[2023-09-16 19:20:47.453] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-16 19:20:47.453] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-16 19:20:47.453] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-16 19:20:47.453] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-16 19:20:47.453] [jointLog] [info] parsing read library format
[2023-09-16 19:20:47.453] [jointLog] [info] There is 1 library.
[2023-09-16 19:20:47.453] [jointLog] [info] Loading pufferfish index
[2023-09-16 19:20:47.453] [jointLog] [info] Loading dense pufferfish index.
[2023-09-16 19:22:04.211] [jointLog] [info] done
[2023-09-16 19:22:04.390] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-16 19:22:46.524] [jointLog] [info] Number of decoys : 194
[2023-09-16 19:22:46.524] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-16 19:22:49.643] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-16 19:22:50.447] [jointLog] [info] Automatically detected most likely library type as SR

[2023-09-16 19:23:19.190] [jointLog] [info] Thread saw mini-batch with a maximum of 5.32% zero probability fragments
[2023-09-16 19:23:19.205] [jointLog] [info] Thread saw mini-batch with a maximum of 5.50% zero probability fragments
[2023-09-16 19:23:19.254] [jointLog] [info] Thread saw mini-batch with a maximum of 5.12% zero probability fragments
[2023-09-16 19:23:19.360] [jointLog] [info] Thread saw mini-batch with a maximum of 5.36% zero probability fragments
[2023-09-16 19:23:19.361] [jointLog] [info] Thread saw mini-batch with a maximum of 5.22% zero probability fragments
[2023-09-16 19:23:19.367] [jointLog] [info] Thread saw mini-batch with a maximum of 5.26% zero probability fragments
[2023-09-16 19:23:19.376] [jointLog] [info] Thread saw mini-batch with a maximum of 5.50% zero probability fragments
[2023-09-16 19:23:19.385] [jointLog] [info] Thread saw mini-batch with a maximum of 5.50% zero probability fragments
[2023-09-16 19:23:19.646] [jointLog] [info] Computed 189,596 rich equivalence classes for further processing
[2023-09-16 19:23:19.646] [jointLog] [info] Counted 3,910,142 total reads in the equivalence classes 
[2023-09-16 19:23:19.656] [jointLog] [info] Number of mappings discarded because of alignment score : 7,415,762
[2023-09-16 19:23:19.656] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 43,915
[2023-09-16 19:23:19.656] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 32,018
[2023-09-16 19:23:19.656] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-16 19:23:19.647] [fileLog] [info] 
At end of round 0
==================
Observed 4343898 total fragments (4343898 in most recent round)

[2023-09-16 19:23:21.323] [jointLog] [warning] Only 3910142 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-16 19:23:21.323] [jointLog] [info] Mapping rate = 90.0146%

[2023-09-16 19:23:21.323] [jointLog] [info] finished quantifyLibrary()
[2023-09-16 19:23:21.323] [jointLog] [info] Starting optimizer
[2023-09-16 19:23:26.474] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-16 19:23:26.841] [jointLog] [info] iteration = 0 | max rel diff. = 92.7501
[2023-09-16 19:23:30.467] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-16 19:24:39.202] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-16 19:24:39.203] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-16 19:24:45.389] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-16 19:24:51.798] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-16 19:24:58.055] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-16 19:25:04.609] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-16 19:25:10.873] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-16 19:25:17.442] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-16 19:25:23.626] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-16 19:25:29.921] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-16 19:25:36.259] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-16 19:25:42.737] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-16 19:25:42.743] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-16 19:26:16.723] [jointLog] [info] iteration = 100 | max rel diff. = 12.8098
[2023-09-16 19:26:52.887] [jointLog] [info] iteration = 200 | max rel diff. = 6.38655
[2023-09-16 19:27:28.877] [jointLog] [info] iteration = 300 | max rel diff. = 4.7628
[2023-09-16 19:28:05.318] [jointLog] [info] iteration = 400 | max rel diff. = 0.263498
[2023-09-16 19:28:43.051] [jointLog] [info] iteration = 500 | max rel diff. = 0.227928
[2023-09-16 19:29:20.666] [jointLog] [info] iteration = 600 | max rel diff. = 0.733203
[2023-09-16 19:29:58.181] [jointLog] [info] iteration = 700 | max rel diff. = 0.675813
[2023-09-16 19:30:35.107] [jointLog] [info] iteration = 800 | max rel diff. = 0.145014
[2023-09-16 19:31:11.762] [jointLog] [info] iteration = 900 | max rel diff. = 0.291864
[2023-09-16 19:31:48.410] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0566722
[2023-09-16 19:31:55.314] [jointLog] [info] iteration = 1,019 | max rel diff. = 0.00672207
[2023-09-16 19:31:57.862] [jointLog] [info] Finished optimizer
[2023-09-16 19:31:57.862] [jointLog] [info] writing output