[2023-09-25 04:14:26.789] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-09-25 04:14:26.789] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-09-25 04:14:26.789] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-09-25 04:14:26.789] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-09-25 04:14:26.789] [jointLog] [info] parsing read library format
[2023-09-25 04:14:26.789] [jointLog] [info] There is 1 library.
[2023-09-25 04:14:26.789] [jointLog] [info] Loading pufferfish index
[2023-09-25 04:14:26.789] [jointLog] [info] Loading dense pufferfish index.
[2023-09-25 04:15:40.076] [jointLog] [info] done
[2023-09-25 04:15:40.194] [jointLog] [info] Index contained 5,382,683 targets
[2023-09-25 04:16:15.669] [jointLog] [info] Number of decoys : 194
[2023-09-25 04:16:15.669] [jointLog] [info] First decoy index : 5,185,409 
[2023-09-25 04:16:17.535] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-09-25 04:16:18.383] [jointLog] [info] Automatically detected most likely library type as SF

[2023-09-25 04:16:48.769] [jointLog] [info] Thread saw mini-batch with a maximum of 3.34% zero probability fragments
[2023-09-25 04:16:48.929] [jointLog] [info] Thread saw mini-batch with a maximum of 3.76% zero probability fragments
[2023-09-25 04:16:49.064] [jointLog] [info] Thread saw mini-batch with a maximum of 3.26% zero probability fragments
[2023-09-25 04:16:49.076] [jointLog] [info] Thread saw mini-batch with a maximum of 3.46% zero probability fragments
[2023-09-25 04:16:49.090] [jointLog] [info] Thread saw mini-batch with a maximum of 3.58% zero probability fragments
[2023-09-25 04:16:49.101] [jointLog] [info] Thread saw mini-batch with a maximum of 3.58% zero probability fragments
[2023-09-25 04:16:49.116] [jointLog] [info] Thread saw mini-batch with a maximum of 3.32% zero probability fragments
[2023-09-25 04:16:49.173] [jointLog] [info] Thread saw mini-batch with a maximum of 3.36% zero probability fragments
[2023-09-25 04:16:49.323] [jointLog] [info] Computed 69,323 rich equivalence classes for further processing
[2023-09-25 04:16:49.323] [jointLog] [info] Counted 1,803,420 total reads in the equivalence classes 
[2023-09-25 04:16:49.330] [jointLog] [info] Number of mappings discarded because of alignment score : 37,653,145
[2023-09-25 04:16:49.330] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 232,721
[2023-09-25 04:16:49.330] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 64,045
[2023-09-25 04:16:49.330] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-09-25 04:16:49.324] [fileLog] [info] 
At end of round 0
==================
Observed 2363993 total fragments (2363993 in most recent round)

[2023-09-25 04:16:50.353] [jointLog] [warning] Only 1803420 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 04:16:50.353] [jointLog] [info] Mapping rate = 76.287%

[2023-09-25 04:16:50.353] [jointLog] [info] finished quantifyLibrary()
[2023-09-25 04:16:50.353] [jointLog] [info] Starting optimizer
[2023-09-25 04:16:53.790] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-09-25 04:16:54.107] [jointLog] [info] iteration = 0 | max rel diff. = 35.8118
[2023-09-25 04:16:57.284] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-09-25 04:17:42.693] [jointLog] [info] Computed expected counts (for bias correction)
[2023-09-25 04:17:42.693] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-09-25 04:17:46.723] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-09-25 04:17:50.689] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-09-25 04:17:54.761] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-09-25 04:17:59.256] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-09-25 04:18:03.514] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-09-25 04:18:07.740] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-09-25 04:18:11.993] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-09-25 04:18:15.942] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-09-25 04:18:19.927] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-09-25 04:18:23.782] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-09-25 04:18:52.708] [jointLog] [info] iteration = 100 | max rel diff. = 13.3008
[2023-09-25 04:19:24.790] [jointLog] [info] iteration = 200 | max rel diff. = 1.5603
[2023-09-25 04:19:56.660] [jointLog] [info] iteration = 300 | max rel diff. = 0.145451
[2023-09-25 04:20:28.603] [jointLog] [info] iteration = 400 | max rel diff. = 0.377655
[2023-09-25 04:21:00.836] [jointLog] [info] iteration = 500 | max rel diff. = 0.218036
[2023-09-25 04:21:14.511] [jointLog] [info] iteration = 544 | max rel diff. = 0.00484471
[2023-09-25 04:21:16.306] [jointLog] [info] Finished optimizer
[2023-09-25 04:21:16.306] [jointLog] [info] writing output