3.24% zero probability fragments
[2023-10-03 05:47:21.450] [jointLog] [info] Thread saw mini-batch with a maximum of 3.08% zero probability fragments
[2023-10-03 05:47:21.580] [jointLog] [info] Thread saw mini-batch with a maximum of 3.12% zero probability fragments
[2023-10-03 05:47:21.729] [jointLog] [info] Computed 88,750 rich equivalence classes for further processing
[2023-10-03 05:47:21.729] [jointLog] [info] Counted 2,387,987 total reads in the equivalence classes 
[2023-10-03 05:47:21.736] [jointLog] [info] Number of mappings discarded because of alignment score : 40,212,317
[2023-10-03 05:47:21.736] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 255,636
[2023-10-03 05:47:21.736] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 57,883
[2023-10-03 05:47:21.736] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-03 05:47:21.729] [fileLog] [info] 
At end of round 0
==================
Observed 3110955 total fragments (3110955 in most recent round)

[2023-10-03 05:47:22.967] [jointLog] [warning] Only 2387987 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 05:47:22.967] [jointLog] [info] Mapping rate = 76.7606%

[2023-10-03 05:47:22.967] [jointLog] [info] finished quantifyLibrary()
[2023-10-03 05:47:22.967] [jointLog] [info] Starting optimizer
[2023-10-03 05:47:27.285] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-03 05:47:27.613] [jointLog] [info] iteration = 0 | max rel diff. = 48.4597
[2023-10-03 05:47:30.902] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-03 05:48:26.276] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-03 05:48:26.276] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-03 05:48:31.004] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-03 05:48:35.830] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-03 05:48:41.171] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-03 05:48:46.210] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-03 05:48:51.621] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-03 05:48:57.133] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-03 05:49:01.899] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-03 05:49:07.264] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-03 05:49:12.596] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-03 05:49:17.425] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-03 05:49:47.689] [jointLog] [info] iteration = 100 | max rel diff. = 2.8774
[2023-10-03 05:50:20.776] [jointLog] [info] iteration = 200 | max rel diff. = 2.6778
[2023-10-03 05:50:53.974] [jointLog] [info] iteration = 300 | max rel diff. = 2.20982
[2023-10-03 05:51:27.413] [jointLog] [info] iteration = 400 | max rel diff. = 0.224851
[2023-10-03 05:52:01.352] [jointLog] [info] iteration = 500 | max rel diff. = 0.0906027
[2023-10-03 05:52:34.953] [jointLog] [info] iteration = 600 | max rel diff. = 0.151246
[2023-10-03 05:53:07.871] [jointLog] [info] iteration = 700 | max rel diff. = 0.0130463
[2023-10-03 05:53:41.004] [jointLog] [info] iteration = 800 | max rel diff. = 10.6697
[2023-10-03 05:54:14.469] [jointLog] [info] iteration = 900 | max rel diff. = 0.0331074
[2023-10-03 05:54:25.772] [jointLog] [info] iteration = 935 | max rel diff. = 0.00118894
[2023-10-03 05:54:27.782] [jointLog] [info] Finished optimizer
[2023-10-03 05:54:27.782] [jointLog] [info] writing output