[2023-09-23 19:04:33.827] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-23 19:04:33.827] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-23 19:04:33.827] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-23 19:04:33.827] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-23 19:04:33.827] [jointLog] [info] parsing read library format
[2023-09-23 19:04:33.827] [jointLog] [info] There is 1 library.
[2023-09-23 19:04:33.827] [jointLog] [info] Loading pufferfish index
[2023-09-23 19:04:33.827] [jointLog] [info] Loading dense pufferfish index.
[2023-09-23 19:05:58.492] [jointLog] [info] done
[2023-09-23 19:05:58.628] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-23 19:06:36.983] [jointLog] [info] Number of decoys : 194
[2023-09-23 19:06:36.983] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-23 19:06:38.785] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-23 19:06:40.114] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-23 19:07:27.903] [jointLog] [info] Thread saw mini-batch with a maximum of 4.00% zero probability fragments
[2023-09-23 19:07:27.952] [jointLog] [info] Thread saw mini-batch with a maximum of 4.12% zero probability fragments
[2023-09-23 19:07:27.992] [jointLog] [info] Thread saw mini-batch with a maximum of 4.02% zero probability fragments
[2023-09-23 19:07:28.078] [jointLog] [info] Thread saw mini-batch with a maximum of 4.04% zero probability fragments
[2023-09-23 19:07:28.128] [jointLog] [info] Thread saw mini-batch with a maximum of 4.02% zero probability fragments
[2023-09-23 19:07:28.239] [jointLog] [info] Thread saw mini-batch with a maximum of 3.88% zero probability fragments
[2023-09-23 19:07:28.272] [jointLog] [info] Thread saw mini-batch with a maximum of 4.12% zero probability fragments
[2023-09-23 19:07:28.285] [jointLog] [info] Thread saw mini-batch with a maximum of 3.92% zero probability fragments
[2023-09-23 19:07:28.455] [jointLog] [info] Computed 77,768 rich equivalence classes for further processing
[2023-09-23 19:07:28.455] [jointLog] [info] Counted 2,057,706 total reads in the equivalence classes 
[2023-09-23 19:07:28.464] [jointLog] [info] Number of mappings discarded because of alignment score : 36,312,351
[2023-09-23 19:07:28.464] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 190,999
[2023-09-23 19:07:28.464] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 68,307
[2023-09-23 19:07:28.464] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-23 19:07:28.456] [fileLog] [info] 
At end of round 0
==================
Observed 2774522 total fragments (2774522 in most recent round)

[2023-09-23 19:07:29.475] [jointLog] [warning] Only 2057706 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-23 19:07:29.475] [jointLog] [info] Mapping rate = 74.1643%

[2023-09-23 19:07:29.475] [jointLog] [info] finished quantifyLibrary()
[2023-09-23 19:07:29.476] [jointLog] [info] Starting optimizer
[2023-09-23 19:07:35.038] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-23 19:07:35.395] [jointLog] [info] iteration = 0 | max rel diff. = 44.4627
[2023-09-23 19:07:38.969] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-23 19:08:46.208] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-23 19:08:46.208] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-23 19:08:52.620] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-23 19:08:59.792] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-23 19:09:05.456] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-23 19:09:11.546] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-23 19:09:17.647] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-23 19:09:23.133] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-23 19:09:29.154] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-23 19:09:35.898] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-23 19:09:42.740] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-23 19:09:48.670] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-23 19:10:21.293] [jointLog] [info] iteration = 100 | max rel diff. = 4.62906
[2023-09-23 19:10:57.164] [jointLog] [info] iteration = 200 | max rel diff. = 1.19583
[2023-09-23 19:11:33.724] [jointLog] [info] iteration = 300 | max rel diff. = 17.5787
[2023-09-23 19:12:10.091] [jointLog] [info] iteration = 400 | max rel diff. = 0.0658553
[2023-09-23 19:12:46.298] [jointLog] [info] iteration = 500 | max rel diff. = 0.602561
[2023-09-23 19:13:22.370] [jointLog] [info] iteration = 600 | max rel diff. = 0.0134469
[2023-09-23 19:13:58.200] [jointLog] [info] iteration = 700 | max rel diff. = 0.0605883
[2023-09-23 19:14:24.062] [jointLog] [info] iteration = 773 | max rel diff. = 0.0049413
[2023-09-23 19:14:26.203] [jointLog] [info] Finished optimizer
[2023-09-23 19:14:26.203] [jointLog] [info] writing output