[2023-10-05 02:16:06.509] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-05 02:16:06.509] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-05 02:16:06.509] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-05 02:16:06.509] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-05 02:16:06.509] [jointLog] [info] parsing read library format
[2023-10-05 02:16:06.510] [jointLog] [info] There is 1 library.
[2023-10-05 02:16:06.510] [jointLog] [info] Loading pufferfish index
[2023-10-05 02:16:06.510] [jointLog] [info] Loading dense pufferfish index.
[2023-10-05 02:17:23.622] [jointLog] [info] done
[2023-10-05 02:17:23.813] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-05 02:18:03.649] [jointLog] [info] Number of decoys : 194
[2023-10-05 02:18:03.649] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-05 02:18:05.489] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-05 02:18:06.491] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-05 02:18:40.344] [jointLog] [info] Thread saw mini-batch with a maximum of 2.84% zero probability fragments
[2023-10-05 02:18:40.361] [jointLog] [info] Thread saw mini-batch with a maximum of 2.92% zero probability fragments
[2023-10-05 02:18:40.392] [jointLog] [info] Thread saw mini-batch with a maximum of 2.74% zero probability fragments
[2023-10-05 02:18:40.413] [jointLog] [info] Thread saw mini-batch with a maximum of 2.90% zero probability fragments
[2023-10-05 02:18:40.696] [jointLog] [info] Thread saw mini-batch with a maximum of 2.62% zero probability fragments
[2023-10-05 02:18:40.746] [jointLog] [info] Thread saw mini-batch with a maximum of 2.72% zero probability fragments
[2023-10-05 02:18:40.747] [jointLog] [info] Thread saw mini-batch with a maximum of 2.70% zero probability fragments
[2023-10-05 02:18:40.808] [jointLog] [info] Thread saw mini-batch with a maximum of 2.82% zero probability fragments
[2023-10-05 02:18:40.968] [jointLog] [info] Computed 71,653 rich equivalence classes for further processing
[2023-10-05 02:18:40.968] [jointLog] [info] Counted 1,526,719 total reads in the equivalence classes 
[2023-10-05 02:18:40.976] [jointLog] [warning] 4.72921e-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 18.


[2023-10-05 02:18:40.976] [jointLog] [info] Number of mappings discarded because of alignment score : 39,117,862
[2023-10-05 02:18:40.976] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 190,852
[2023-10-05 02:18:40.976] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 58,246
[2023-10-05 02:18:40.976] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-05 02:18:40.969] [fileLog] [info] 
At end of round 0
==================
Observed 2114516 total fragments (2114516 in most recent round)

[2023-10-05 02:18:42.193] [jointLog] [warning] Only 1526719 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-10-05 02:18:42.193] [jointLog] [info] Mapping rate = 72.2018%

[2023-10-05 02:18:42.193] [jointLog] [info] finished quantifyLibrary()
[2023-10-05 02:18:42.193] [jointLog] [info] Starting optimizer
[2023-10-05 02:18:47.112] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-05 02:18:47.462] [jointLog] [info] iteration = 0 | max rel diff. = 31.2368
[2023-10-05 02:18:50.872] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-05 02:19:38.899] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-05 02:19:38.900] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-05 02:19:43.591] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-05 02:19:48.028] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-05 02:19:52.926] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-05 02:19:57.955] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-05 02:20:02.861] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-05 02:20:07.451] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-05 02:20:12.027] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-05 02:20:16.261] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-05 02:20:20.552] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-05 02:20:25.201] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-05 02:20:57.331] [jointLog] [info] iteration = 100 | max rel diff. = 14.4369
[2023-10-05 02:21:32.480] [jointLog] [info] iteration = 200 | max rel diff. = 1.6386
[2023-10-05 02:22:07.188] [jointLog] [info] iteration = 300 | max rel diff. = 0.110337
[2023-10-05 02:22:42.912] [jointLog] [info] iteration = 400 | max rel diff. = 0.171605
[2023-10-05 02:23:17.981] [jointLog] [info] iteration = 500 | max rel diff. = 0.718412
[2023-10-05 02:23:52.634] [jointLog] [info] iteration = 600 | max rel diff. = 0.0736766
[2023-10-05 02:23:57.923] [jointLog] [info] iteration = 616 | max rel diff. = 0.00872979
[2023-10-05 02:24:00.198] [jointLog] [info] Finished optimizer
[2023-10-05 02:24:00.198] [jointLog] [info] writing output