[2023-09-29 19:17:58.395] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-29 19:17:58.395] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-29 19:17:58.395] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-29 19:17:58.396] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-29 19:17:58.396] [jointLog] [info] parsing read library format
[2023-09-29 19:17:58.396] [jointLog] [info] There is 1 library.
[2023-09-29 19:17:58.396] [jointLog] [info] Loading pufferfish index
[2023-09-29 19:17:58.396] [jointLog] [info] Loading dense pufferfish index.
[2023-09-29 19:19:17.501] [jointLog] [info] done
[2023-09-29 19:19:17.625] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-29 19:19:52.972] [jointLog] [info] Number of decoys : 194
[2023-09-29 19:19:52.972] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-29 19:19:54.014] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-29 19:19:55.188] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-29 19:20:11.896] [jointLog] [info] Thread saw mini-batch with a maximum of 3.90% zero probability fragments
[2023-09-29 19:20:12.131] [jointLog] [info] Thread saw mini-batch with a maximum of 4.16% zero probability fragments
[2023-09-29 19:20:12.279] [jointLog] [info] Thread saw mini-batch with a maximum of 3.98% zero probability fragments
[2023-09-29 19:20:12.295] [jointLog] [info] Thread saw mini-batch with a maximum of 3.86% zero probability fragments
[2023-09-29 19:20:12.306] [jointLog] [info] Thread saw mini-batch with a maximum of 3.84% zero probability fragments
[2023-09-29 19:20:12.316] [jointLog] [info] Thread saw mini-batch with a maximum of 3.84% zero probability fragments
[2023-09-29 19:20:12.410] [jointLog] [info] Thread saw mini-batch with a maximum of 3.86% zero probability fragments
[2023-09-29 19:20:12.524] [jointLog] [info] Thread saw mini-batch with a maximum of 4.02% zero probability fragments
[2023-09-29 19:20:12.684] [jointLog] [info] Computed 79,783 rich equivalence classes for further processing
[2023-09-29 19:20:12.684] [jointLog] [info] Counted 976,598 total reads in the equivalence classes 
[2023-09-29 19:20:12.691] [jointLog] [warning] 7.69222e-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.


[2023-09-29 19:20:12.691] [jointLog] [info] Number of mappings discarded because of alignment score : 14,433,247
[2023-09-29 19:20:12.691] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 88,965
[2023-09-29 19:20:12.691] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 27,238
[2023-09-29 19:20:12.691] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-29 19:20:12.685] [fileLog] [info] 
At end of round 0
==================
Observed 1300014 total fragments (1300014 in most recent round)

[2023-09-29 19:20:13.452] [jointLog] [warning] Only 976598 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-09-29 19:20:13.452] [jointLog] [info] Mapping rate = 75.1221%

[2023-09-29 19:20:13.452] [jointLog] [info] finished quantifyLibrary()
[2023-09-29 19:20:13.454] [jointLog] [info] Starting optimizer
[2023-09-29 19:20:17.591] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-29 19:20:17.970] [jointLog] [info] iteration = 0 | max rel diff. = 19.2387
[2023-09-29 19:20:21.223] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-29 19:21:19.711] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-29 19:21:19.711] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-29 19:21:24.946] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-29 19:21:29.984] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-29 19:21:35.614] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-29 19:21:40.835] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-29 19:21:46.242] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-29 19:21:51.515] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-29 19:21:56.625] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-29 19:22:01.951] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-29 19:22:07.027] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-29 19:22:12.347] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-29 19:22:41.188] [jointLog] [info] iteration = 100 | max rel diff. = 8.11253
[2023-09-29 19:23:12.762] [jointLog] [info] iteration = 200 | max rel diff. = 0.756905
[2023-09-29 19:23:44.436] [jointLog] [info] iteration = 300 | max rel diff. = 0.0193764
[2023-09-29 19:24:16.133] [jointLog] [info] iteration = 400 | max rel diff. = 0.253398
[2023-09-29 19:24:40.479] [jointLog] [info] iteration = 477 | max rel diff. = 0.00596476
[2023-09-29 19:24:42.142] [jointLog] [info] Finished optimizer
[2023-09-29 19:24:42.142] [jointLog] [info] writing output