[2023-09-25 18:24:35.719] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-25 18:24:35.719] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-25 18:24:35.719] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-25 18:24:35.719] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-25 18:24:35.719] [jointLog] [info] parsing read library format
[2023-09-25 18:24:35.719] [jointLog] [info] There is 1 library.
[2023-09-25 18:24:35.719] [jointLog] [info] Loading pufferfish index
[2023-09-25 18:24:35.719] [jointLog] [info] Loading dense pufferfish index.
[2023-09-25 18:25:48.379] [jointLog] [info] done
[2023-09-25 18:25:48.504] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-25 18:26:24.296] [jointLog] [info] Number of decoys : 194
[2023-09-25 18:26:24.296] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-25 18:26:25.332] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-25 18:26:26.043] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-25 18:26:49.588] [jointLog] [info] Thread saw mini-batch with a maximum of 2.78% zero probability fragments
[2023-09-25 18:26:49.625] [jointLog] [info] Thread saw mini-batch with a maximum of 2.62% zero probability fragments
[2023-09-25 18:26:49.843] [jointLog] [info] Thread saw mini-batch with a maximum of 2.70% zero probability fragments
[2023-09-25 18:26:49.852] [jointLog] [info] Thread saw mini-batch with a maximum of 3.08% zero probability fragments
[2023-09-25 18:26:49.861] [jointLog] [info] Thread saw mini-batch with a maximum of 2.72% zero probability fragments
[2023-09-25 18:26:49.914] [jointLog] [info] Thread saw mini-batch with a maximum of 2.70% zero probability fragments
[2023-09-25 18:26:49.933] [jointLog] [info] Thread saw mini-batch with a maximum of 2.68% zero probability fragments
[2023-09-25 18:26:49.935] [jointLog] [info] Thread saw mini-batch with a maximum of 2.64% zero probability fragments
[2023-09-25 18:26:50.041] [jointLog] [info] Computed 60,293 rich equivalence classes for further processing
[2023-09-25 18:26:50.041] [jointLog] [info] Counted 1,400,207 total reads in the equivalence classes 
[2023-09-25 18:26:50.046] [jointLog] [warning] 5.18188e-05% of fragments were shorter than the k used to build the index.
If this fraction is too large, consider re-building the index with a smaller k.
The minimum read size found was 10.


[2023-09-25 18:26:50.046] [jointLog] [info] Number of mappings discarded because of alignment score : 34,556,678
[2023-09-25 18:26:50.046] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 223,069
[2023-09-25 18:26:50.046] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 47,445
[2023-09-25 18:26:50.046] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-25 18:26:50.041] [fileLog] [info] 
At end of round 0
==================
Observed 1929800 total fragments (1929800 in most recent round)

[2023-09-25 18:26:50.814] [jointLog] [warning] Only 1400207 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 18:26:50.814] [jointLog] [info] Mapping rate = 72.5571%

[2023-09-25 18:26:50.814] [jointLog] [info] finished quantifyLibrary()
[2023-09-25 18:26:50.814] [jointLog] [info] Starting optimizer
[2023-09-25 18:26:54.090] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-25 18:26:54.412] [jointLog] [info] iteration = 0 | max rel diff. = 30.4545
[2023-09-25 18:26:57.544] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-25 18:27:38.184] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-25 18:27:38.185] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-25 18:27:42.013] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-25 18:27:45.635] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-25 18:27:49.481] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-25 18:27:53.306] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-25 18:27:57.363] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-25 18:28:01.168] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-25 18:28:04.699] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-25 18:28:08.252] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-25 18:28:12.063] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-25 18:28:15.954] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-25 18:28:43.836] [jointLog] [info] iteration = 100 | max rel diff. = 15.8789
[2023-09-25 18:29:15.128] [jointLog] [info] iteration = 200 | max rel diff. = 0.411008
[2023-09-25 18:29:45.797] [jointLog] [info] iteration = 300 | max rel diff. = 0.660809
[2023-09-25 18:30:16.778] [jointLog] [info] iteration = 400 | max rel diff. = 0.111275
[2023-09-25 18:30:48.738] [jointLog] [info] iteration = 500 | max rel diff. = 2.87833
[2023-09-25 18:31:20.838] [jointLog] [info] iteration = 600 | max rel diff. = 0.0646504
[2023-09-25 18:31:52.989] [jointLog] [info] iteration = 700 | max rel diff. = 0.0150608
[2023-09-25 18:32:17.693] [jointLog] [info] iteration = 778 | max rel diff. = 0.0033448
[2023-09-25 18:32:19.442] [jointLog] [info] Finished optimizer
[2023-09-25 18:32:19.442] [jointLog] [info] writing output