[2023-10-04 11:31:39.687] [jointLog] [info] setting maxHashResizeThreads to 8
[2023-10-04 11:31:39.687] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2023-10-04 11:31:39.687] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2023-10-04 11:31:39.687] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2023-10-04 11:31:39.687] [jointLog] [info] parsing read library format
[2023-10-04 11:31:39.687] [jointLog] [info] There is 1 library.
[2023-10-04 11:31:39.687] [jointLog] [info] Loading pufferfish index
[2023-10-04 11:31:39.688] [jointLog] [info] Loading dense pufferfish index.
[2023-10-04 11:33:06.288] [jointLog] [info] done
[2023-10-04 11:33:06.408] [jointLog] [info] Index contained 5,382,683 targets
[2023-10-04 11:33:44.585] [jointLog] [info] Number of decoys : 194
[2023-10-04 11:33:44.585] [jointLog] [info] First decoy index : 5,185,409 
[2023-10-04 11:33:47.137] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in single-end libraries.  Please use this option with caution.
[2023-10-04 11:33:47.843] [jointLog] [info] Automatically detected most likely library type as SF

[2023-10-04 11:34:42.478] [jointLog] [info] Thread saw mini-batch with a maximum of 3.92% zero probability fragments
[2023-10-04 11:34:42.609] [jointLog] [info] Thread saw mini-batch with a maximum of 3.42% zero probability fragments
[2023-10-04 11:34:42.732] [jointLog] [info] Thread saw mini-batch with a maximum of 3.72% zero probability fragments
[2023-10-04 11:34:42.815] [jointLog] [info] Thread saw mini-batch with a maximum of 3.62% zero probability fragments
[2023-10-04 11:34:42.881] [jointLog] [info] Thread saw mini-batch with a maximum of 3.60% zero probability fragments
[2023-10-04 11:34:42.908] [jointLog] [info] Thread saw mini-batch with a maximum of 3.64% zero probability fragments
[2023-10-04 11:34:42.938] [jointLog] [info] Thread saw mini-batch with a maximum of 3.54% zero probability fragments
[2023-10-04 11:34:42.954] [jointLog] [info] Thread saw mini-batch with a maximum of 3.66% zero probability fragments
[2023-10-04 11:34:43.164] [jointLog] [info] Computed 87,608 rich equivalence classes for further processing
[2023-10-04 11:34:43.164] [jointLog] [info] Counted 3,546,377 total reads in the equivalence classes 
[2023-10-04 11:34:43.172] [jointLog] [info] Number of mappings discarded because of alignment score : 48,975,289
[2023-10-04 11:34:43.172] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 314,396
[2023-10-04 11:34:43.172] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 97,538
[2023-10-04 11:34:43.172] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
[2023-10-04 11:34:43.165] [fileLog] [info] 
At end of round 0
==================
Observed 4607553 total fragments (4607553 in most recent round)

[2023-10-04 11:34:44.831] [jointLog] [warning] Only 3546377 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2023-10-04 11:34:44.831] [jointLog] [info] Mapping rate = 76.9688%

[2023-10-04 11:34:44.832] [jointLog] [info] finished quantifyLibrary()
[2023-10-04 11:34:44.832] [jointLog] [info] Starting optimizer
[2023-10-04 11:34:49.344] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2023-10-04 11:34:49.682] [jointLog] [info] iteration = 0 | max rel diff. = 76.7286
[2023-10-04 11:34:53.025] [jointLog] [info] iteration 11, adjusting effective lengths to account for biases
[2023-10-04 11:35:51.770] [jointLog] [info] Computed expected counts (for bias correction)
[2023-10-04 11:35:51.770] [jointLog] [info] processed bias for 0.0% of the transcripts
[2023-10-04 11:35:56.719] [jointLog] [info] processed bias for 10.0% of the transcripts
[2023-10-04 11:36:02.277] [jointLog] [info] processed bias for 20.0% of the transcripts
[2023-10-04 11:36:08.002] [jointLog] [info] processed bias for 30.0% of the transcripts
[2023-10-04 11:36:13.416] [jointLog] [info] processed bias for 40.0% of the transcripts
[2023-10-04 11:36:17.976] [jointLog] [info] processed bias for 50.0% of the transcripts
[2023-10-04 11:36:23.382] [jointLog] [info] processed bias for 60.0% of the transcripts
[2023-10-04 11:36:28.722] [jointLog] [info] processed bias for 70.0% of the transcripts
[2023-10-04 11:36:34.096] [jointLog] [info] processed bias for 80.0% of the transcripts
[2023-10-04 11:36:39.226] [jointLog] [info] processed bias for 90.0% of the transcripts
[2023-10-04 11:36:44.963] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-04 11:36:44.965] [jointLog] [info] processed bias for 100.0% of the transcripts
[2023-10-04 11:37:15.758] [jointLog] [info] iteration = 100 | max rel diff. = 15.9665
[2023-10-04 11:37:49.321] [jointLog] [info] iteration = 200 | max rel diff. = 14.7707
[2023-10-04 11:38:22.840] [jointLog] [info] iteration = 300 | max rel diff. = 0.679803
[2023-10-04 11:38:58.462] [jointLog] [info] iteration = 400 | max rel diff. = 0.0534184
[2023-10-04 11:39:34.474] [jointLog] [info] iteration = 500 | max rel diff. = 0.212947
[2023-10-04 11:40:09.602] [jointLog] [info] iteration = 600 | max rel diff. = 0.110431
[2023-10-04 11:40:44.667] [jointLog] [info] iteration = 700 | max rel diff. = 0.351962
[2023-10-04 11:40:46.105] [jointLog] [info] iteration = 705 | max rel diff. = 0.00938665
[2023-10-04 11:40:48.172] [jointLog] [info] Finished optimizer
[2023-10-04 11:40:48.172] [jointLog] [info] writing output